Renamed "atoms" to "particles"

62c4fd53 · Peter Eastman · ad75a390 · 62c4fd53 · 62c4fd53 · 62c4fd53
Commit 62c4fd53 authored Oct 22, 2008 by Peter Eastman
20 changed files
--- a/openmmapi/src/HarmonicBondForce.cpp
+++ b/openmmapi/src/HarmonicBondForce.cpp
@@ -39,16 +39,16 @@ using namespace OpenMM;
 HarmonicBondForce::HarmonicBondForce(int numBonds) : bonds(numBonds) {
 }
-void HarmonicBondForce::getBondParameters(int index, int& atom1, int& atom2, double& length, double& k) const {
+void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const {
-    atom1 = bonds[index].atom1;
+    particle1 = bonds[index].particle1;
-    atom2 = bonds[index].atom2;
+    particle2 = bonds[index].particle2;
    length = bonds[index].length;
    k = bonds[index].k;
 }
-void HarmonicBondForce::setBondParameters(int index, int atom1, int atom2, double length, double k) {
+void HarmonicBondForce::setBondParameters(int index, int particle1, int particle2, double length, double k) {
-    bonds[index].atom1 = atom1;
+    bonds[index].particle1 = particle1;
-    bonds[index].atom2 = atom2;
+    bonds[index].particle2 = particle2;
    bonds[index].length = length;
    bonds[index].k = k;
 }

--- a/openmmapi/src/NonbondedForce.cpp
+++ b/openmmapi/src/NonbondedForce.cpp
@@ -36,7 +36,7 @@
 using namespace OpenMM;
-NonbondedForce::NonbondedForce(int numAtoms, int numNonbonded14) : atoms(numAtoms), nb14s(numNonbonded14),
+NonbondedForce::NonbondedForce(int numParticles, int numNonbonded14) : particles(numParticles), nb14s(numNonbonded14),
        nonbondedMethod(NoCutoff), cutoffDistance(1.0) {
    periodicBoxVectors[0] = Vec3(2, 0, 0);
    periodicBoxVectors[1] = Vec3(0, 2, 0);
@@ -77,29 +77,29 @@ void NonbondedForce::setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c) {
    periodicBoxVectors[2] = c;
 }
-void NonbondedForce::getAtomParameters(int index, double& charge, double& radius, double& depth) const {
+void NonbondedForce::getParticleParameters(int index, double& charge, double& radius, double& depth) const {
-    charge = atoms[index].charge;
+    charge = particles[index].charge;
-    radius = atoms[index].radius;
+    radius = particles[index].radius;
-    depth = atoms[index].depth;
+    depth = particles[index].depth;
 }
-void NonbondedForce::setAtomParameters(int index, double charge, double radius, double depth) {
+void NonbondedForce::setParticleParameters(int index, double charge, double radius, double depth) {
-    atoms[index].charge = charge;
+    particles[index].charge = charge;
-    atoms[index].radius = radius;
+    particles[index].radius = radius;
-    atoms[index].depth = depth;
+    particles[index].depth = depth;
 }
-void NonbondedForce::getNonbonded14Parameters(int index, int& atom1, int& atom2, double& charge, double& radius, double& depth) const {
+void NonbondedForce::getNonbonded14Parameters(int index, int& particle1, int& particle2, double& charge, double& radius, double& depth) const {
-    atom1 = nb14s[index].atom1;
+    particle1 = nb14s[index].particle1;
-    atom2 = nb14s[index].atom2;
+    particle2 = nb14s[index].particle2;
    charge = nb14s[index].charge;
    radius = nb14s[index].radius;
    depth = nb14s[index].depth;
 }
-void NonbondedForce::setNonbonded14Parameters(int index, int atom1, int atom2, double charge, double radius, double depth) {
+void NonbondedForce::setNonbonded14Parameters(int index, int particle1, int particle2, double charge, double radius, double depth) {
-    nb14s[index].atom1 = atom1;
+    nb14s[index].particle1 = particle1;
-    nb14s[index].atom2 = atom2;
+    nb14s[index].particle2 = particle2;
    nb14s[index].charge = charge;
    nb14s[index].radius = radius;
    nb14s[index].depth = depth;

--- a/openmmapi/src/NonbondedForceImpl.cpp
+++ b/openmmapi/src/NonbondedForceImpl.cpp
@@ -50,23 +50,23 @@ void NonbondedForceImpl::initialize(OpenMMContextImpl& context) {
    // See if the system contains a HarmonicBondForce.  If so, use it to identify exclusions.
    System& system = context.getSystem();
-    vector<set<int> > exclusions(owner.getNumAtoms());
+    vector<set<int> > exclusions(owner.getNumParticles());
    for (int i = 0; i < system.getNumForces(); i++) {
        if (dynamic_cast<HarmonicBondForce*>(&system.getForce(i)) != NULL) {
            const HarmonicBondForce& force = dynamic_cast<const HarmonicBondForce&>(system.getForce(i));
            vector<vector<int> > bondIndices(force.getNumBonds());
            set<pair<int, int> > bonded14set;
            for (int i = 0; i < force.getNumBonds(); ++i) {
-                int atom1, atom2;
+                int particle1, particle2;
                double length, k;
-                force.getBondParameters(i, atom1, atom2, length, k);
+                force.getBondParameters(i, particle1, particle2, length, k);
-                bondIndices[i].push_back(atom1);
+                bondIndices[i].push_back(particle1);
-                bondIndices[i].push_back(atom2);
+                bondIndices[i].push_back(particle2);
            }
            findExclusions(bondIndices, exclusions, bonded14set);
        }
    }
-            dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner, exclusions);
+    dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner, exclusions);
 }
 void NonbondedForceImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
@@ -100,12 +100,12 @@ void NonbondedForceImpl::findExclusions(const vector<vector<int> >& bondIndices,
    }
 }
-void NonbondedForceImpl::addExclusionsToSet(const vector<set<int> >& bonded12, set<int>& exclusions, int baseAtom, int fromAtom, int currentLevel) const {
+void NonbondedForceImpl::addExclusionsToSet(const vector<set<int> >& bonded12, set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const {
-    for (set<int>::const_iterator iter = bonded12[fromAtom].begin(); iter != bonded12[fromAtom].end(); ++iter) {
+    for (set<int>::const_iterator iter = bonded12[fromParticle].begin(); iter != bonded12[fromParticle].end(); ++iter) {
-        if (*iter != baseAtom)
+        if (*iter != baseParticle)
            exclusions.insert(*iter);
        if (currentLevel > 0)
-            addExclusionsToSet(bonded12, exclusions, baseAtom, *iter, currentLevel-1);
+            addExclusionsToSet(bonded12, exclusions, baseParticle, *iter, currentLevel-1);
    }
 }
--- a/openmmapi/src/OpenMMContext.cpp
+++ b/openmmapi/src/OpenMMContext.cpp
@@ -66,7 +66,7 @@ Integrator& OpenMMContext::getIntegrator() {
 }
 State OpenMMContext::getState(int types) const {
-    State state(impl->getTime(), impl->getSystem().getNumAtoms(), State::DataType(types));
+    State state(impl->getTime(), impl->getSystem().getNumParticles(), State::DataType(types));
    if (types&State::Energy)
        state.setEnergy(impl->calcKineticEnergy(), impl->calcPotentialEnergy());
    if (types&State::Forces) {
@@ -93,13 +93,13 @@ void OpenMMContext::setTime(double time) {
 }
 void OpenMMContext::setPositions(const vector<Vec3>& positions) {
-    if ((int) positions.size() != impl->getSystem().getNumAtoms())
+    if ((int) positions.size() != impl->getSystem().getNumParticles())
        throw OpenMMException("Called setPositions() on an OpenMMContext with the wrong number of positions");
    impl->getPositions().loadFromArray(&positions[0]);
 }
 void OpenMMContext::setVelocities(const vector<Vec3>& velocities) {
-    if ((int) velocities.size() != impl->getSystem().getNumAtoms())
+    if ((int) velocities.size() != impl->getSystem().getNumParticles())
        throw OpenMMException("Called setVelocities() on an OpenMMContext with the wrong number of velocities");
    impl->getVelocities().loadFromArray(&velocities[0]);
 }

