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/reference/tests/TestReferenceBrownianIntegrator.cpp

@@ -52,13 +52,13 @@ const double TOL = 1e-5;
 
 void testSingleBond() {
     ReferencePlatform 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);
@@ -89,14 +89,14 @@ void testTemperature() {
     const int numBonds = numParticles-1;
     const double temp = 10.0;
     ReferencePlatform 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);
@@ -126,16 +126,16 @@ void testConstraints() {
     const int numParticles = 8;
     const double temp = 100.0;
     ReferencePlatform platform;
-    System system(numParticles, numParticles-1);
+    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);
     }
     for (int i = 0; i < numParticles-1; ++i)
-        system.setConstraintParameters(i, i, i+1, 1.0);
+        system.addConstraint(i, i+1, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
@@ -167,11 +167,11 @@ void testRandomSeed() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     ReferencePlatform 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/reference/tests/TestReferenceCMMotionRemover.cpp

@@ -64,14 +64,14 @@ void testMotionRemoval() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     ReferencePlatform platform;
-    System system(numParticles, 0);
+    System system;
     VerletIntegrator integrator(0.01);
-    HarmonicBondForce* bonds = new HarmonicBondForce(1);
-    bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
+    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/reference/tests/TestReferenceEwald.cpp

@@ -51,7 +51,9 @@ const double TOL = 1e-5;
 
 void testEwald() {
     ReferencePlatform 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);

platforms/reference/tests/TestReferenceGBSAOBCForce.cpp

@@ -52,11 +52,11 @@ const double TOL = 1e-5;
 
 void testSingleParticle() {
     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);
@@ -73,13 +73,15 @@ void testSingleParticle() {
 
 void testCutoffAndPeriodic() {
     ReferencePlatform platform;
-    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;
@@ -124,11 +126,13 @@ void testCutoffAndPeriodic() {
 void testForce() {
     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/reference/tests/TestReferenceGBVIForce.cpp

@@ -54,16 +54,16 @@ const double TOL = 1e-5;
 
 void testSingleParticle() {
     ReferencePlatform platform;
-    System system(1, 0);
-    system.setParticleMass(0, 2.0);
+    System system;
+    system.addParticle(2.0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
 
-    GBVIForce* forceField = new GBVIForce(1);
+    GBVIForce* forceField = new GBVIForce();
 
     double charge         = 0.0;
     double radius         = 0.15;
     double gamma          = 1.0;
-    forceField->setParticleParameters(0, charge, radius, gamma);
+    forceField->addParticle(charge, radius, gamma);
     system.addForce(forceField);
 
     OpenMMContext context(system, integrator, platform);
@@ -143,22 +143,22 @@ void testEnergyEthane() {
 
     ReferencePlatform platform;
     const int numParticles = 8;
-    System system(numParticles, 0);
+    System system;
     LangevinIntegrator integrator(0, 0.1, 0.01);
 
     //void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k)
     double C_HBondDistance   = 0.1097;
     double C_CBondDistance   = 0.1504;
-    HarmonicBondForce* bonds = new HarmonicBondForce(7);
-    bonds->setBondParameters(0, 0, 1, C_HBondDistance, 0.0); 
-    bonds->setBondParameters(1, 2, 1, C_HBondDistance, 0.0); 
-    bonds->setBondParameters(2, 3, 1, C_HBondDistance, 0.0); 
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    bonds->addBond(0, 1, C_HBondDistance, 0.0);
+    bonds->addBond(2, 1, C_HBondDistance, 0.0);
+    bonds->addBond(3, 1, C_HBondDistance, 0.0);
 
-    bonds->setBondParameters(3, 1, 4, C_CBondDistance, 0.0); 
+    bonds->addBond(1, 4, C_CBondDistance, 0.0);
 
