Renamed "atoms" to "particles"

platforms/reference/tests/TestReferenceBrownianIntegrator.cpp

@@ -53,8 +53,8 @@ const double TOL = 1e-5;
 void testSingleBond() {
     ReferencePlatform platform;
     System system(2, 0);
-    system.setAtomMass(0, 2.0);
-    system.setAtomMass(1, 2.0);
+    system.setParticleMass(0, 2.0);
+    system.setParticleMass(1, 2.0);
     double dt = 0.01;
     BrownianIntegrator integrator(0, 0.1, dt);
     HarmonicBondForce* forceField = new HarmonicBondForce(1);
@@ -85,23 +85,23 @@ void testSingleBond() {
 }
 
 void testTemperature() {
-    const int numAtoms = 8;
-    const int numBonds = numAtoms-1;
+    const int numParticles = 8;
+    const int numBonds = numParticles-1;
     const double temp = 100.0;
     ReferencePlatform platform;
-    System system(numAtoms, 0);
+    System system(numParticles, 0);
     BrownianIntegrator integrator(temp, 2.0, 0.01);
     HarmonicBondForce* forceField = new HarmonicBondForce(numBonds);
-    for (int i = 0; i < numAtoms; ++i) {
-        system.setAtomMass(i, 2.0);
-//        forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.setParticleMass(i, 2.0);
+//        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     for (int i = 0; i < numBonds; ++i)
         forceField->setBondParameters(i, i, i+1, 1.0, i);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
-    vector<Vec3> positions(numAtoms);
-    for (int i = 0; i < numAtoms; ++i)
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; ++i)
         positions[i] = Vec3(i, 0, 0);
     context.setPositions(positions);
     
@@ -123,24 +123,24 @@ void testTemperature() {
 }
 
 void testConstraints() {
-    const int numAtoms = 8;
+    const int numParticles = 8;
     const double temp = 100.0;
     ReferencePlatform platform;
-    System system(numAtoms, numAtoms-1);
+    System system(numParticles, numParticles-1);
     BrownianIntegrator integrator(temp, 2.0, 0.001);
-    NonbondedForce* forceField = new NonbondedForce(numAtoms, 0);
-    for (int i = 0; i < numAtoms; ++i) {
-        system.setAtomMass(i, 10.0);
-        forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.setParticleMass(i, 10.0);
+        forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
-    for (int i = 0; i < numAtoms-1; ++i)
+    for (int i = 0; i < numParticles-1; ++i)
         system.setConstraintParameters(i, i, i+1, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
-    vector<Vec3> positions(numAtoms);
-    vector<Vec3> velocities(numAtoms);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
     init_gen_rand(0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
         positions[i] = Vec3(i/2, (i+1)/2, 0);
         velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
     }
@@ -151,7 +151,7 @@ void testConstraints() {
     
     for (int i = 0; i < 1000; ++i) {
         State state = context.getState(State::Positions);
-        for (int j = 0; j < numAtoms-1; ++j) {
+        for (int j = 0; j < numParticles-1; ++j) {
             Vec3 p1 = state.getPositions()[j];
             Vec3 p2 = state.getPositions()[j+1];
             double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));

platforms/reference/tests/TestReferenceCMMotionRemover.cpp

@@ -51,37 +51,37 @@ using namespace std;
 
 Vec3 calcCM(const vector<Vec3>& values, System& system) {
     Vec3 cm;
-    for (int j = 0; j < system.getNumAtoms(); ++j) {
-        cm[0] += values[j][0]*system.getAtomMass(j);
-        cm[1] += values[j][1]*system.getAtomMass(j);
-        cm[2] += values[j][2]*system.getAtomMass(j);
+    for (int j = 0; j < system.getNumParticles(); ++j) {
+        cm[0] += values[j][0]*system.getParticleMass(j);
+        cm[1] += values[j][1]*system.getParticleMass(j);
+        cm[2] += values[j][2]*system.getParticleMass(j);
     }
     return cm;
 }
 
