Modified the API for lots of classes so that the number of...

Modified the API for lots of classes so that the number of particles/bonds/etc. need not be specified in the constructor.

platforms/brook/tests/TestBrookNonbondedForce.cpp

@@ -68,7 +68,9 @@ void testBrookCoulomb( FILE* log ){
    }   
 
    BrookPlatform platform( 32, "cal", log );
-   System system( numberOfParticles, 0 ); 
+   System system;
+   system.addParticle(1.0);
+   system.addParticle(1.0);
    LangevinIntegrator integrator( 0, 0.1, 0.01 );
 
    // int index, double charge, double radius, double depth
@@ -136,7 +138,9 @@ void testBrookLJ( FILE* log ){
 
    BrookPlatform platform( 32, "cal", log );
    // ReferencePlatform platform;
-   System system( numberOfParticles, 0 ); 
+   System system;
+   system.addParticle(1.0);
+   system.addParticle(1.0);
    LangevinIntegrator integrator( 0, 0.1, 0.01 );
 
    // int index, double charge, double radius, double depth
@@ -203,14 +207,16 @@ void testBrookExclusionsAnd14( FILE* log ){
 
    BrookPlatform platform( 32, "cpu", log );
    //ReferencePlatform platform;
-   System system( numberOfParticles, 0 ); 
+   System system;
    LangevinIntegrator integrator( 0, 0.1, 0.01 );
 
    // int index, double charge, double radius, double depth
 
    NonbondedForce* nonbonded = new NonbondedForce();
-   for (int i = 0; i < numberOfParticles; i++)
+   for (int i = 0; i < numberOfParticles; i++) {
+       system.addParticle(1.0);
        nonbonded->addParticle(0, 1.5, 0)
+   }
    vector<pair<int, int> > bonds;
    bonds.push_back(pair<int, int>(0, 1));
    bonds.push_back(pair<int, int>(1, 2));

platforms/brook/tests/TestBrookPeriodicTorsionForce.cpp

@@ -68,15 +68,19 @@ void testBrookPeriodicTorsions( FILE* log ){
    }   
 
    BrookPlatform platform( 32, "cal", log );
-   System system( numberOfParticles, 0 ); 
+   System system;
+   system.addParticle(1.0);
+   system.addParticle(1.0);
+   system.addParticle(1.0);
+   system.addParticle(1.0);
    LangevinIntegrator integrator( 0, 0.1, 0.01 );
 
    // int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
 
-   PeriodicTorsionForce* forceField = new PeriodicTorsionForce( 1 ); 
+   PeriodicTorsionForce* forceField = new PeriodicTorsionForce(); 
 
    // int index, int atom1, int atom2, int atom3, double angle, double k
-   forceField->setTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
+   forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
    system.addForce(forceField);
 
    OpenMMContext context(system, integrator, platform);

platforms/brook/tests/TestBrookRBTorsionForce.cpp

@@ -69,11 +69,15 @@ void testBrookRBTorsions( FILE* log ){
 
    BrookPlatform platform( 32, "cal", log );
    //ReferencePlatform platform;
-   System system( numberOfParticles, 0 ); 
+   System system;
+   system.addParticle(1.0);
+   system.addParticle(1.0);
+   system.addParticle(1.0);
+   system.addParticle(1.0);
    LangevinIntegrator integrator( 0, 0.1, 0.01 );
 
-   RBTorsionForce* forceField = new RBTorsionForce( 1 );
-   forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
+   RBTorsionForce* forceField = new RBTorsionForce();
+   forceField->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
    system.addForce(forceField);
 
    OpenMMContext context(system, integrator, platform);

platforms/brook/tests/TestBrookVerletIntegrator.cpp

@@ -73,14 +73,14 @@ void testVerletSingleBond( FILE* log ){
 
    BrookPlatform platform( 32, "cal", log );
 
-   System system( numberOfParticles, 0 ); 
-   system.setParticleMass(0, 2.0);
-   system.setParticleMass(1, 2.0);
+   System system; 
+   system.addParticle(2.0);
+   system.addParticle(2.0);
 