--- a/openmmapi/src/OpenMMContextImpl.cpp
+++ b/openmmapi/src/OpenMMContextImpl.cpp
@@ -67,16 +67,16 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
        throw OpenMMException("Specified a Platform for an OpenMMContext which does not support all required kernels");
    platform->contextCreated(*this);
    kineticEnergyKernel = platform->createKernel(CalcKineticEnergyKernel::Name(), *this);
-    vector<double> masses(system.getNumAtoms());
+    vector<double> masses(system.getNumParticles());
    for (size_t i = 0; i < masses.size(); ++i)
-        masses[i] = system.getAtomMass(i);
+        masses[i] = system.getParticleMass(i);
    dynamic_cast<CalcKineticEnergyKernel&>(kineticEnergyKernel.getImpl()).initialize(system);
    for (size_t i = 0; i < forceImpls.size(); ++i)
        forceImpls[i]->initialize(*this);
    integrator.initialize(*this);
-    positions = platform->createStream("atomPositions", system.getNumAtoms(), Stream::Double3, *this);
+    positions = platform->createStream("particlePositions", system.getNumParticles(), Stream::Double3, *this);
-    velocities = platform->createStream("atomVelocities", system.getNumAtoms(), Stream::Double3, *this);
+    velocities = platform->createStream("particleVelocities", system.getNumParticles(), Stream::Double3, *this);
-    forces = platform->createStream("atomForces", system.getNumAtoms(), Stream::Double3, *this);
+    forces = platform->createStream("particleForces", system.getNumParticles(), Stream::Double3, *this);
    double zero[] = {0.0, 0.0, 0.0};
    velocities.fillWithValue(&zero);
 }

--- a/openmmapi/src/PeriodicTorsionForce.cpp
+++ b/openmmapi/src/PeriodicTorsionForce.cpp
@@ -39,21 +39,21 @@ using namespace OpenMM;
 PeriodicTorsionForce::PeriodicTorsionForce(int numTorsions) : periodicTorsions(numTorsions) {
 }
-void PeriodicTorsionForce::getTorsionParameters(int index, int& atom1, int& atom2, int& atom3, int& atom4, int& periodicity, double& phase, double& k) const {
+void PeriodicTorsionForce::getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& periodicity, double& phase, double& k) const {
-    atom1 = periodicTorsions[index].atom1;
+    particle1 = periodicTorsions[index].particle1;
-    atom2 = periodicTorsions[index].atom2;
+    particle2 = periodicTorsions[index].particle2;
-    atom3 = periodicTorsions[index].atom3;
+    particle3 = periodicTorsions[index].particle3;
-    atom4 = periodicTorsions[index].atom4;
+    particle4 = periodicTorsions[index].particle4;
    periodicity = periodicTorsions[index].periodicity;
    phase = periodicTorsions[index].phase;
    k = periodicTorsions[index].k;
 }
-void PeriodicTorsionForce::setTorsionParameters(int index, int atom1, int atom2, int atom3, int atom4, int periodicity, double phase, double k) {
+void PeriodicTorsionForce::setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k) {
-    periodicTorsions[index].atom1 = atom1;
+    periodicTorsions[index].particle1 = particle1;
-    periodicTorsions[index].atom2 = atom2;
+    periodicTorsions[index].particle2 = particle2;
-    periodicTorsions[index].atom3 = atom3;
+    periodicTorsions[index].particle3 = particle3;
-    periodicTorsions[index].atom4 = atom4;
+    periodicTorsions[index].particle4 = particle4;
    periodicTorsions[index].periodicity = periodicity;
    periodicTorsions[index].phase = phase;
    periodicTorsions[index].k = k;

--- a/openmmapi/src/RBTorsionForce.cpp
+++ b/openmmapi/src/RBTorsionForce.cpp
@@ -39,11 +39,11 @@ using namespace OpenMM;
 RBTorsionForce::RBTorsionForce(int numTorsions) : rbTorsions(numTorsions) {
 }
-void RBTorsionForce::getTorsionParameters(int index, int& atom1, int& atom2, int& atom3, int& atom4, double& c0, double& c1, double& c2, double& c3, double& c4, double& c5) const {
+void RBTorsionForce::getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& c0, double& c1, double& c2, double& c3, double& c4, double& c5) const {
-    atom1 = rbTorsions[index].atom1;
+    particle1 = rbTorsions[index].particle1;
-    atom2 = rbTorsions[index].atom2;
+    particle2 = rbTorsions[index].particle2;
-    atom3 = rbTorsions[index].atom3;
+    particle3 = rbTorsions[index].particle3;
-    atom4 = rbTorsions[index].atom4;
+    particle4 = rbTorsions[index].particle4;
    c0 = rbTorsions[index].c[0];
    c1 = rbTorsions[index].c[1];
    c2 = rbTorsions[index].c[2];
@@ -52,11 +52,11 @@ void RBTorsionForce::getTorsionParameters(int index, int& atom1, int& atom2, int
    c5 = rbTorsions[index].c[5];
 }
-void RBTorsionForce::setTorsionParameters(int index, int atom1, int atom2, int atom3, int atom4, double c0, double c1, double c2, double c3, double c4, double c5) {
+void RBTorsionForce::setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5) {
-    rbTorsions[index].atom1 = atom1;
+    rbTorsions[index].particle1 = particle1;
-    rbTorsions[index].atom2 = atom2;
+    rbTorsions[index].particle2 = particle2;
-    rbTorsions[index].atom3 = atom3;
+    rbTorsions[index].particle3 = particle3;
-    rbTorsions[index].atom4 = atom4;
+    rbTorsions[index].particle4 = particle4;
    rbTorsions[index].c[0] = c0;
    rbTorsions[index].c[1] = c1;
    rbTorsions[index].c[2] = c2;

--- a/openmmapi/src/State.cpp
+++ b/openmmapi/src/State.cpp
@@ -68,9 +68,9 @@ const map<string, double>& State::getParameters() const {
        throw OpenMMException("Invoked getParameters() on a State which does not contain parameters.");
    return parameters;
 }
-State::State(double time, int numAtoms, DataType types) : types(types), time(time), ke(0), pe(0),
+State::State(double time, int numParticles, DataType types) : types(types), time(time), ke(0), pe(0),
-        positions( (types & Positions) == 0 ? 0 : numAtoms), velocities( (types & Velocities) == 0 ? 0 : numAtoms),
+        positions( (types & Positions) == 0 ? 0 : numParticles), velocities( (types & Velocities) == 0 ? 0 : numParticles),
-        forces( (types & Forces) == 0 ? 0 : numAtoms) {
+        forces( (types & Forces) == 0 ? 0 : numParticles) {
 }
 vector<Vec3>& State::updPositions() {
    return positions;

