Renamed "atoms" to "particles"

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 {
-    atom1 = bonds[index].atom1;
-    atom2 = bonds[index].atom2;
+void HarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const {
+    particle1 = bonds[index].particle1;
+    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) {
-    bonds[index].atom1 = atom1;
-    bonds[index].atom2 = atom2;
+void HarmonicBondForce::setBondParameters(int index, int particle1, int particle2, double length, double k) {
+    bonds[index].particle1 = particle1;
+    bonds[index].particle2 = particle2;
     bonds[index].length = length;
     bonds[index].k = k;
 }

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 {
-    charge = atoms[index].charge;
-    radius = atoms[index].radius;
-    depth = atoms[index].depth;
+void NonbondedForce::getParticleParameters(int index, double& charge, double& radius, double& depth) const {
+    charge = particles[index].charge;
+    radius = particles[index].radius;
+    depth = particles[index].depth;
 }
 
-void NonbondedForce::setAtomParameters(int index, double charge, double radius, double depth) {
-    atoms[index].charge = charge;
-    atoms[index].radius = radius;
-    atoms[index].depth = depth;
+void NonbondedForce::setParticleParameters(int index, double charge, double radius, double depth) {
+    particles[index].charge = charge;
+    particles[index].radius = radius;
+    particles[index].depth = depth;
 }
 
-void NonbondedForce::getNonbonded14Parameters(int index, int& atom1, int& atom2, double& charge, double& radius, double& depth) const {
-    atom1 = nb14s[index].atom1;
-    atom2 = nb14s[index].atom2;
+void NonbondedForce::getNonbonded14Parameters(int index, int& particle1, int& particle2, double& charge, double& radius, double& depth) const {
+    particle1 = nb14s[index].particle1;
+    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) {
-    nb14s[index].atom1 = atom1;
-    nb14s[index].atom2 = atom2;
+void NonbondedForce::setNonbonded14Parameters(int index, int particle1, int particle2, double charge, double radius, double depth) {
+    nb14s[index].particle1 = particle1;
+    nb14s[index].particle2 = particle2;
     nb14s[index].charge = charge;
     nb14s[index].radius = radius;
     nb14s[index].depth = depth;

openmmapi/src/NonbondedForceImpl.cpp

@@ -50,18 +50,18 @@ 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);
-                bondIndices[i].push_back(atom1);
-                bondIndices[i].push_back(atom2);
+                force.getBondParameters(i, particle1, particle2, length, k);
+                bondIndices[i].push_back(particle1);
+                bondIndices[i].push_back(particle2);
             }
             findExclusions(bondIndices, exclusions, bonded14set);
         }
@@ -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 {
-    for (set<int>::const_iterator iter = bonded12[fromAtom].begin(); iter != bonded12[fromAtom].end(); ++iter) {
-        if (*iter != baseAtom)
+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[fromParticle].begin(); iter != bonded12[fromParticle].end(); ++iter) {
+        if (*iter != baseParticle)
             exclusions.insert(*iter);
         if (currentLevel > 0)
-            addExclusionsToSet(bonded12, exclusions, baseAtom, *iter, currentLevel-1);
+            addExclusionsToSet(bonded12, exclusions, baseParticle, *iter, currentLevel-1);
     }
 }
 

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]);
 }

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);
-    velocities = platform->createStream("atomVelocities", system.getNumAtoms(), Stream::Double3, *this);
-    forces = platform->createStream("atomForces", system.getNumAtoms(), Stream::Double3, *this);
+    positions = platform->createStream("particlePositions", system.getNumParticles(), Stream::Double3, *this);
+    velocities = platform->createStream("particleVelocities", system.getNumParticles(), Stream::Double3, *this);
+    forces = platform->createStream("particleForces", system.getNumParticles(), Stream::Double3, *this);
     double zero[] = {0.0, 0.0, 0.0};
     velocities.fillWithValue(&zero);
 }