    VerletIntegrator integrator(0.001);
 
-   HarmonicBondForce* forceField = new HarmonicBondForce(1);
-   forceField->setBondParameters(0, 0, 1, 1.5, 1); 
+   HarmonicBondForce* forceField = new HarmonicBondForce();
+   forceField->addBond(0, 1, 1.5, 1);
    system.addForce(forceField);
 
 //   CMMotionRemover* remover = new CMMotionRemover();
@@ -180,16 +180,16 @@ void testVerletConstraints( FILE* log ){
 
    //ReferencePlatform platform;
    BrookPlatform platform( 32, "cal", log );
-   System system(numParticles, numConstraints);
+   System system;
    VerletIntegrator integrator(0.001);
    integrator.setConstraintTolerance(1e-5);
    NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numParticles; ++i) {
-       system.setParticleMass(i, mass );
+       system.addParticle(mass);
        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
    }
    for (int i = 0; i < numConstraints; ++i){
-       system.setConstraintParameters(i, 2*i, 2*i+1, 1.0);
+       system.addConstraint(2*i, 2*i+1, 1.0);
    }
    system.addForce(forceField);
 

platforms/brook/tests/TstBrookGBSAOBCForce.cpp

@@ -154,13 +154,15 @@ static OpenMMContext* testObcForceSetup( int numParticles, int brookContext, FIL
       platform = new ReferencePlatform();
    }
 
-   System* system                 = new System( numParticles, 0 );
+   System* system                 = new System();
+   for (int i = 0; i < numParticles; i++)
+       system.addParticle(1.0);
    LangevinIntegrator* integrator = new LangevinIntegrator(0, 0.1, 0.01);
-   GBSAOBCForce* forceField  = new GBSAOBCForce(numParticles);
+   GBSAOBCForce* forceField  = new GBSAOBCForce();
 
    for (int i = 0; i < numParticles; ++i){
        // charge radius scalingFactor
-       forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
+       forceField->addParticle(i%2 == 0 ? -1 : 1, 0.15, 1);
        //forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 1.5, 1);
    }
    system->addForce(forceField);
@@ -280,8 +282,10 @@ static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookCont
    *numParticles           = numberOfParticles;
    lineCount++;
 
-   System* system                 = new System( *numParticles, 0 );
-   GBSAOBCForce* forceField       = new GBSAOBCForce(numberOfParticles);
+   System* system                 = new System();
+   for (int i = 0; i < numberOfParticles; i++)
+       system.addParticle(1.0);
+   GBSAOBCForce* forceField       = new GBSAOBCForce();
 
    vector<Vec3> positions(numberOfParticles);
    int index                      = 0;
@@ -309,7 +313,7 @@ static OpenMMContext* testObcForceFileSetup( std::string fileName, int brookCont
    
       positions[index++]        = Vec3( coordX, coordY, coordZ );
       // charge radius scalingFactor
-      forceField->setParticleParameters( i, charge, radius, scalingFactor );
+      forceField->addParticle( charge, radius, scalingFactor );
 
       if( log ){
          (void) fprintf( log, "%d [%.6f %.6f %.6f] q=%.6f rad=%.6f scl=%.6f bR=%.6f\n", i,
@@ -431,11 +435,11 @@ void testObcSingleParticle( FILE* log ){
    BrookPlatform platform( 32, "cal", log );
    //ReferencePlatform platform;
 
-   System system(1, 0);
-   system.setParticleMass(0, 2.0);
+   System system;
+   system.addParticle(2.0);
    LangevinIntegrator integrator(0, 0.1, 0.01);
-   GBSAOBCForce* forceField = new GBSAOBCForce(1);
-   forceField->setParticleParameters(0, 0.5, 0.15, 1);
+   GBSAOBCForce* forceField = new GBSAOBCForce();
+   forceField->addParticle(0.5, 0.15, 1);
    system.addForce(forceField);
    OpenMMContext context(system, integrator, platform);
    vector<Vec3> positions(1);
@@ -468,11 +472,13 @@ void testObcEConsistentForce( FILE* log ){
 