--- a/openmmapi/src/System.cpp
+++ b/openmmapi/src/System.cpp
@@ -34,8 +34,8 @@
 using namespace OpenMM;
-System::System(int numAtoms, int numConstraints) : masses(numAtoms), constraints(numConstraints), forces(0) {
+System::System(int numParticles, int numConstraints) : masses(numParticles), constraints(numConstraints), forces(0) {
-    for (int i = 0; i < numAtoms; ++i)
+    for (int i = 0; i < numParticles; ++i)
        masses[i] = 0.0;
 }
@@ -44,14 +44,14 @@ System::~System() {
        delete forces[i];
 }
-void System::getConstraintParameters(int index, int& atom1, int& atom2, double& distance) const {
+void System::getConstraintParameters(int index, int& particle1, int& particle2, double& distance) const {
-    atom1 = constraints[index].atom1;
+    particle1 = constraints[index].particle1;
-    atom2 = constraints[index].atom2;
+    particle2 = constraints[index].particle2;
    distance = constraints[index].distance;
 }
-void System::setConstraintParameters(int index, int atom1, int atom2, double distance) {
+void System::setConstraintParameters(int index, int particle1, int particle2, double distance) {
-    constraints[index].atom1 = atom1;
+    constraints[index].particle1 = particle1;
-    constraints[index].atom2 = atom2;
+    constraints[index].particle2 = particle2;
    constraints[index].distance = distance;
 }
--- a/platforms/cuda/src/CudaKernels.cpp
+++ b/platforms/cuda/src/CudaKernels.cpp
@@ -86,17 +86,17 @@ void CudaCalcHarmonicBondForceKernel::initialize(const System& system, const Har
        data.primaryKernel = this;
    data.hasBonds = true;
    numBonds = force.getNumBonds();
-    vector<int> atom1(numBonds);
+    vector<int> particle1(numBonds);
-    vector<int> atom2(numBonds);
+    vector<int> particle2(numBonds);
    vector<float> length(numBonds);
    vector<float> k(numBonds);
    for (int i = 0; i < numBonds; i++) {
        double lengthValue, kValue;
-        force.getBondParameters(i, atom1[i], atom2[i], lengthValue, kValue);
+        force.getBondParameters(i, particle1[i], particle2[i], lengthValue, kValue);
        length[i] = (float) lengthValue;
        k[i] = (float) kValue;
    }
-    gpuSetBondParameters(data.gpu, atom1, atom2, length, k);
+    gpuSetBondParameters(data.gpu, particle1, particle2, length, k);
 }
 void CudaCalcHarmonicBondForceKernel::executeForces(OpenMMContextImpl& context) {
@@ -119,18 +119,18 @@ void CudaCalcHarmonicAngleForceKernel::initialize(const System& system, const Ha
    data.hasAngles = true;
    numAngles = force.getNumAngles();
    const float RadiansToDegrees = 180.0/3.14159265;
-    vector<int> atom1(numAngles);
+    vector<int> particle1(numAngles);
-    vector<int> atom2(numAngles);
+    vector<int> particle2(numAngles);
-    vector<int> atom3(numAngles);
+    vector<int> particle3(numAngles);
    vector<float> angle(numAngles);
    vector<float> k(numAngles);
    for (int i = 0; i < numAngles; i++) {
        double angleValue, kValue;
-        force.getAngleParameters(i, atom1[i], atom2[i], atom3[i], angleValue, kValue);
+        force.getAngleParameters(i, particle1[i], particle2[i], particle3[i], angleValue, kValue);
        angle[i] = (float) (angleValue*RadiansToDegrees);
        k[i] = (float) kValue;
    }
-    gpuSetBondAngleParameters(data.gpu, atom1, atom2, atom3, angle, k);
+    gpuSetBondAngleParameters(data.gpu, particle1, particle2, particle3, angle, k);
 }
 void CudaCalcHarmonicAngleForceKernel::executeForces(OpenMMContextImpl& context) {
@@ -153,20 +153,20 @@ void CudaCalcPeriodicTorsionForceKernel::initialize(const System& system, const
    data.hasPeriodicTorsions = true;
    numTorsions = force.getNumTorsions();
    const float RadiansToDegrees = 180.0/3.14159265;
-    vector<int> atom1(numTorsions);
+    vector<int> particle1(numTorsions);
-    vector<int> atom2(numTorsions);
+    vector<int> particle2(numTorsions);
-    vector<int> atom3(numTorsions);
+    vector<int> particle3(numTorsions);
-    vector<int> atom4(numTorsions);
+    vector<int> particle4(numTorsions);
    vector<float> k(numTorsions);
    vector<float> phase(numTorsions);
    vector<int> periodicity(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        double kValue, phaseValue;
-        force.getTorsionParameters(i, atom1[i], atom2[i], atom3[i], atom4[i], periodicity[i], phaseValue, kValue);
+        force.getTorsionParameters(i, particle1[i], particle2[i], particle3[i], particle4[i], periodicity[i], phaseValue, kValue);
        k[i] = (float) kValue;
        phase[i] = (float) (phaseValue*RadiansToDegrees);
    }
-    gpuSetDihedralParameters(data.gpu, atom1, atom2, atom3, atom4, k, phase, periodicity);
+    gpuSetDihedralParameters(data.gpu, particle1, particle2, particle3, particle4, k, phase, periodicity);
 }
 void CudaCalcPeriodicTorsionForceKernel::executeForces(OpenMMContextImpl& context) {
@@ -188,10 +188,10 @@ void CudaCalcRBTorsionForceKernel::initialize(const System& system, const RBTors
        data.primaryKernel = this;
    data.hasRB = true;
    numTorsions = force.getNumTorsions();
-    vector<int> atom1(numTorsions);
+    vector<int> particle1(numTorsions);
-    vector<int> atom2(numTorsions);
+    vector<int> particle2(numTorsions);
-    vector<int> atom3(numTorsions);
+    vector<int> particle3(numTorsions);
-    vector<int> atom4(numTorsions);
+    vector<int> particle4(numTorsions);
    vector<float> c0(numTorsions);
    vector<float> c1(numTorsions);
    vector<float> c2(numTorsions);
@@ -200,7 +200,7 @@ void CudaCalcRBTorsionForceKernel::initialize(const System& system, const RBTors
    vector<float> c5(numTorsions);
    for (int i = 0; i < numTorsions; i++) {
        double c[6];
-        force.getTorsionParameters(i, atom1[i], atom2[i], atom3[i], atom4[i], c[0], c[1], c[2], c[3], c[4], c[5]);
+        force.getTorsionParameters(i, particle1[i], particle2[i], particle3[i], particle4[i], c[0], c[1], c[2], c[3], c[4], c[5]);
        c0[i] = (float) c[0];
        c1[i] = (float) c[1];
        c2[i] = (float) c[2];
@@ -208,7 +208,7 @@ void CudaCalcRBTorsionForceKernel::initialize(const System& system, const RBTors
        c4[i] = (float) c[4];
        c5[i] = (float) c[5];
    }
-    gpuSetRbDihedralParameters(data.gpu, atom1, atom2, atom3, atom4, c0, c1, c2, c3, c4, c5);
+    gpuSetRbDihedralParameters(data.gpu, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
 }
 void CudaCalcRBTorsionForceKernel::executeForces(OpenMMContextImpl& context) {
@@ -229,51 +229,51 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
    if (data.primaryKernel == NULL)
        data.primaryKernel = this;
    data.hasNonbonded = true;
-    numAtoms = force.getNumAtoms();
+    numParticles = force.getNumParticles();
    num14 = force.getNumNonbonded14();
    _gpuContext* gpu = data.gpu;
    // Initialize nonbonded interactions.
    {
-        vector<int> atom(numAtoms);
+        vector<int> particle(numParticles);
-        vector<float> c6(numAtoms);
+        vector<float> c6(numParticles);
-        vector<float> c12(numAtoms);
+        vector<float> c12(numParticles);
-        vector<float> q(numAtoms);
+        vector<float> q(numParticles);
        vector<char> symbol;
-        vector<vector<int> > exclusionList(numAtoms);
+        vector<vector<int> > exclusionList(numParticles);
-        for (int i = 0; i < numAtoms; i++) {
+        for (int i = 0; i < numParticles; i++) {
            double charge, radius, depth;
-            force.getAtomParameters(i, charge, radius, depth);
+            force.getParticleParameters(i, charge, radius, depth);
-            atom[i] = i;
+            particle[i] = i;
            q[i] = (float) charge;
            c6[i] = (float) (4*depth*pow(radius, 6.0));
            c12[i] = (float) (4*depth*pow(radius, 12.0));
            exclusionList[i] = vector<int>(exclusions[i].begin(), exclusions[i].end());
            exclusionList[i].push_back(i);
        }
-        gpuSetCoulombParameters(gpu, 138.935485f, atom, c6, c12, q, symbol, exclusionList);
+        gpuSetCoulombParameters(gpu, 138.935485f, particle, c6, c12, q, symbol, exclusionList);
    }
    // Initialize 1-4 nonbonded interactions.
    {
-        vector<int> atom1(num14);
+        vector<int> particle1(num14);
-        vector<int> atom2(num14);
+        vector<int> particle2(num14);
        vector<float> c6(num14);
        vector<float> c12(num14);
        vector<float> q1(num14);
        vector<float> q2(num14);
        for (int i = 0; i < num14; i++) {
            double charge, sig, eps;
-            force.getNonbonded14Parameters(i, atom1[i], atom2[i], charge, sig, eps);
+            force.getNonbonded14Parameters(i, particle1[i], particle2[i], charge, sig, eps);
            c6[i] = (float) (4*eps*pow(sig, 6.0));
            c12[i] = (float) (4*eps*pow(sig, 12.0));
            float q = (float) std::sqrt(charge);
            q1[i] = q;
            q2[i] = q;
        }
-        gpuSetLJ14Parameters(gpu, 138.935485f, 1.0f, atom1, atom2, c6, c12, q1, q2);
+        gpuSetLJ14Parameters(gpu, 138.935485f, 1.0f, particle1, particle2, c6, c12, q1, q2);
    }
 }
@@ -292,19 +292,19 @@ CudaCalcGBSAOBCForceFieldKernel::~CudaCalcGBSAOBCForceFieldKernel() {
 }
 void CudaCalcGBSAOBCForceFieldKernel::initialize(const System& system, const GBSAOBCForceField& force) {
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
    _gpuContext* gpu = data.gpu;
-    vector<int> atom(numAtoms);
+    vector<int> particle(numParticles);
-    vector<float> radius(numAtoms);
+    vector<float> radius(numParticles);
-    vector<float> scale(numAtoms);
+    vector<float> scale(numParticles);
-    for (int i = 0; i < numAtoms; i++) {
+    for (int i = 0; i < numParticles; i++) {
-        double charge, atomRadius, scalingFactor;
+        double charge, particleRadius, scalingFactor;
-        force.getAtomParameters(i, charge, atomRadius, scalingFactor);
+        force.getParticleParameters(i, charge, particleRadius, scalingFactor);
-        atom[i] = i;
+        particle[i] = i;
-        radius[i] = (float) atomRadius;
+        radius[i] = (float) particleRadius;
        scale[i] = (float) scalingFactor;
    }
-    gpuSetObcParameters(gpu, force.getSoluteDielectric(), force.getSolventDielectric(), atom, radius, scale);
+    gpuSetObcParameters(gpu, force.getSoluteDielectric(), force.getSolventDielectric(), particle, radius, scale);
    data.useOBC = true;
 }
@@ -331,31 +331,31 @@ void CudaIntegrateLangevinStepKernel::initialize(const System& system, const Lan
    // Set masses.
    _gpuContext* gpu = data.gpu;
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
-    vector<float> mass(numAtoms);
+    vector<float> mass(numParticles);
-    for (int i = 0; i < numAtoms; i++)
+    for (int i = 0; i < numParticles; i++)
-        mass[i] = (float) system.getAtomMass(i);
+        mass[i] = (float) system.getParticleMass(i);
    gpuSetMass(gpu, mass);
    // Set constraints.
    int numConstraints = system.getNumConstraints();
-    vector<int> atom1(numConstraints);
+    vector<int> particle1(numConstraints);
-    vector<int> atom2(numConstraints);
+    vector<int> particle2(numConstraints);
    vector<float> distance(numConstraints);
    vector<float> invMass1(numConstraints);
    vector<float> invMass2(numConstraints);
    for (int i = 0; i < numConstraints; i++) {
-        int atom1Index, atom2Index;
+        int particle1Index, particle2Index;
        double constraintDistance;
-        system.getConstraintParameters(i, atom1Index, atom2Index, constraintDistance);
+        system.getConstraintParameters(i, particle1Index, particle2Index, constraintDistance);
-        atom1[i] = atom1Index;
+        particle1[i] = particle1Index;
-        atom2[i] = atom2Index;
+        particle2[i] = particle2Index;
        distance[i] = (float) constraintDistance;
-        invMass1[i] = 1.0f/mass[atom1Index];
+        invMass1[i] = 1.0f/mass[particle1Index];
-        invMass2[i] = 1.0f/mass[atom2Index];
+        invMass2[i] = 1.0f/mass[particle2Index];
    }
-    gpuSetShakeParameters(gpu, atom1, atom2, distance, invMass1, invMass2);
+    gpuSetShakeParameters(gpu, particle1, particle2, distance, invMass1, invMass2);
    // Initialize any terms that haven't already been handled by a Force.
@@ -433,10 +433,10 @@ void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const
 //}
 void CudaCalcKineticEnergyKernel::initialize(const System& system) {
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
-    masses.resize(numAtoms);
+    masses.resize(numParticles);
-    for (size_t i = 0; i < numAtoms; ++i)
+    for (size_t i = 0; i < numParticles; ++i)
-        masses[i] = system.getAtomMass(i);
+        masses[i] = system.getParticleMass(i);
 }
 double CudaCalcKineticEnergyKernel::execute(OpenMMContextImpl& context) {