-    bonds->setBondParameters(4, 5, 4, C_HBondDistance, 0.0); 
-    bonds->setBondParameters(5, 6, 4, C_HBondDistance, 0.0); 
-    bonds->setBondParameters(6, 7, 4, C_HBondDistance, 0.0); 
+    bonds->addBond(5, 4, C_HBondDistance, 0.0);
+    bonds->addBond(6, 4, C_HBondDistance, 0.0);
+    bonds->addBond(7, 4, C_HBondDistance, 0.0);
 
     system.addForce(bonds);
 
@@ -182,20 +182,22 @@ void testEnergyEthane() {
     int VI = 1;
     if( VI ){
        (void) fprintf( stderr, "Applying GB/VI\n" );
-       GBVIForce* forceField = new GBVIForce(numParticles);
+       GBVIForce* forceField = new GBVIForce();
        for( int i = 0; i < numParticles; i++ ){
-          forceField->setParticleParameters(i, H_charge, H_radius, H_gamma);
+          system.addParticle(1.0);
+          forceField->addParticle( H_charge, H_radius, H_gamma);
        }
        forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
        forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
        system.addForce(forceField);
     } else {
        (void) fprintf( stderr, "Applying GBSA OBC\n" );
-       GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
+       GBSAOBCForce* forceField = new GBSAOBCForce();
        double H_scale           =  0.85;
        double C_scale           =  0.72;
        for( int i = 0; i < numParticles; i++ ){
-          forceField->setParticleParameters(i, H_charge, H_radius, H_scale );
+          system.addParticle(1.0);
+          forceField->addParticle(H_charge, H_radius, H_scale );
        }
        forceField->setParticleParameters(1, C_charge, C_radius, C_scale);
        forceField->setParticleParameters(4, C_charge, C_radius, C_scale);
@@ -266,13 +268,15 @@ void testEnergyTwoParticle() {
 
     ReferencePlatform platform;
     const int numParticles = 2;
-    System system(numParticles, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
 
     //void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k)
     double C_HBondDistance   = 3.0;
-    HarmonicBondForce* bonds = new HarmonicBondForce(1);
-    bonds->setBondParameters(0, 0, 1, C_HBondDistance, 0.0); 
+    HarmonicBondForce* bonds = new HarmonicBondForce();
+    bonds->addBond(0, 1, C_HBondDistance, 0.0);
     system.addForce(bonds);
 
     double C_radius, C_gamma, C_charge, H_radius, H_gamma, H_charge;
@@ -298,15 +302,15 @@ void testEnergyTwoParticle() {
     int VI = 1;
     if( VI ){
        (void) fprintf( stderr, "Applying GB/VI\n" );
-       GBVIForce* forceField = new GBVIForce(numParticles);
-       forceField->setParticleParameters(0, H_charge, H_radius, H_gamma);
-       forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
+       GBVIForce* forceField = new GBVIForce();
+       forceField->addParticle(H_charge, H_radius, H_gamma);
+       forceField->addParticle(C_charge, C_radius, C_gamma);
        system.addForce(forceField);
     } else {
        (void) fprintf( stderr, "Applying GBSA OBC\n" );
-       GBSAOBCForce* forceField = new GBSAOBCForce(numParticles);
-       forceField->setParticleParameters(0, H_charge, H_radius, 1.0);
-       forceField->setParticleParameters(1, C_charge, C_radius, 1.0);
+       GBSAOBCForce* forceField = new GBSAOBCForce();
+       forceField->addParticle(H_charge, H_radius, 1.0);
+       forceField->addParticle(C_charge, C_radius, 1.0);
        system.addForce(forceField);
     }
 

platforms/reference/tests/TestReferenceHarmonicAngleForce.cpp

@@ -50,11 +50,15 @@ const double TOL = 1e-5;
 
 void testAngles() {
     ReferencePlatform platform;
-    System system(4, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(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/reference/tests/TestReferenceHarmonicBondForce.cpp

@@ -50,11 +50,14 @@ const double TOL = 1e-5;
 
 void testBonds() {
     ReferencePlatform platform;
-    System system(3, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(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/reference/tests/TestReferenceKineticEnergy.cpp