    //ReferencePlatform platform;
    const int numParticles = 10; 
-   System system(numParticles, 0); 
+   System system; 
    LangevinIntegrator integrator(0, 0.1, 0.01);
-   GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
-   for (int i = 0; i < numParticles; ++i)
-       forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1); 
+   GBSAOBCForce* forceField = new GBSAOBCForce();
+   for (int i = 0; i < numParticles; ++i) {
+       system.addParticle(1.0);
+       forceField->addParticle(i%2 == 0 ? -1 : 1, 0.15, 1);
+   }
    system.addForce(forceField);
    OpenMMContext context(system, integrator, platform);
    

platforms/cuda/tests/TestCudaAndersenThermostat.cpp

@@ -53,11 +53,11 @@ void testTemperature() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     CudaPlatform platform;
-    System system(numParticles, 0);
+    System system;
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 2.0);
+        system.addParticle(2.0);
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
@@ -91,11 +91,11 @@ void testRandomSeed() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     CudaPlatform platform;
-    System system(numParticles, 0);
+    System system;
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 2.0);
+        system.addParticle(2.0);
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);

platforms/cuda/tests/TestCudaBrownianIntegrator.cpp

@@ -55,13 +55,13 @@ const double TOL = 1e-5;
 
 void testSingleBond() {
     CudaPlatform platform;
-    System system(2, 0);
-    system.setParticleMass(0, 2.0);
-    system.setParticleMass(1, 2.0);
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
     double dt = 0.01;
     BrownianIntegrator integrator(0, 0.1, dt);
-    HarmonicBondForce* forceField = new HarmonicBondForce(1);
-    forceField->setBondParameters(0, 0, 1, 1.5, 1);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
+    forceField->addBond(0, 1, 1.5, 1);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -92,13 +92,13 @@ void testTemperature() {
     const int numBonds = numParticles-1;
     const double temp = 10.0;
     CudaPlatform platform;
-    System system(numParticles, 0);
+    System system;
     BrownianIntegrator integrator(temp, 2.0, 0.01);
-    HarmonicBondForce* forceField = new HarmonicBondForce(numBonds);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
     for (int i = 0; i < numParticles; ++i)
-        system.setParticleMass(i, 2.0);
+        system.addParticle(2.0);
     for (int i = 0; i < numBonds; ++i)
-        forceField->setBondParameters(i, i, i+1, 1.0, 5.0);
+        forceField->addBond(i, i+1, 1.0, 5.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
@@ -129,19 +129,19 @@ void testConstraints() {
     const int numConstraints = 5;
     const double temp = 20.0;
     CudaPlatform platform;
-    System system(numParticles, numConstraints);
+    System system;
     BrownianIntegrator integrator(temp, 2.0, 0.001);
     integrator.setConstraintTolerance(1e-5);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 10.0);
+        system.addParticle(10.0);
         forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
-    system.setConstraintParameters(0, 0, 1, 1.0);
-    system.setConstraintParameters(1, 1, 2, 1.0);
-    system.setConstraintParameters(2, 2, 3, 1.0);
-    system.setConstraintParameters(3, 4, 5, 1.0);
-    system.setConstraintParameters(4, 6, 7, 1.0);
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(1, 2, 1.0);
+    system.addConstraint(2, 3, 1.0);
+    system.addConstraint(4, 5, 1.0);
+    system.addConstraint(6, 7, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
@@ -176,11 +176,11 @@ void testRandomSeed() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     CudaPlatform platform;
-    System system(numParticles, 0);
+    System system;
     BrownianIntegrator integrator(temp, 2.0, 0.001);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 2.0);
+        system.addParticle(2.0);
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);