--- a/platforms/cuda/src/CudaKernels.h
+++ b/platforms/cuda/src/CudaKernels.h
@@ -195,7 +195,7 @@ public:
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the NonbondedForce this kernel will be used for
-     * @param exclusions the i'th element lists the indices of all atoms with which the i'th atom should not interact through
+     * @param exclusions the i'th element lists the indices of all particles with which the i'th particle should not interact through
     *                   nonbonded forces.  Bonded 1-4 pairs are also included in this list, since they should be omitted from
     *                   the standard nonbonded calculation.
     */
@@ -215,7 +215,7 @@ public:
    double executeEnergy(OpenMMContextImpl& context);
 private:
    CudaPlatform::PlatformData& data;
-    int numAtoms, num14;
+    int numParticles, num14;
    System& system;
 };
@@ -293,7 +293,7 @@ public:
    }
    ~CudaIntegrateLangevinStepKernel();
    /**
-     * Initialize the kernel, setting up the atomic masses.
+     * Initialize the kernel, setting up the particle masses.
     * 
     * @param system     the System this kernel will be applied to
     * @param integrator the LangevinIntegrator this kernel will be used for
@@ -345,7 +345,7 @@ private:
 //};
 //
 ///**
-// * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the atom velocities.
+// * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
 // */
 //class CudaApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
 //public:
@@ -401,7 +401,7 @@ public:
    CudaRemoveCMMotionKernel(std::string name, const Platform& platform, CudaPlatform::PlatformData& data) : RemoveCMMotionKernel(name, platform), data(data) {
    }
    /**
-     * Initialize the kernel, setting up the atomic masses.
+     * Initialize the kernel, setting up the particle masses.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the CMMotionRemover this kernel will be used for

--- a/platforms/cuda/src/CudaPlatform.cpp
+++ b/platforms/cuda/src/CudaPlatform.cpp
@@ -63,8 +63,8 @@ const StreamFactory& CudaPlatform::getDefaultStreamFactory() const {
 }
 void CudaPlatform::contextCreated(OpenMMContextImpl& context) const {
-    int numAtoms = context.getSystem().getNumAtoms();
+    int numParticles = context.getSystem().getNumParticles();
-    _gpuContext* gpu = (_gpuContext*) gpuInit(numAtoms);
+    _gpuContext* gpu = (_gpuContext*) gpuInit(numParticles);
    context.setPlatformData(new PlatformData(gpu));
 }

--- a/platforms/cuda/src/CudaStreamFactory.cpp
+++ b/platforms/cuda/src/CudaStreamFactory.cpp
@@ -39,17 +39,17 @@
 using namespace OpenMM;
 StreamImpl* CudaStreamFactory::createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, OpenMMContextImpl& context) const {
-    if (name == "atomPositions") {
+    if (name == "particlePositions") {
        CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
        float padding[] = {100000.0f, 100000.0f, 100000.0f, 0.2f};
        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psPosq4, 4, padding);
    }
-    if (name == "atomVelocities") {
+    if (name == "particleVelocities") {
        CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
        float padding[] = {0.0f, 0.0f, 0.0f, 0.0f};
        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psVelm4, 4, padding);
    }
-    if (name == "atomForces") {
+    if (name == "particleForces") {
        CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
        float padding[] = {0.0f, 0.0f, 0.0f, 0.0f};
        return new CudaStreamImpl<float4>(name, size, type, platform, data.gpu->psForce4, 4, padding);

--- a/platforms/cuda/tests/TestCudaCMMotionRemover.cpp
+++ b/platforms/cuda/tests/TestCudaCMMotionRemover.cpp
@@ -51,35 +51,35 @@ using namespace std;
 Vec3 calcCM(const vector<Vec3>& values, System& system) {
    Vec3 cm;
-    for (int j = 0; j < system.getNumAtoms(); ++j) {
+    for (int j = 0; j < system.getNumParticles(); ++j) {
-        cm[0] += values[j][0]*system.getAtomMass(j);
+        cm[0] += values[j][0]*system.getParticleMass(j);
-        cm[1] += values[j][1]*system.getAtomMass(j);
+        cm[1] += values[j][1]*system.getParticleMass(j);
-        cm[2] += values[j][2]*system.getAtomMass(j);
+        cm[2] += values[j][2]*system.getParticleMass(j);
    }
    return cm;
 }
 void testMotionRemoval() {
-    const int numAtoms = 8;
+    const int numParticles = 8;
    CudaPlatform platform;
-    System system(numAtoms, 0);
+    System system(numParticles, 0);
    LangevinIntegrator integrator(0.0, 1e-5, 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);
+    NonbondedForce* nonbonded = new NonbondedForce(numParticles, 0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
-        system.setAtomMass(i, i+1);
+        system.setParticleMass(i, i+1);
-        nonbonded->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        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> positions(numParticles);
-    vector<Vec3> velocities(numAtoms);
+    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);
    }