 void testMotionRemoval() {
-    const int numAtoms = 8;
+    const int numParticles = 8;
     const double temp = 100.0;
     const double collisionFreq = 10.0;
     ReferencePlatform platform;
-    System system(numAtoms, 0);
+    System system(numParticles, 0);
     VerletIntegrator integrator(0.01);
     HarmonicBondForce* bonds = new HarmonicBondForce(1);
     bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
     system.addForce(bonds);
-    NonbondedForce* nonbonded = new NonbondedForce(numAtoms, 0);
-    for (int i = 0; i < numAtoms; ++i) {
-        system.setAtomMass(i, i+1);
-        nonbonded->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    NonbondedForce* nonbonded = new NonbondedForce(numParticles, 0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.setParticleMass(i, i+1);
+        nonbonded->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(nonbonded);
     CMMotionRemover* remover = new CMMotionRemover();
     system.addForce(remover);
     OpenMMContext context(system, integrator, platform);
-    vector<Vec3> positions(numAtoms);
-    vector<Vec3> velocities(numAtoms);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
     init_gen_rand(0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
         positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
         velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
     }

platforms/reference/tests/TestReferenceGBSAOBCForceField.cpp

@@ -49,13 +49,13 @@ using namespace std;
 
 const double TOL = 1e-5;
 
-void testSingleAtom() {
+void testSingleParticle() {
     ReferencePlatform platform;
     System system(1, 0);
-    system.setAtomMass(0, 2.0);
+    system.setParticleMass(0, 2.0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
     GBSAOBCForceField* forceField = new GBSAOBCForceField(1);
-    forceField->setAtomParameters(0, 0.5, 0.15, 1);
+    forceField->setParticleParameters(0, 0.5, 0.15, 1);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(1);
@@ -72,20 +72,20 @@ void testSingleAtom() {
 
 void testForce() {
     ReferencePlatform platform;
-    const int numAtoms = 10;
-    System system(numAtoms, 0);
+    const int numParticles = 10;
+    System system(numParticles, 0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForceField* forceField = new GBSAOBCForceField(numAtoms);
-    for (int i = 0; i < numAtoms; ++i)
-        forceField->setAtomParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
+    GBSAOBCForceField* forceField = new GBSAOBCForceField(numParticles);
+    for (int i = 0; i < numParticles; ++i)
+        forceField->setParticleParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     
-    // Set random positions for all the atoms.
+    // Set random positions for all the particles.
     
-    vector<Vec3> positions(numAtoms);
+    vector<Vec3> positions(numParticles);
     init_gen_rand(0);
-    for (int i = 0; i < numAtoms; ++i)
+    for (int i = 0; i < numParticles; ++i)
         positions[i] = Vec3(5.0*genrand_real2(), 5.0*genrand_real2(), 5.0*genrand_real2());
     context.setPositions(positions);
     State state = context.getState(State::Forces | State::Energy);
@@ -93,14 +93,14 @@ void testForce() {
     // Take a small step in the direction of the energy gradient.
     
     double norm = 0.0;
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
         Vec3 f = state.getForces()[i];
         norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
     }
     norm = std::sqrt(norm);
     const double delta = 1e-3;
     double step = delta/norm;
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
         Vec3 p = positions[i];
         Vec3 f = state.getForces()[i];
         positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
@@ -115,7 +115,7 @@ void testForce() {
 
 int main() {
     try {
-        testSingleAtom();
+        testSingleParticle();
         testForce();
     }
     catch(const exception& e) {

platforms/reference/tests/TestReferenceKineticEnergy.cpp

@@ -50,7 +50,7 @@ void testCalcKE() {
     ReferencePlatform platform;
     System system(4, 0);
     for (int i = 0; i < 4; ++i)
-        system.setAtomMass(i, i+1);
+        system.setParticleMass(i, i+1);
     VerletIntegrator integrator(0.01);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> velocities(4);

platforms/reference/tests/TestReferenceLangevinIntegrator.cpp

@@ -53,8 +53,8 @@ const double TOL = 1e-5;
 void testSingleBond() {
     ReferencePlatform platform;
     System system(2, 0);
-    system.setAtomMass(0, 2.0);
-    system.setAtomMass(1, 2.0);
+    system.setParticleMass(0, 2.0);
+    system.setParticleMass(1, 2.0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
     HarmonicBondForce* forceField = new HarmonicBondForce(1);
     forceField->setBondParameters(0, 0, 1, 1.5, 1);
@@ -95,20 +95,20 @@ void testSingleBond() {
 }
 