platforms/cuda/tests/TestCudaCMMotionRemover.cpp

@@ -63,13 +63,13 @@ Vec3 calcCM(const vector<Vec3>& values, System& system) {
 void testMotionRemoval(Integrator& integrator) {
     const int numParticles = 8;
     CudaPlatform platform;
-    System system(numParticles, 0);
-    HarmonicBondForce* bonds = new HarmonicBondForce(1);
-    bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
+    System system;
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    bonds->addBond(2, 3, 2.0, 0.5);
     system.addForce(bonds);
     NonbondedForce* nonbonded = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, i+1);
+        system.addParticle(i+1);
         nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(nonbonded);

platforms/cuda/tests/TestCudaEwald.cpp

@@ -56,7 +56,9 @@ const double TOL = 1e-5;
 
 void testEwald() {
     CudaPlatform platform;
-    System system(2, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* nonbonded = new NonbondedForce();
     nonbonded->addParticle(1.0, 1, 0);
@@ -85,10 +87,13 @@ void testEwald() {
 
 void testPeriodic() {
     CudaPlatform platform;
-    System system(3, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
-    HarmonicBondForce* bonds = new HarmonicBondForce(1);
-    bonds->setBondParameters(0, 0, 1, 1, 0);
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    bonds->addBond(0, 1, 1, 0);
     system.addForce(bonds);
     NonbondedForce* nonbonded = new NonbondedForce();
     nonbonded->addParticle(1.0, 1, 0);

platforms/cuda/tests/TestCudaGBSAOBCForce.cpp

@@ -53,12 +53,12 @@ const double TOL = 1e-5;
 
 void testSingleParticle() {
     CudaPlatform platform;
-    System system(1, 0);
-    system.setParticleMass(0, 2.0);
+    System system;
+    system.addParticle(2.0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* gbsa = new GBSAOBCForce(1);
+    GBSAOBCForce* gbsa = new GBSAOBCForce();
     NonbondedForce* nonbonded = new NonbondedForce();
-    gbsa->setParticleParameters(0, 0.5, 0.15, 1);
+    gbsa->addParticle( 0.5, 0.15, 1);
     nonbonded->addParticle(0.5, 1, 0);
     system.addForce(gbsa);
     system.addForce(nonbonded);
@@ -77,13 +77,15 @@ void testSingleParticle() {
 
 void testCutoffAndPeriodic() {
     CudaPlatform cuda;
-    System system(2, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* gbsa = new GBSAOBCForce(2);
+    GBSAOBCForce* gbsa = new GBSAOBCForce();
     NonbondedForce* nonbonded = new NonbondedForce();
-    gbsa->setParticleParameters(0, -1, 0.15, 1);
+    gbsa->addParticle(-1, 0.15, 1);
     nonbonded->addParticle(-1, 1, 0);
-    gbsa->setParticleParameters(1, 1, 0.15, 1);
+    gbsa->addParticle(1, 0.15, 1);
     nonbonded->addParticle(1, 1, 0);
     const double cutoffDistance = 3.0;
     const double boxSize = 10.0;
@@ -128,13 +130,14 @@ void testCutoffAndPeriodic() {
 void testForce(int numParticles, NonbondedForce::NonbondedMethod method) {
     CudaPlatform cuda;
     ReferencePlatform reference;
-    System system(numParticles, 0);
+    System system;
     LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* gbsa = new GBSAOBCForce(numParticles);
+    GBSAOBCForce* gbsa = new GBSAOBCForce();
     NonbondedForce* nonbonded = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(1.0);
         double charge = i%2 == 0 ? -1 : 1;
-        gbsa->setParticleParameters(i, charge, 0.15, 1);
+        gbsa->addParticle(charge, 0.15, 1);
         nonbonded->addParticle(charge, 1, 0);
     }
     nonbonded->setNonbondedMethod(method);

platforms/cuda/tests/TestCudaHarmonicAngleForce.cpp

@@ -50,11 +50,15 @@ const double TOL = 1e-5;
 