--- a/platforms/cuda/tests/TestCudaGBSAOBCForceField.cpp
+++ b/platforms/cuda/tests/TestCudaGBSAOBCForceField.cpp
@@ -50,15 +50,15 @@ using namespace std;
 const double TOL = 1e-5;
-void testSingleAtom() {
+void testSingleParticle() {
    CudaPlatform 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);
    NonbondedForce* standard = new NonbondedForce(1, 0);
-    forceField->setAtomParameters(0, 0.5, 0.15, 1);
+    forceField->setParticleParameters(0, 0.5, 0.15, 1);
-    standard->setAtomParameters(0, 0.5, 1, 0);
+    standard->setParticleParameters(0, 0.5, 1, 0);
    system.addForce(forceField);
    system.addForce(standard);
    OpenMMContext context(system, integrator, platform);
@@ -76,25 +76,25 @@ void testSingleAtom() {
 void testForce() {
    CudaPlatform platform;
-    const int numAtoms = 10;
+    const int numParticles = 10;
-    System system(numAtoms, 0);
+    System system(numParticles, 0);
    LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForceField* forceField = new GBSAOBCForceField(numAtoms);
+    GBSAOBCForceField* forceField = new GBSAOBCForceField(numParticles);
-    NonbondedForce* standard = new NonbondedForce(numAtoms, 0);
+    NonbondedForce* standard = new NonbondedForce(numParticles, 0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
        double charge = i%2 == 0 ? -1 : 1;
-        forceField->setAtomParameters(i, charge, 0.15, 1);
+        forceField->setParticleParameters(i, charge, 0.15, 1);
-        standard->setAtomParameters(i, charge, 1, 0);
+        standard->setParticleParameters(i, charge, 1, 0);
    }
    system.addForce(forceField);
    system.addForce(standard);
    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);
@@ -102,14 +102,14 @@ 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);
@@ -124,7 +124,7 @@ void testForce() {
 int main() {
    try {
-        testSingleAtom();
+        testSingleParticle();
        testForce();
    }
    catch(const exception& e) {

--- a/platforms/cuda/tests/TestCudaLangevinIntegrator.cpp
+++ b/platforms/cuda/tests/TestCudaLangevinIntegrator.cpp
@@ -53,8 +53,8 @@ const double TOL = 1e-5;
 void testSingleBond() {
    CudaPlatform platform;
    System system(2, 0);
-    system.setAtomMass(0, 2.0);
+    system.setParticleMass(0, 2.0);
-    system.setAtomMass(1, 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;
    CudaPlatform platform;
-    System system(numAtoms, 0);
+    System system(numParticles, 0);
    LangevinIntegrator integrator(temp, 2.0, 0.01);
-    NonbondedForce* forceField = new NonbondedForce(numAtoms, 0);
+    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
-        system.setAtomMass(i, 2.0);
+        system.setParticleMass(i, 2.0);
-        forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        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);
+    vector<Vec3> positions(numParticles);
-    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));
    context.setPositions(positions);
@@ -125,30 +125,30 @@ 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 int numConstraints = 4;
    const double temp = 100.0;
    CudaPlatform platform;
-    System system(numAtoms, numConstraints);
+    System system(numParticles, numConstraints);
    LangevinIntegrator integrator(temp, 2.0, 0.01);
-    NonbondedForce* forceField = new NonbondedForce(numAtoms, 0);
+    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
-        system.setAtomMass(i, 10.0);
+        system.setParticleMass(i, 10.0);
-        forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+        forceField->setParticleParameters(i, (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.addForce(forceField);
    OpenMMContext context(system, integrator, platform);
-    vector<Vec3> positions(numAtoms);
+    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numAtoms);
+    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);
    }
@@ -160,11 +160,11 @@ void testConstraints() {
    for (int i = 0; i < 1000; ++i) {
        State state = context.getState(State::Positions);
        for (int j = 0; j < numConstraints; ++j) {
-            int atom1, atom2;
+            int particle1, particle2;
            double distance;
-            system.getConstraintParameters(j, atom1, atom2, distance);
+            system.getConstraintParameters(j, particle1, particle2, distance);
-            Vec3 p1 = state.getPositions()[atom1];
+            Vec3 p1 = state.getPositions()[particle1];
-            Vec3 p2 = state.getPositions()[atom2];
+            Vec3 p2 = state.getPositions()[particle2];
            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]));
            ASSERT_EQUAL_TOL(distance, dist, 2e-4);
        }

--- a/platforms/cuda/tests/TestCudaNonbondedForce.cpp
+++ b/platforms/cuda/tests/TestCudaNonbondedForce.cpp
@@ -54,8 +54,8 @@ void testCoulomb() {
    System system(2, 0);
    LangevinIntegrator integrator(0.0, 0.1, 0.01);
    NonbondedForce* forceField = new NonbondedForce(2, 0);
-    forceField->setAtomParameters(0, 0.5, 1, 0);
+    forceField->setParticleParameters(0, 0.5, 1, 0);
-    forceField->setAtomParameters(1, -1.5, 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);
    LangevinIntegrator integrator(0.0, 0.1, 0.01);
    NonbondedForce* forceField = new NonbondedForce(2, 0);
-    forceField->setAtomParameters(0, 0, 1.2, 1);
+    forceField->setParticleParameters(0, 0, 1.2, 1);
-    forceField->setAtomParameters(1, 0, 1.4, 2);
+    forceField->setParticleParameters(1, 0, 1.4, 2);
    system.addForce(forceField);
    OpenMMContext context(system, integrator, platform);
    vector<Vec3> positions(2);
@@ -112,11 +112,11 @@ 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->setParticleParameters(0, 0, 1.5, 1);
-        nonbonded->setAtomParameters(i, 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);
@@ -142,8 +142,8 @@ void testExclusionsAnd14() {
        // Test Coulomb forces
-        nonbonded->setAtomParameters(0, 2, 1.5, 0);
+        nonbonded->setParticleParameters(0, 2, 1.5, 0);
-        nonbonded->setAtomParameters(i, 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);
        OpenMMContext context2(system, integrator, platform);
@@ -171,9 +171,9 @@ void testCutoff() {
    System system(3, 0);
    LangevinIntegrator integrator(0.0, 0.1, 0.01);
    NonbondedForce* forceField = new NonbondedForce(3, 0);
-    forceField->setAtomParameters(0, 1.0, 1, 0);
+    forceField->setParticleParameters(0, 1.0, 1, 0);
-    forceField->setAtomParameters(1, 1.0, 1, 0);
+    forceField->setParticleParameters(1, 1.0, 1, 0);
-    forceField->setAtomParameters(2, 1.0, 1, 0);
+    forceField->setParticleParameters(2, 1.0, 1, 0);
    forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
    const double cutoff = 2.9;
    forceField->setCutoffDistance(cutoff);
@@ -225,10 +225,10 @@ 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->setParticleParameters(j, 0, 1.5, 0);
-        nonbonded->setAtomParameters(i, 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);
        context.reinitialize();
@@ -255,8 +255,8 @@ void testCutoff14() {
        // Test Coulomb forces
        const double q = 0.7;
-        nonbonded->setAtomParameters(0, q, 1.5, 0);
+        nonbonded->setParticleParameters(0, q, 1.5, 0);
-        nonbonded->setAtomParameters(i, 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();
@@ -290,9 +290,9 @@ 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->setParticleParameters(0, 1.0, 1, 0);
-    nonbonded->setAtomParameters(1, 1.0, 1, 0);
+    nonbonded->setParticleParameters(1, 1.0, 1, 0);
-    nonbonded->setAtomParameters(2, 1.0, 1, 0);
+    nonbonded->setParticleParameters(2, 1.0, 1, 0);
    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
    const double cutoff = 2.0;
    nonbonded->setCutoffDistance(cutoff);