@@ -48,9 +48,9 @@ const double TOL = 1e-5;
 
 void testCalcKE() {
     ReferencePlatform platform;
-    System system(4, 0);
+    System system;
     for (int i = 0; i < 4; ++i)
-        system.setParticleMass(i, i+1);
+        system.addParticle(i+1);
     VerletIntegrator integrator(0.01);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> velocities(4);

platforms/reference/tests/TestReferenceLangevinIntegrator.cpp

@@ -52,12 +52,12 @@ const double TOL = 1e-5;
 
 void testSingleBond() {
     ReferencePlatform 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;
     ReferencePlatform 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);
@@ -133,16 +133,16 @@ void testConstraints() {
     const int numParticles = 8;
     const double temp = 100.0;
     ReferencePlatform platform;
-    System system(numParticles, numParticles-1);
+    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);
     }
     for (int i = 0; i < numParticles-1; ++i)
-        system.setConstraintParameters(i, i, i+1, 1.0);
+        system.addConstraint(i, i+1, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(numParticles);
@@ -174,11 +174,11 @@ void testRandomSeed() {
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     ReferencePlatform 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/reference/tests/TestReferenceNonbondedForce.cpp

@@ -51,7 +51,9 @@ const double TOL = 1e-5;
 
 void testCoulomb() {
     ReferencePlatform platform;
-    System system(2, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce();
     forceField->addParticle(0.5, 1, 0);
@@ -72,7 +74,9 @@ void testCoulomb() {
 
 void testLJ() {
     ReferencePlatform platform;
-    System system(2, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce();
     forceField->addParticle(0, 1.2, 1);
@@ -95,11 +99,13 @@ void testLJ() {
 
 void testExclusionsAnd14() {
     ReferencePlatform platform;
-    System system(5, 0);
+    System system;
     VerletIntegrator integrator(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));
@@ -181,7 +187,10 @@ void testExclusionsAnd14() {
 
 void testCutoff() {
     ReferencePlatform platform;
-    System system(3, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce();
     forceField->addParticle(1.0, 1, 0);
@@ -214,11 +223,13 @@ void testCutoff() {
 
 void testCutoff14() {
     ReferencePlatform platform;
-    System system(5, 0);
+    System system;
     VerletIntegrator integrator(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);
+    }
     nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
     const double cutoff = 3.5;
     nonbonded->setCutoffDistance(cutoff);
@@ -309,7 +320,10 @@ void testCutoff14() {
 
 void testPeriodic() {
     ReferencePlatform platform;
-    System system(3, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* nonbonded = new NonbondedForce();
     nonbonded->addParticle(1.0, 1, 0);

platforms/reference/tests/TestReferencePeriodicTorsionForce.cpp

@@ -50,10 +50,14 @@ const double TOL = 1e-5;
 
 void testPeriodicTorsions() {
     ReferencePlatform platform;
-    System system(4, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(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/reference/tests/TestReferenceRBTorsionForce.cpp

@@ -50,10 +50,14 @@ const double TOL = 1e-5;
 
 void testRBTorsions() {
     ReferencePlatform platform;
-    System system(4, 0);
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
     VerletIntegrator integrator(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/reference/tests/TestReferenceVerletIntegrator.cpp

@@ -52,12 +52,12 @@ const double TOL = 1e-5;
 
 void testSingleBond() {
     ReferencePlatform 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);
@@ -89,16 +89,16 @@ void testConstraints() {
     const int numParticles = 8;
     const double temp = 100.0;
     ReferencePlatform platform;
-    System system(numParticles, numParticles-1);
+    System system;
     VerletIntegrator integrator(0.002);
     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);
     }
     for (int i = 0; i < numParticles-1; ++i)
-        system.setConstraintParameters(i, i, i+1, 1.0);
+        system.addConstraint(i, i+1, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(numParticles);