 void testTemperature() {
-    const int numAtoms = 8;
+    const int numParticles = 8;
     const double temp = 100.0;
     ReferencePlatform platform;
-    System system(numAtoms, 0);
+    System system(numParticles, 0);
     LangevinIntegrator integrator(temp, 2.0, 0.01);
-    NonbondedForce* forceField = new NonbondedForce(numAtoms, 0);
-    for (int i = 0; i < numAtoms; ++i) {
-        system.setAtomMass(i, 2.0);
-        forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.setParticleMass(i, 2.0);
+        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
-    vector<Vec3> positions(numAtoms);
-    for (int i = 0; i < numAtoms; ++i)
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; ++i)
         positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
     context.setPositions(positions);
     
@@ -125,29 +125,29 @@ void testTemperature() {
         integrator.step(1);
     }
     ke /= 1000;
-    double expected = 0.5*numAtoms*3*BOLTZ*temp;
+    double expected = 0.5*numParticles*3*BOLTZ*temp;
     ASSERT_EQUAL_TOL(expected, ke, 3*expected/std::sqrt(1000.0));
 }
 
 void testConstraints() {
-    const int numAtoms = 8;
+    const int numParticles = 8;
     const double temp = 100.0;
     ReferencePlatform platform;
-    System system(numAtoms, numAtoms-1);
+    System system(numParticles, numParticles-1);
     LangevinIntegrator integrator(temp, 2.0, 0.01);
-    NonbondedForce* forceField = new NonbondedForce(numAtoms, 0);
-    for (int i = 0; i < numAtoms; ++i) {
-        system.setAtomMass(i, 10.0);
-        forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.setParticleMass(i, 10.0);
+        forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
-    for (int i = 0; i < numAtoms-1; ++i)
+    for (int i = 0; i < numParticles-1; ++i)
         system.setConstraintParameters(i, i, i+1, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
-    vector<Vec3> positions(numAtoms);
-    vector<Vec3> velocities(numAtoms);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
     init_gen_rand(0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
         positions[i] = Vec3(i/2, (i+1)/2, 0);
         velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
     }
@@ -158,7 +158,7 @@ void testConstraints() {
     
     for (int i = 0; i < 1000; ++i) {
         State state = context.getState(State::Positions);
-        for (int j = 0; j < numAtoms-1; ++j) {
+        for (int j = 0; j < numParticles-1; ++j) {
             Vec3 p1 = state.getPositions()[j];
             Vec3 p2 = state.getPositions()[j+1];
             double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));

platforms/reference/tests/TestReferenceNeighborList.cpp

@@ -9,35 +9,35 @@ using namespace OpenMM;
 
 void testNeighborList()
 {
-    RealOpenMM* atomList[2];
-    atomList[0] = new RealOpenMM[3];
-    atomList[1] = new RealOpenMM[3];
-    atomList[2] = new RealOpenMM[3];
-    atomList[0][0] = 13.6f;
-    atomList[0][1] = 0;
-    atomList[0][2] = 0;
-    atomList[1][0] = 0;
-    atomList[1][1] = 0;
-    atomList[1][2] = 0;
+    RealOpenMM* particleList[2];
+    particleList[0] = new RealOpenMM[3];
+    particleList[1] = new RealOpenMM[3];
+    particleList[2] = new RealOpenMM[3];
+    particleList[0][0] = 13.6f;
+    particleList[0][1] = 0;
+    particleList[0][2] = 0;
+    particleList[1][0] = 0;
+    particleList[1][1] = 0;
+    particleList[1][2] = 0;
     vector<set<int> > exclusions(2);
     
     NeighborList neighborList;
     
-    computeNeighborListNaive(neighborList, 2, atomList, exclusions, NULL, 13.7, 0.01);
+    computeNeighborListNaive(neighborList, 2, particleList, exclusions, NULL, 13.7, 0.01);
     assert(neighborList.size() == 1);
     