--- a/platforms/reference/src/ReferenceKernels.cpp
+++ b/platforms/reference/src/ReferenceKernels.cpp
@@ -114,11 +114,11 @@ void ReferenceCalcHarmonicBondForceKernel::initialize(const System& system, cons
    bondIndexArray = allocateIntArray(numBonds, 2);
    bondParamArray = allocateRealArray(numBonds, 2);
    for (int i = 0; i < force.getNumBonds(); ++i) {
-        int atom1, atom2;
+        int particle1, particle2;
        double length, k;
-        force.getBondParameters(i, atom1, atom2, length, k);
+        force.getBondParameters(i, particle1, particle2, length, k);
-        bondIndexArray[i][0] = atom1;
+        bondIndexArray[i][0] = particle1;
-        bondIndexArray[i][1] = atom2;
+        bondIndexArray[i][1] = particle2;
        bondParamArray[i][0] = length;
        bondParamArray[i][1] = k;
    }
@@ -134,7 +134,7 @@ void ReferenceCalcHarmonicBondForceKernel::executeForces(OpenMMContextImpl& cont
 double ReferenceCalcHarmonicBondForceKernel::executeEnergy(OpenMMContextImpl& context) {
    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
-    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumAtoms(), 3);
+    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
    RealOpenMM* energyArray = new RealOpenMM[numBonds];
    RealOpenMM energy = 0;
    ReferenceBondForce refBondForce;
@@ -142,7 +142,7 @@ double ReferenceCalcHarmonicBondForceKernel::executeEnergy(OpenMMContextImpl& co
    for (int i = 0; i < numBonds; ++i)
        energyArray[i] = 0;
    refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, energyArray, 0, &energy, harmonicBond);
-    disposeRealArray(forceData, context.getSystem().getNumAtoms());
+    disposeRealArray(forceData, context.getSystem().getNumParticles());
    delete[] energyArray;
    return energy;
 }
@@ -157,12 +157,12 @@ void ReferenceCalcHarmonicAngleForceKernel::initialize(const System& system, con
    angleIndexArray = allocateIntArray(numAngles, 3);
    angleParamArray = allocateRealArray(numAngles, 2);
    for (int i = 0; i < force.getNumAngles(); ++i) {
-        int atom1, atom2, atom3;
+        int particle1, particle2, particle3;
        double angle, k;
-        force.getAngleParameters(i, atom1, atom2, atom3, angle, k);
+        force.getAngleParameters(i, particle1, particle2, particle3, angle, k);
-        angleIndexArray[i][0] = atom1;
+        angleIndexArray[i][0] = particle1;
-        angleIndexArray[i][1] = atom2;
+        angleIndexArray[i][1] = particle2;
-        angleIndexArray[i][2] = atom3;
+        angleIndexArray[i][2] = particle3;
        angleParamArray[i][0] = angle;
        angleParamArray[i][1] = k;
    }
@@ -178,7 +178,7 @@ void ReferenceCalcHarmonicAngleForceKernel::executeForces(OpenMMContextImpl& con
 double ReferenceCalcHarmonicAngleForceKernel::executeEnergy(OpenMMContextImpl& context) {
    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
-    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumAtoms(), 3);
+    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
    RealOpenMM* energyArray = new RealOpenMM[numAngles];
    RealOpenMM energy = 0;
    ReferenceBondForce refBondForce;
@@ -186,7 +186,7 @@ double ReferenceCalcHarmonicAngleForceKernel::executeEnergy(OpenMMContextImpl& c
    for (int i = 0; i < numAngles; ++i)
        energyArray[i] = 0;
    refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, energyArray, 0, &energy, angleBond);
-    disposeRealArray(forceData, context.getSystem().getNumAtoms());
+    disposeRealArray(forceData, context.getSystem().getNumParticles());
    delete[] energyArray;
    return energy;
 }
@@ -201,13 +201,13 @@ void ReferenceCalcPeriodicTorsionForceKernel::initialize(const System& system, c
    torsionIndexArray = allocateIntArray(numTorsions, 4);
    torsionParamArray = allocateRealArray(numTorsions, 3);
    for (int i = 0; i < force.getNumTorsions(); ++i) {
-        int atom1, atom2, atom3, atom4, periodicity;
+        int particle1, particle2, particle3, particle4, periodicity;
        double phase, k;
-        force.getTorsionParameters(i, atom1, atom2, atom3, atom4, periodicity, phase, k);
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, periodicity, phase, k);
-        torsionIndexArray[i][0] = atom1;
+        torsionIndexArray[i][0] = particle1;
-        torsionIndexArray[i][1] = atom2;
+        torsionIndexArray[i][1] = particle2;
-        torsionIndexArray[i][2] = atom3;
+        torsionIndexArray[i][2] = particle3;
-        torsionIndexArray[i][3] = atom4;
+        torsionIndexArray[i][3] = particle4;
        torsionParamArray[i][0] = k;
        torsionParamArray[i][1] = phase;
        torsionParamArray[i][2] = periodicity;
@@ -224,7 +224,7 @@ void ReferenceCalcPeriodicTorsionForceKernel::executeForces(OpenMMContextImpl& c
 double ReferenceCalcPeriodicTorsionForceKernel::executeEnergy(OpenMMContextImpl& context) {
    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
-    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumAtoms(), 3);
+    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
    RealOpenMM* energyArray = new RealOpenMM[numTorsions];
    RealOpenMM energy = 0;
    ReferenceBondForce refBondForce;
@@ -232,7 +232,7 @@ double ReferenceCalcPeriodicTorsionForceKernel::executeEnergy(OpenMMContextImpl&
    for (int i = 0; i < numTorsions; ++i)
        energyArray[i] = 0;
    refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, energyArray, 0, &energy, periodicTorsionBond);
-    disposeRealArray(forceData, context.getSystem().getNumAtoms());
+    disposeRealArray(forceData, context.getSystem().getNumParticles());
    delete[] energyArray;
    return energy;
 }
@@ -247,13 +247,13 @@ void ReferenceCalcRBTorsionForceKernel::initialize(const System& system, const R
    torsionIndexArray = allocateIntArray(numTorsions, 4);
    torsionParamArray = allocateRealArray(numTorsions, 6);
    for (int i = 0; i < force.getNumTorsions(); ++i) {
-        int atom1, atom2, atom3, atom4;
+        int particle1, particle2, particle3, particle4;
        double c0, c1, c2, c3, c4, c5;
-        force.getTorsionParameters(i, atom1, atom2, atom3, atom4, c0, c1, c2, c3, c4, c5);
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
-        torsionIndexArray[i][0] = atom1;
+        torsionIndexArray[i][0] = particle1;
-        torsionIndexArray[i][1] = atom2;
+        torsionIndexArray[i][1] = particle2;
-        torsionIndexArray[i][2] = atom3;
+        torsionIndexArray[i][2] = particle3;
-        torsionIndexArray[i][3] = atom4;
+        torsionIndexArray[i][3] = particle4;
        torsionParamArray[i][0] = c0;
        torsionParamArray[i][1] = c1;
        torsionParamArray[i][2] = c2;
@@ -273,7 +273,7 @@ void ReferenceCalcRBTorsionForceKernel::executeForces(OpenMMContextImpl& context
 double ReferenceCalcRBTorsionForceKernel::executeEnergy(OpenMMContextImpl& context) {
    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
-    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumAtoms(), 3);
+    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
    RealOpenMM* energyArray = new RealOpenMM[numTorsions];
    RealOpenMM energy = 0;
    ReferenceBondForce refBondForce;
@@ -281,14 +281,14 @@ double ReferenceCalcRBTorsionForceKernel::executeEnergy(OpenMMContextImpl& conte
    for (int i = 0; i < numTorsions; ++i)
        energyArray[i] = 0;
    refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, energyArray, 0, &energy, rbTorsionBond);
-    disposeRealArray(forceData, context.getSystem().getNumAtoms());
+    disposeRealArray(forceData, context.getSystem().getNumParticles());
    delete[] energyArray;
    return energy;
 }
 ReferenceCalcNonbondedForceKernel::~ReferenceCalcNonbondedForceKernel() {
-    disposeRealArray(atomParamArray, numAtoms);
+    disposeRealArray(particleParamArray, numParticles);
-    disposeIntArray(exclusionArray, numAtoms);
+    disposeIntArray(exclusionArray, numParticles);
    disposeIntArray(bonded14IndexArray, num14);
    disposeRealArray(bonded14ParamArray, num14);
    if (neighborList != NULL)
@@ -296,22 +296,22 @@ ReferenceCalcNonbondedForceKernel::~ReferenceCalcNonbondedForceKernel() {
 }
 void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force, const std::vector<std::set<int> >& exclusions) {
-    numAtoms = force.getNumAtoms();
+    numParticles = force.getNumParticles();
    num14 = force.getNumNonbonded14();
    bonded14IndexArray = allocateIntArray(num14, 2);
    bonded14ParamArray = allocateRealArray(num14, 3);
-    atomParamArray = allocateRealArray(numAtoms, 3);
+    particleParamArray = allocateRealArray(numParticles, 3);
    RealOpenMM sqrtEps = static_cast<RealOpenMM>( std::sqrt(138.935485) );
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
        double charge, radius, depth;
-        force.getAtomParameters(i, charge, radius, depth);
+        force.getParticleParameters(i, charge, radius, depth);
-        atomParamArray[i][0] = static_cast<RealOpenMM>(0.5*radius);
+        particleParamArray[i][0] = static_cast<RealOpenMM>(0.5*radius);
-        atomParamArray[i][1] = static_cast<RealOpenMM>(2.0*sqrt(depth));
+        particleParamArray[i][1] = static_cast<RealOpenMM>(2.0*sqrt(depth));
-        atomParamArray[i][2] = static_cast<RealOpenMM>(charge*sqrtEps);
+        particleParamArray[i][2] = static_cast<RealOpenMM>(charge*sqrtEps);
    }
    this->exclusions = exclusions;
-    exclusionArray = new int*[numAtoms];
+    exclusionArray = new int*[numParticles];
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
        exclusionArray[i] = new int[exclusions[i].size()+1];
        exclusionArray[i][0] = exclusions[i].size();
        int index = 0;
@@ -319,11 +319,11 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
            exclusionArray[i][++index] = *iter;
    }
    for (int i = 0; i < num14; ++i) {
-        int atom1, atom2;
+        int particle1, particle2;
        double charge, radius, depth;
-        force.getNonbonded14Parameters(i, atom1, atom2, charge, radius, depth);
+        force.getNonbonded14Parameters(i, particle1, particle2, charge, radius, depth);
-        bonded14IndexArray[i][0] = atom1;
+        bonded14IndexArray[i][0] = particle1;
-        bonded14IndexArray[i][1] = atom2;
+        bonded14IndexArray[i][1] = particle2;
        bonded14ParamArray[i][0] = static_cast<RealOpenMM>(radius);
        bonded14ParamArray[i][1] = static_cast<RealOpenMM>(4.0*depth);
        bonded14ParamArray[i][2] = static_cast<RealOpenMM>(charge*sqrtEps*sqrtEps);
@@ -348,12 +348,12 @@ void ReferenceCalcNonbondedForceKernel::executeForces(OpenMMContextImpl& context
    ReferenceLJCoulombIxn clj;
    bool periodic = (nonbondedMethod == CutoffPeriodic);
    if (nonbondedMethod != NoCutoff) {
-        computeNeighborListVoxelHash(*neighborList, numAtoms, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
+        computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
        clj.setUseCutoff(nonbondedCutoff, *neighborList, 78.3f);
    }
    if (periodic)
        clj.setPeriodic(periodicBoxSize);
-    clj.calculatePairIxn(numAtoms, posData, atomParamArray, exclusionArray, 0, forceData, 0, 0);
+    clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, 0);
    ReferenceBondForce refBondForce;
    ReferenceLJCoulomb14 nonbonded14;
    if (nonbondedMethod != NoCutoff)
@@ -363,26 +363,26 @@ void ReferenceCalcNonbondedForceKernel::executeForces(OpenMMContextImpl& context
 double ReferenceCalcNonbondedForceKernel::executeEnergy(OpenMMContextImpl& context) {