 void testAngles() {
     CudaPlatform platform;
-    System system(4, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
-    HarmonicAngleForce* forceField = new HarmonicAngleForce(2);
-    forceField->setAngleParameters(0, 0, 1, 2, PI_M/3, 1.1);
-    forceField->setAngleParameters(1, 1, 2, 3, PI_M/2, 1.2);
+    HarmonicAngleForce* forceField = new HarmonicAngleForce();
+    forceField->addAngle(0, 1, 2, PI_M/3, 1.1);
+    forceField->addAngle(1, 2, 3, PI_M/2, 1.2);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(4);

platforms/cuda/tests/TestCudaHarmonicBondForce.cpp

@@ -50,11 +50,14 @@ const double TOL = 1e-5;
 
 void testBonds() {
     CudaPlatform platform;
-    System system(3, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
-    HarmonicBondForce* forceField = new HarmonicBondForce(2);
-    forceField->setBondParameters(0, 0, 1, 1.5, 0.8);
-    forceField->setBondParameters(1, 1, 2, 1.2, 0.7);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
+    forceField->addBond(0, 1, 1.5, 0.8);
+    forceField->addBond(1, 2, 1.2, 0.7);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(3);

platforms/cuda/tests/TestCudaLangevinIntegrator.cpp

@@ -52,12 +52,12 @@ const double TOL = 1e-5;
 
 void testSingleBond() {
     CudaPlatform platform;
-    System system(2, 0);
-    system.setParticleMass(0, 2.0);
-    system.setParticleMass(1, 2.0);
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
-    HarmonicBondForce* forceField = new HarmonicBondForce(1);
-    forceField->setBondParameters(0, 0, 1, 1.5, 1);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
+    forceField->addBond(0, 1, 1.5, 1);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -98,11 +98,11 @@ void testTemperature() {
     const int numParticles = 8;
     const double temp = 100.0;
     CudaPlatform platform;
-    System system(numParticles, 0);
+    System system;
     LangevinIntegrator integrator(temp, 2.0, 0.01);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 2.0);
+        system.addParticle(2.0);
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
@@ -134,19 +134,19 @@ void testConstraints() {
     const int numConstraints = 5;
     const double temp = 100.0;
     CudaPlatform platform;
-    System system(numParticles, numConstraints);
+    System system;
     LangevinIntegrator integrator(temp, 2.0, 0.01);
     integrator.setConstraintTolerance(1e-5);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 10.0);
+        system.addParticle(10.0);
         forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
-    system.setConstraintParameters(0, 0, 1, 1.0);
-    system.setConstraintParameters(1, 1, 2, 1.0);
-    system.setConstraintParameters(2, 2, 3, 1.0);
-    system.setConstraintParameters(3, 4, 5, 1.0);
-    system.setConstraintParameters(4, 6, 7, 1.0);
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(1, 2, 1.0);
+    system.addConstraint(2, 3, 1.0);
+    system.addConstraint(4, 5, 1.0);
+    system.addConstraint(6, 7, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
@@ -181,11 +181,11 @@ void testRandomSeed() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     CudaPlatform platform;
-    System system(numParticles, 0);
+    System system;
     LangevinIntegrator integrator(temp, 2.0, 0.01);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 2.0);
+        system.addParticle(2.0);
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);

platforms/cuda/tests/TestCudaNonbondedForce.cpp

@@ -56,7 +56,9 @@ const double TOL = 1e-5;
 
 void testCoulomb() {
     CudaPlatform platform;
-    System system(2, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     NonbondedForce* forceField = new NonbondedForce();
     forceField->addParticle(0.5, 1, 0);
@@ -77,7 +79,9 @@ void testCoulomb() {
 
 void testLJ() {
     CudaPlatform platform;
-    System system(2, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     NonbondedForce* forceField = new NonbondedForce();
     forceField->addParticle(0, 1.2, 1);
@@ -100,11 +104,13 @@ void testLJ() {
 