-    computeNeighborListNaive(neighborList, 2, atomList, exclusions, NULL, 13.5, 0.01);
+    computeNeighborListNaive(neighborList, 2, particleList, exclusions, NULL, 13.5, 0.01);
     assert(neighborList.size() == 0);
     
-    computeNeighborListVoxelHash(neighborList, 2, atomList, exclusions, NULL, 13.7, 0.01);
+    computeNeighborListVoxelHash(neighborList, 2, particleList, exclusions, NULL, 13.7, 0.01);
     assert(neighborList.size() == 1);
     
-    computeNeighborListVoxelHash(neighborList, 2, atomList, exclusions, NULL, 13.5, 0.01);
+    computeNeighborListVoxelHash(neighborList, 2, particleList, exclusions, NULL, 13.5, 0.01);
     assert(neighborList.size() == 0);
     
-    delete[] atomList[0];
-    delete[] atomList[1];
-    delete[] atomList[2];
+    delete[] particleList[0];
+    delete[] particleList[1];
+    delete[] particleList[2];
 }
 
 double periodicDifference(double val1, double val2, double period) {
@@ -53,40 +53,40 @@ double distance2(RealOpenMM* pos1, RealOpenMM* pos2, const RealOpenMM* periodicB
     return dx*dx+dy*dy+dz*dz;
 }
 
-void verifyNeighborList(NeighborList& list, int numAtoms, RealOpenMM** positions, const RealOpenMM* periodicBoxSize, double cutoff) {
+void verifyNeighborList(NeighborList& list, int numParticles, RealOpenMM** positions, const RealOpenMM* periodicBoxSize, double cutoff) {
     for (int i = 0; i < (int) list.size(); i++) {
-        int atom1 = list[i].first;
-        int atom2 = list[i].second;
-        ASSERT(distance2(positions[atom1], positions[atom2], periodicBoxSize) <= cutoff*cutoff);
+        int particle1 = list[i].first;
+        int particle2 = list[i].second;
+        ASSERT(distance2(positions[particle1], positions[particle2], periodicBoxSize) <= cutoff*cutoff);
     }
     int count = 0;
-    for (int i = 0; i < numAtoms; i++)
-        for (int j = i+1; j < numAtoms; j++)
+    for (int i = 0; i < numParticles; i++)
+        for (int j = i+1; j < numParticles; j++)
             if (distance2(positions[i], positions[j], periodicBoxSize) <= cutoff*cutoff)
                 count++;
     ASSERT(count == list.size());
 }
 
 void testPeriodic() {
-    const int numAtoms = 100;
+    const int numParticles = 100;
     const double cutoff = 3.0;
     const RealOpenMM periodicBoxSize[3] = {20.0, 15.0, 22.0};
-    RealOpenMM* atomList[numAtoms];
+    RealOpenMM* particleList[numParticles];
     init_gen_rand(0);
-    for (int i = 0; i <numAtoms; i++) {
-        atomList[i] = new RealOpenMM[3];
-        atomList[i][0] = (RealOpenMM) (genrand_real2()*periodicBoxSize[0]*3);
-        atomList[i][1] = (RealOpenMM) (genrand_real2()*periodicBoxSize[1]*3);
-        atomList[i][2] = (RealOpenMM) (genrand_real2()*periodicBoxSize[2]*3);
+    for (int i = 0; i <numParticles; i++) {
+        particleList[i] = new RealOpenMM[3];
+        particleList[i][0] = (RealOpenMM) (genrand_real2()*periodicBoxSize[0]*3);
+        particleList[i][1] = (RealOpenMM) (genrand_real2()*periodicBoxSize[1]*3);
+        particleList[i][2] = (RealOpenMM) (genrand_real2()*periodicBoxSize[2]*3);
     }
-    vector<set<int> > exclusions(numAtoms);
+    vector<set<int> > exclusions(numParticles);
     NeighborList neighborList;
-    computeNeighborListNaive(neighborList, numAtoms, atomList, exclusions, periodicBoxSize, cutoff);
-    verifyNeighborList(neighborList, numAtoms, atomList, periodicBoxSize, cutoff);
-    computeNeighborListVoxelHash(neighborList, numAtoms, atomList, exclusions, periodicBoxSize, cutoff);
-    verifyNeighborList(neighborList, numAtoms, atomList, periodicBoxSize, cutoff);
-    for (int i = 0; i <numAtoms; i++)
-        delete[] atomList[i];
+    computeNeighborListNaive(neighborList, numParticles, particleList, exclusions, periodicBoxSize, cutoff);
+    verifyNeighborList(neighborList, numParticles, particleList, periodicBoxSize, cutoff);
+    computeNeighborListVoxelHash(neighborList, numParticles, particleList, exclusions, periodicBoxSize, cutoff);
+    verifyNeighborList(neighborList, numParticles, particleList, periodicBoxSize, cutoff);
+    for (int i = 0; i <numParticles; i++)
+        delete[] particleList[i];
 }
 