    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
-    RealOpenMM** forceData = allocateRealArray(numAtoms, 3);
+    RealOpenMM** forceData = allocateRealArray(numParticles, 3);
    RealOpenMM energy = 0;
    ReferenceLJCoulombIxn clj;
    bool periodic = (nonbondedMethod == CutoffPeriodic);
    if (nonbondedMethod != NoCutoff) {
-        computeNeighborListVoxelHash(*neighborList, numAtoms, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
+        computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
        clj.setUseCutoff(nonbondedCutoff, *neighborList, 78.3f);
    }
    if (periodic)
        clj.setPeriodic(periodicBoxSize);
-    clj.calculatePairIxn(numAtoms, posData, atomParamArray, exclusionArray, 0, forceData, 0, &energy);
+    clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, &energy);
    ReferenceBondForce refBondForce;
    ReferenceLJCoulomb14 nonbonded14;
    if (nonbondedMethod != NoCutoff)
        nonbonded14.setUseCutoff(nonbondedCutoff, 78.3f);
-    RealOpenMM* energyArray = new RealOpenMM[numAtoms];
+    RealOpenMM* energyArray = new RealOpenMM[numParticles];
-    for (int i = 0; i < numAtoms; ++i)
+    for (int i = 0; i < numParticles; ++i)
        energyArray[i] = 0;
    refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, energyArray, 0, &energy, nonbonded14);
-    disposeRealArray(forceData, numAtoms);
+    disposeRealArray(forceData, numParticles);
    delete[] energyArray;
    return energy;
 }
@@ -395,18 +395,18 @@ ReferenceCalcGBSAOBCForceFieldKernel::~ReferenceCalcGBSAOBCForceFieldKernel() {
 }
 void ReferenceCalcGBSAOBCForceFieldKernel::initialize(const System& system, const GBSAOBCForceField& force) {
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
-    charges.resize(numAtoms);
+    charges.resize(numParticles);
-    vector<RealOpenMM> atomicRadii(numAtoms);
+    vector<RealOpenMM> atomicRadii(numParticles);
-    vector<RealOpenMM> scaleFactors(numAtoms);
+    vector<RealOpenMM> scaleFactors(numParticles);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
        double charge, radius, scalingFactor;
-        force.getAtomParameters(i, charge, radius, scalingFactor);
+        force.getParticleParameters(i, charge, radius, scalingFactor);
        charges[i] = static_cast<RealOpenMM>(charge);
        atomicRadii[i] = static_cast<RealOpenMM>(radius);
        scaleFactors[i] = static_cast<RealOpenMM>(scalingFactor);
    }
-    ObcParameters* obcParameters  = new ObcParameters(numAtoms, ObcParameters::ObcTypeII);
+    ObcParameters* obcParameters  = new ObcParameters(numParticles, ObcParameters::ObcTypeII);
    obcParameters->setAtomicRadii(atomicRadii);
    obcParameters->setScaledRadiusFactors(scaleFactors);
    obcParameters->setSolventDielectric( static_cast<RealOpenMM>(force.getSolventDielectric()) );
@@ -423,9 +423,9 @@ void ReferenceCalcGBSAOBCForceFieldKernel::executeForces(OpenMMContextImpl& cont
 double ReferenceCalcGBSAOBCForceFieldKernel::executeEnergy(OpenMMContextImpl& context) {
    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
-    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumAtoms(), 3);
+    RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
    obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
-    disposeRealArray(forceData, context.getSystem().getNumAtoms());
+    disposeRealArray(forceData, context.getSystem().getNumParticles());
    return obc->getEnergy();
 }
@@ -443,19 +443,19 @@ ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() {
 }
 void ReferenceIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) {
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
-    masses = new RealOpenMM[numAtoms];
+    masses = new RealOpenMM[numParticles];
-    for (size_t i = 0; i < numAtoms; ++i)
+    for (size_t i = 0; i < numParticles; ++i)
-        masses[i] = static_cast<RealOpenMM>(system.getAtomMass(i));
+        masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
    numConstraints = system.getNumConstraints();
    constraintIndices = allocateIntArray(numConstraints, 2);
    shakeParameters = allocateRealArray(numConstraints, 1);
    for (int i = 0; i < numConstraints; ++i) {
-        int atom1, atom2;
+        int particle1, particle2;
        double distance;
-        system.getConstraintParameters(i, atom1, atom2, distance);
+        system.getConstraintParameters(i, particle1, particle2, distance);
-        constraintIndices[i][0] = atom1;
+        constraintIndices[i][0] = particle1;
-        constraintIndices[i][1] = atom2;
+        constraintIndices[i][1] = particle2;
        shakeParameters[i][0] = static_cast<RealOpenMM>(distance);
    }
 }
@@ -472,12 +472,12 @@ void ReferenceIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, con
            delete dynamics;
            delete shake;
        }
-        dynamics = new ReferenceVerletDynamics(context.getSystem().getNumAtoms(), static_cast<RealOpenMM>(stepSize) );
+        dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) );
        shake = new ReferenceShakeAlgorithm(numConstraints, constraintIndices, shakeParameters);
        dynamics->setReferenceShakeAlgorithm(shake);
        prevStepSize = stepSize;
    }
-    dynamics->update(context.getSystem().getNumAtoms(), posData, velData, forceData, masses);
+    dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
 }
 ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() {
@@ -494,19 +494,19 @@ ReferenceIntegrateLangevinStepKernel::~ReferenceIntegrateLangevinStepKernel() {
 }
 void ReferenceIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
-    masses = new RealOpenMM[numAtoms];
+    masses = new RealOpenMM[numParticles];
-    for (size_t i = 0; i < numAtoms; ++i)
+    for (size_t i = 0; i < numParticles; ++i)
-        masses[i] = static_cast<RealOpenMM>(system.getAtomMass(i));
+        masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
    numConstraints = system.getNumConstraints();
    constraintIndices = allocateIntArray(numConstraints, 2);
    shakeParameters = allocateRealArray(numConstraints, 1);
    for (int i = 0; i < numConstraints; ++i) {
-        int atom1, atom2;
+        int particle1, particle2;
        double distance;
-        system.getConstraintParameters(i, atom1, atom2, distance);
+        system.getConstraintParameters(i, particle1, particle2, distance);
-        constraintIndices[i][0] = atom1;
+        constraintIndices[i][0] = particle1;
-        constraintIndices[i][1] = atom2;
+        constraintIndices[i][1] = particle2;
        shakeParameters[i][0] = static_cast<RealOpenMM>(distance);
    }
 }
@@ -527,7 +527,7 @@ void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, c
        }
        RealOpenMM tau = static_cast<RealOpenMM>( friction == 0.0 ? 0.0 : 1.0/friction );
        dynamics = new ReferenceStochasticDynamics(
-				context.getSystem().getNumAtoms(), 
+				context.getSystem().getNumParticles(), 
 				static_cast<RealOpenMM>(stepSize), 
 				static_cast<RealOpenMM>(tau), 
 				static_cast<RealOpenMM>(temperature) );
@@ -537,7 +537,7 @@ void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, c
        prevFriction = friction;
        prevStepSize = stepSize;
    }
-    dynamics->update(context.getSystem().getNumAtoms(), posData, velData, forceData, masses);
+    dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
 }
 ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() {
@@ -554,19 +554,19 @@ ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() {
 }
 void ReferenceIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
-    masses = new RealOpenMM[numAtoms];
+    masses = new RealOpenMM[numParticles];
-    for (size_t i = 0; i < numAtoms; ++i)
+    for (size_t i = 0; i < numParticles; ++i)
-        masses[i] = static_cast<RealOpenMM>(system.getAtomMass(i));
+        masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
    numConstraints = system.getNumConstraints();
    constraintIndices = allocateIntArray(numConstraints, 2);
    shakeParameters = allocateRealArray(numConstraints, 1);
    for (int i = 0; i < numConstraints; ++i) {
-        int atom1, atom2;
+        int particle1, particle2;
        double distance;
-        system.getConstraintParameters(i, atom1, atom2, distance);
+        system.getConstraintParameters(i, particle1, particle2, distance);
-        constraintIndices[i][0] = atom1;
+        constraintIndices[i][0] = particle1;
-        constraintIndices[i][1] = atom2;
+        constraintIndices[i][1] = particle2;
        shakeParameters[i][0] = static_cast<RealOpenMM>(distance);
    }
 }
@@ -586,7 +586,7 @@ void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, c
            delete shake;
        }
        dynamics = new ReferenceBrownianDynamics(
-				context.getSystem().getNumAtoms(), 
+				context.getSystem().getNumParticles(), 
 				static_cast<RealOpenMM>(stepSize), 
 				static_cast<RealOpenMM>(friction), 
 				static_cast<RealOpenMM>(temperature) );
@@ -596,7 +596,7 @@ void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, c
        prevFriction = friction;
        prevStepSize = stepSize;
    }
-    dynamics->update(context.getSystem().getNumAtoms(), posData, velData, forceData, masses);
+    dynamics->update(context.getSystem().getNumParticles(), posData, velData, forceData, masses);
 }
 ReferenceApplyAndersenThermostatKernel::~ReferenceApplyAndersenThermostatKernel() {
@@ -607,10 +607,10 @@ ReferenceApplyAndersenThermostatKernel::~ReferenceApplyAndersenThermostatKernel(
 }
 void ReferenceApplyAndersenThermostatKernel::initialize(const System& system, const AndersenThermostat& thermostat) {
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
-    masses = new RealOpenMM[numAtoms];
+    masses = new RealOpenMM[numParticles];
-    for (size_t i = 0; i < numAtoms; ++i)
+    for (size_t i = 0; i < numParticles; ++i)
-        masses[i] = static_cast<RealOpenMM>(system.getAtomMass(i));
+        masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
    this->thermostat = new ReferenceAndersenThermostat();
 }
@@ -626,10 +626,10 @@ void ReferenceApplyAndersenThermostatKernel::execute(OpenMMContextImpl& context)
 }
 void ReferenceCalcKineticEnergyKernel::initialize(const System& system) {
-    int numAtoms = system.getNumAtoms();
+    int numParticles = system.getNumParticles();
-    masses.resize(numAtoms);
+    masses.resize(numParticles);
-    for (size_t i = 0; i < numAtoms; ++i)
+    for (size_t i = 0; i < numParticles; ++i)
-        masses[i] = system.getAtomMass(i);
+        masses[i] = system.getParticleMass(i);
 }
 double ReferenceCalcKineticEnergyKernel::execute(OpenMMContextImpl& context) {
@@ -642,9 +642,9 @@ double ReferenceCalcKineticEnergyKernel::execute(OpenMMContextImpl& context) {
 void ReferenceRemoveCMMotionKernel::initialize(const System& system, const CMMotionRemover& force) {
    frequency = force.getFrequency();
-    masses.resize(system.getNumAtoms());
+    masses.resize(system.getNumParticles());
    for (size_t i = 0; i < masses.size(); ++i)
-        masses[i] = system.getAtomMass(i);
+        masses[i] = system.getParticleMass(i);
 }
 void ReferenceRemoveCMMotionKernel::execute(OpenMMContextImpl& context) {
@@ -662,7 +662,7 @@ void ReferenceRemoveCMMotionKernel::execute(OpenMMContextImpl& context) {
        momentum[2] += static_cast<RealOpenMM>( masses[i]*velData[i][2] );
    }
-    // Adjust the atom velocities.
+    // Adjust the particle velocities.
    momentum[0] /= static_cast<RealOpenMM>( masses.size() );
    momentum[1] /= static_cast<RealOpenMM>( masses.size() );