 void testExclusionsAnd14() {
     CudaPlatform platform;
-    System system(5, 0);
+    System system;
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     NonbondedForce* nonbonded = new NonbondedForce();
-    for (int i = 0; i < 5; ++i)
+    for (int i = 0; i < 5; ++i) {
+        system.addParticle(1.0);
         nonbonded->addParticle(0, 1.5, 0);
+    }
     vector<pair<int, int> > bonds;
     bonds.push_back(pair<int, int>(0, 1));
     bonds.push_back(pair<int, int>(1, 2));
@@ -185,7 +191,10 @@ void testExclusionsAnd14() {
 
 void testCutoff() {
     CudaPlatform platform;
-    System system(3, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     NonbondedForce* forceField = new NonbondedForce();
     forceField->addParticle(1.0, 1, 0);
@@ -218,12 +227,14 @@ void testCutoff() {
 
 void testCutoff14() {
     CudaPlatform platform;
-    System system(5, 0);
+    System system;
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     NonbondedForce* nonbonded = new NonbondedForce();
     nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
-    for (int i = 0; i < 5; ++i)
+    for (int i = 0; i < 5; ++i) {
+        system.addParticle(1.0);
         nonbonded->addParticle(0, 1.5, 0);
+    }
     const double cutoff = 3.5;
     nonbonded->setCutoffDistance(cutoff);
     vector<pair<int, int> > bonds;
@@ -313,7 +324,10 @@ void testCutoff14() {
 
 void testPeriodic() {
     CudaPlatform platform;
-    System system(3, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     NonbondedForce* nonbonded = new NonbondedForce();
     nonbonded->addParticle(1.0, 1, 0);
@@ -351,10 +365,12 @@ void testLargeSystem() {
     const double tol = 1e-3;
     CudaPlatform cuda;
     ReferencePlatform reference;
-    System system(numParticles, 0);
+    System system;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* nonbonded = new NonbondedForce();
-    HarmonicBondForce* bonds = new HarmonicBondForce(numMolecules);
+    HarmonicBondForce* bonds = new HarmonicBondForce();
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
     init_gen_rand(0);
@@ -371,7 +387,7 @@ void testLargeSystem() {
         positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
         velocities[2*i] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
         velocities[2*i+1] = Vec3(genrand_real2(), genrand_real2(), genrand_real2());
-        bonds->setBondParameters(i, 2*i, 2*i+1, 1.0, 0.1);
+        bonds->addBond(2*i, 2*i+1, 1.0, 0.1);
     }
 
     // Try with cutoffs but not periodic boundary conditions, and make sure the Cuda and Reference
@@ -423,12 +439,13 @@ void testBlockInteractions(bool periodic) {
     const double cutoff = 1.0;
     const double boxSize = (periodic ? 5.1 : 1.1);
     CudaPlatform cuda;
-    System system(numParticles, 0);
+    System system;
     VerletIntegrator integrator(0.01);
     NonbondedForce* nonbonded = new NonbondedForce();
     vector<Vec3> positions(numParticles);
     init_gen_rand(0);
     for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
         nonbonded->addParticle(1.0, 0.2, 0.2);
         positions[i] = Vec3(boxSize*(3*genrand_real2()-1), boxSize*(3*genrand_real2()-1), boxSize*(3*genrand_real2()-1));
     }

platforms/cuda/tests/TestCudaPeriodicTorsionForce.cpp

@@ -50,10 +50,14 @@ const double TOL = 1e-5;
 
 void testPeriodicTorsions() {
     CudaPlatform platform;
-    System system(4, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
-    PeriodicTorsionForce* forceField = new PeriodicTorsionForce(1);
-    forceField->setTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
+    PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
+    forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(4);

platforms/cuda/tests/TestCudaRBTorsionForce.cpp

@@ -50,10 +50,14 @@ const double TOL = 1e-5;
 
 void testRBTorsions() {
     CudaPlatform platform;
-    System system(4, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
-    RBTorsionForce* forceField = new RBTorsionForce(1);
-    forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
+    RBTorsionForce* forceField = new RBTorsionForce();
+    forceField->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(4);