 int main() 

platforms/reference/tests/TestReferenceNonbondedForce.cpp

@@ -54,8 +54,8 @@ void testCoulomb() {
     System system(2, 0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce(2, 0);
-    forceField->setAtomParameters(0, 0.5, 1, 0);
-    forceField->setAtomParameters(1, -1.5, 1, 0);
+    forceField->setParticleParameters(0, 0.5, 1, 0);
+    forceField->setParticleParameters(1, -1.5, 1, 0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -75,8 +75,8 @@ void testLJ() {
     System system(2, 0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce(2, 0);
-    forceField->setAtomParameters(0, 0, 1.2, 1);
-    forceField->setAtomParameters(1, 0, 1.4, 2);
+    forceField->setParticleParameters(0, 0, 1.2, 1);
+    forceField->setParticleParameters(1, 0, 1.4, 2);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
     vector<Vec3> positions(2);
@@ -113,11 +113,11 @@ void testExclusionsAnd14() {
         vector<Vec3> positions(5);
         const double r = 1.0;
         for (int j = 0; j < 5; ++j) {
-            nonbonded->setAtomParameters(j, 0, 1.5, 0);
+            nonbonded->setParticleParameters(j, 0, 1.5, 0);
             positions[j] = Vec3(0, j, 0);
         }
-        nonbonded->setAtomParameters(0, 0, 1.5, 1);
-        nonbonded->setAtomParameters(i, 0, 1.5, 1);
+        nonbonded->setParticleParameters(0, 0, 1.5, 1);
+        nonbonded->setParticleParameters(i, 0, 1.5, 1);
         nonbonded->setNonbonded14Parameters(0, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
         nonbonded->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0.0);
         positions[i] = Vec3(r, 0, 0);
@@ -143,8 +143,8 @@ void testExclusionsAnd14() {
 
         // Test Coulomb forces
         
-        nonbonded->setAtomParameters(0, 2, 1.5, 0);
-        nonbonded->setAtomParameters(i, 2, 1.5, 0);
+        nonbonded->setParticleParameters(0, 2, 1.5, 0);
+        nonbonded->setParticleParameters(i, 2, 1.5, 0);
         nonbonded->setNonbonded14Parameters(0, 0, 3, i == 3 ? 4/1.2 : 0, 1.5, 0);
         nonbonded->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0);
         context.reinitialize();
@@ -172,9 +172,9 @@ void testCutoff() {
     System system(3, 0);
     VerletIntegrator integrator(0.01);
     NonbondedForce* forceField = new NonbondedForce(3, 0);
-    forceField->setAtomParameters(0, 1.0, 1, 0);
-    forceField->setAtomParameters(1, 1.0, 1, 0);
-    forceField->setAtomParameters(2, 1.0, 1, 0);
+    forceField->setParticleParameters(0, 1.0, 1, 0);
+    forceField->setParticleParameters(1, 1.0, 1, 0);
+    forceField->setParticleParameters(2, 1.0, 1, 0);
     forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
     const double cutoff = 2.9;
     forceField->setCutoffDistance(cutoff);
@@ -226,10 +226,10 @@ void testCutoff14() {
  