--- a/platforms/reference/src/ReferenceKernels.h
+++ b/platforms/reference/src/ReferenceKernels.h
@@ -194,7 +194,7 @@ public:
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the NonbondedForce this kernel will be used for
-     * @param exclusions the i'th element lists the indices of all atoms with which the i'th atom should not interact through
+     * @param exclusions the i'th element lists the indices of all particles with which the i'th particle should not interact through
     *                   nonbonded forces.  Bonded 1-4 pairs are also included in this list, since they should be omitted from
     *                   the standard nonbonded calculation.
     */
@@ -213,9 +213,9 @@ public:
     */
    double executeEnergy(OpenMMContextImpl& context);
 private:
-    int numAtoms, num14;
+    int numParticles, num14;
    int **exclusionArray, **bonded14IndexArray;
-    RealOpenMM **atomParamArray, **bonded14ParamArray;
+    RealOpenMM **particleParamArray, **bonded14ParamArray;
    RealOpenMM nonbondedCutoff, periodicBoxSize[3];
    std::vector<std::set<int> > exclusions;
    NonbondedMethod nonbondedMethod;
@@ -298,7 +298,7 @@ public:
    }
    ~ReferenceIntegrateLangevinStepKernel();
    /**
-     * Initialize the kernel, setting up the atomic masses.
+     * Initialize the kernel, setting up the particle masses.
     * 
     * @param system     the System this kernel will be applied to
     * @param integrator the LangevinIntegrator this kernel will be used for
@@ -355,7 +355,7 @@ private:
 };
 /**
- * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the atom velocities.
+ * This kernel is invoked by AndersenThermostat at the start of each time step to adjust the particle velocities.
 */
 class ReferenceApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
 public:
@@ -411,7 +411,7 @@ public:
    ReferenceRemoveCMMotionKernel(std::string name, const Platform& platform) : RemoveCMMotionKernel(name, platform) {
    }
    /**
-     * Initialize the kernel, setting up the atomic masses.
+     * Initialize the kernel, setting up the particle masses.
     * 
     * @param system     the System this kernel will be applied to
     * @param force      the CMMotionRemover this kernel will be used for

--- a/platforms/reference/tests/TestReferenceAndersenThermostat.cpp
+++ b/platforms/reference/tests/TestReferenceAndersenThermostat.cpp
@@ -49,23 +49,23 @@ using namespace OpenMM;
 using namespace std;
 void testTemperature() {
-    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);
-    NonbondedForce* forceField = new NonbondedForce(numAtoms, 0);
+    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
-    for (int i = 0; i < numAtoms; ++i) {
+    for (int i = 0; i < numParticles; ++i) {
-        system.setAtomMass(i, 2.0);
+        system.setParticleMass(i, 2.0);
-        forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
    AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
    system.addForce(thermstat);
    OpenMMContext context(system, integrator, platform);
-    vector<Vec3> positions(numAtoms);
+    vector<Vec3> positions(numParticles);
-    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));
    context.setPositions(positions);
@@ -82,7 +82,7 @@ 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));
 }