platforms/cuda/tests/TestCudaSettle.cpp

@@ -53,20 +53,20 @@ void testConstraints() {
     const int numConstraints = numMolecules*3;
     const double temp = 100.0;
     CudaPlatform platform;
-    System system(numParticles, numConstraints);
+    System system;
     LangevinIntegrator integrator(temp, 2.0, 0.001);
     integrator.setConstraintTolerance(1e-5);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numMolecules; ++i) {
-        system.setParticleMass(i*3, 16.0);
-        system.setParticleMass(i*3+1, 1.0);
-        system.setParticleMass(i*3+2, 1.0);
+        system.addParticle(16.0);
+        system.addParticle(1.0);
+        system.addParticle(1.0);
         forceField->addParticle(-0.82, 0.317, 0.65);
         forceField->addParticle(0.41, 1.0, 0.0);
         forceField->addParticle(0.41, 1.0, 0.0);
-        system.setConstraintParameters(i*3, i*3, i*3+1, 0.1);
-        system.setConstraintParameters(i*3+1, i*3, i*3+2, 0.1);
-        system.setConstraintParameters(i*3+2, i*3+1, i*3+2, 0.163);
+        system.addConstraint(i*3, i*3+1, 0.1);
+        system.addConstraint(i*3, i*3+2, 0.1);
+        system.addConstraint(i*3+1, i*3+2, 0.163);
     }
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);

platforms/cuda/tests/TestCudaStreams.cpp

@@ -49,7 +49,9 @@ template <class T, int WIDTH>
 void testStream(Stream::DataType type, T scale) {
     const int size = 100;
     CudaPlatform platform;
-    System system(size, 0);
+    System system;
+    for (int i = 0; i < size; i++)
+        system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
     OpenMMContext context(system, integrator, platform);
     OpenMMContextImpl* impl = *reinterpret_cast<OpenMMContextImpl**>(&context);

platforms/cuda/tests/TestCudaVerletIntegrator.cpp

@@ -52,12 +52,12 @@ const double TOL = 1e-5;
 
 void testSingleBond() {
     CudaPlatform platform;
-    System system(2, 0);
-    system.setParticleMass(0, 2.0);
-    system.setParticleMass(1, 2.0);
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
     VerletIntegrator integrator(0.01);
-    HarmonicBondForce* forceField = new HarmonicBondForce(1);
-    forceField->setBondParameters(0, 0, 1, 1.5, 1);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
+    forceField->addBond(0, 1, 1.5, 1);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -90,19 +90,19 @@ void testConstraints() {
     const int numConstraints = 5;
     const double temp = 100.0;
     CudaPlatform platform;
-    System system(numParticles, numConstraints);
+    System system;
     VerletIntegrator integrator(0.001);
     integrator.setConstraintTolerance(1e-5);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 10.0);
+        system.addParticle(10.0);
         forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
-    system.setConstraintParameters(0, 0, 1, 1.0);
-    system.setConstraintParameters(1, 1, 2, 1.0);
-    system.setConstraintParameters(2, 2, 3, 1.0);
-    system.setConstraintParameters(3, 4, 5, 1.0);
-    system.setConstraintParameters(4, 6, 7, 1.0);
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(1, 2, 1.0);
+    system.addConstraint(2, 3, 1.0);
+    system.addConstraint(4, 5, 1.0);
+    system.addConstraint(6, 7, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(numParticles);

platforms/reference/tests/TestReferenceAndersenThermostat.cpp

@@ -53,11 +53,11 @@ void testTemperature() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     ReferencePlatform platform;
-    System system(numParticles, 0);
+    System system;
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 2.0);
+        system.addParticle(2.0);
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
@@ -91,11 +91,11 @@ void testRandomSeed() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     ReferencePlatform platform;
-    System system(numParticles, 0);
+    System system;
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
-        system.setParticleMass(i, 2.0);
+        system.addParticle(2.0);
         forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);