         // Test LJ forces
         
-        nonbonded->setAtomParameters(0, 0, 1.5, 1);
+        nonbonded->setParticleParameters(0, 0, 1.5, 1);
         for (int j = 1; j < 5; ++j)
-            nonbonded->setAtomParameters(j, 0, 1.5, 0);
-        nonbonded->setAtomParameters(i, 0, 1.5, 1);
+            nonbonded->setParticleParameters(j, 0, 1.5, 0);
+        nonbonded->setParticleParameters(i, 0, 1.5, 1);
         nonbonded->setNonbonded14Parameters(0, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
         nonbonded->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0.0);
         context.reinitialize();
@@ -256,8 +256,8 @@ void testCutoff14() {
         // Test Coulomb forces
         
         const double q = 0.7;
-        nonbonded->setAtomParameters(0, q, 1.5, 0);
-        nonbonded->setAtomParameters(i, q, 1.5, 0);
+        nonbonded->setParticleParameters(0, q, 1.5, 0);
+        nonbonded->setParticleParameters(i, q, 1.5, 0);
         nonbonded->setNonbonded14Parameters(0, 0, 3, i == 3 ? q*q/1.2 : 0, 1.5, 0);
         nonbonded->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0);
         context.reinitialize();
@@ -291,9 +291,9 @@ void testPeriodic() {
     bonds->setBondParameters(0, 0, 1, 1, 0);
     system.addForce(bonds);
     NonbondedForce* nonbonded = new NonbondedForce(3, 0);
-    nonbonded->setAtomParameters(0, 1.0, 1, 0);
-    nonbonded->setAtomParameters(1, 1.0, 1, 0);
-    nonbonded->setAtomParameters(2, 1.0, 1, 0);
+    nonbonded->setParticleParameters(0, 1.0, 1, 0);
+    nonbonded->setParticleParameters(1, 1.0, 1, 0);
+    nonbonded->setParticleParameters(2, 1.0, 1, 0);
     nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
     const double cutoff = 2.0;
     nonbonded->setCutoffDistance(cutoff);

platforms/reference/tests/TestReferenceVerletIntegrator.cpp

@@ -53,8 +53,8 @@ const double TOL = 1e-5;
 void testSingleBond() {
     ReferencePlatform platform;
     System system(2, 0);
-    system.setAtomMass(0, 2.0);
-    system.setAtomMass(1, 2.0);
+    system.setParticleMass(0, 2.0);
+    system.setParticleMass(1, 2.0);
     VerletIntegrator integrator(0.01);
     HarmonicBondForce* forceField = new HarmonicBondForce(1);
     forceField->setBondParameters(0, 0, 1, 1.5, 1);
@@ -86,24 +86,24 @@ void testSingleBond() {
 }
 
 void testConstraints() {
-    const int numAtoms = 8;
+    const int numParticles = 8;
     const double temp = 100.0;
     ReferencePlatform platform;
-    System system(numAtoms, numAtoms-1);
+    System system(numParticles, numParticles-1);
     VerletIntegrator integrator(0.002);
-    NonbondedForce* forceField = new NonbondedForce(numAtoms, 0);
-    for (int i = 0; i < numAtoms; ++i) {
-        system.setAtomMass(i, 10.0);
-        forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    for (int i = 0; i < numParticles; ++i) {
+        system.setParticleMass(i, 10.0);
+        forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
-    for (int i = 0; i < numAtoms-1; ++i)
+    for (int i = 0; i < numParticles-1; ++i)
         system.setConstraintParameters(i, i, i+1, 1.0);
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
-    vector<Vec3> positions(numAtoms);
-    vector<Vec3> velocities(numAtoms);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
     init_gen_rand(0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
         positions[i] = Vec3(i/2, (i+1)/2, 0);
         velocities[i] = Vec3(genrand_real2()-0.5, genrand_real2()-0.5, genrand_real2()-0.5);
     }
@@ -115,7 +115,7 @@ void testConstraints() {
     double initialEnergy = 0.0;
     for (int i = 0; i < 1000; ++i) {
         State state = context.getState(State::Positions | State::Energy);
-        for (int j = 0; j < numAtoms-1; ++j) {
+        for (int j = 0; j < numParticles-1; ++j) {
             Vec3 p1 = state.getPositions()[j];
             Vec3 p2 = state.getPositions()[j+1];
             double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));