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 {
-    atom1 = periodicTorsions[index].atom1;
-    atom2 = periodicTorsions[index].atom2;
-    atom3 = periodicTorsions[index].atom3;
-    atom4 = periodicTorsions[index].atom4;
+void PeriodicTorsionForce::getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& periodicity, double& phase, double& k) const {
+    particle1 = periodicTorsions[index].particle1;
+    particle2 = periodicTorsions[index].particle2;
+    particle3 = periodicTorsions[index].particle3;
+    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) {
-    periodicTorsions[index].atom1 = atom1;
-    periodicTorsions[index].atom2 = atom2;
-    periodicTorsions[index].atom3 = atom3;
-    periodicTorsions[index].atom4 = atom4;
+void PeriodicTorsionForce::setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k) {
+    periodicTorsions[index].particle1 = particle1;
+    periodicTorsions[index].particle2 = particle2;
+    periodicTorsions[index].particle3 = particle3;
+    periodicTorsions[index].particle4 = particle4;
     periodicTorsions[index].periodicity = periodicity;
     periodicTorsions[index].phase = phase;
     periodicTorsions[index].k = k;

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 {
-    atom1 = rbTorsions[index].atom1;
-    atom2 = rbTorsions[index].atom2;
-    atom3 = rbTorsions[index].atom3;
-    atom4 = rbTorsions[index].atom4;
+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 {
+    particle1 = rbTorsions[index].particle1;
+    particle2 = rbTorsions[index].particle2;
+    particle3 = rbTorsions[index].particle3;
+    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) {
-    rbTorsions[index].atom1 = atom1;
-    rbTorsions[index].atom2 = atom2;
-    rbTorsions[index].atom3 = atom3;
-    rbTorsions[index].atom4 = atom4;
+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].particle1 = particle1;
+    rbTorsions[index].particle2 = particle2;
+    rbTorsions[index].particle3 = particle3;
+    rbTorsions[index].particle4 = particle4;
     rbTorsions[index].c[0] = c0;
     rbTorsions[index].c[1] = c1;
     rbTorsions[index].c[2] = c2;

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),
-        positions( (types & Positions) == 0 ? 0 : numAtoms), velocities( (types & Velocities) == 0 ? 0 : numAtoms),
-        forces( (types & Forces) == 0 ? 0 : numAtoms) {
+State::State(double time, int numParticles, DataType types) : types(types), time(time), ke(0), pe(0),
+        positions( (types & Positions) == 0 ? 0 : numParticles), velocities( (types & Velocities) == 0 ? 0 : numParticles),
+        forces( (types & Forces) == 0 ? 0 : numParticles) {
 }
 vector<Vec3>& State::updPositions() {
     return positions;

openmmapi/src/System.cpp

@@ -34,8 +34,8 @@
 
 using namespace OpenMM;
 
-System::System(int numAtoms, int numConstraints) : masses(numAtoms), constraints(numConstraints), forces(0) {
-    for (int i = 0; i < numAtoms; ++i)
+System::System(int numParticles, int numConstraints) : masses(numParticles), constraints(numConstraints), forces(0) {
+    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 {
-    atom1 = constraints[index].atom1;
-    atom2 = constraints[index].atom2;
+void System::getConstraintParameters(int index, int& particle1, int& particle2, double& distance) const {
+    particle1 = constraints[index].particle1;
+    particle2 = constraints[index].particle2;
     distance = constraints[index].distance;
 }
 
-void System::setConstraintParameters(int index, int atom1, int atom2, double distance) {
-    constraints[index].atom1 = atom1;
-    constraints[index].atom2 = atom2;
+void System::setConstraintParameters(int index, int particle1, int particle2, double distance) {
+    constraints[index].particle1 = particle1;
+    constraints[index].particle2 = particle2;
     constraints[index].distance = distance;
 }

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> atom2(numBonds);
+    vector<int> particle1(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> atom2(numAngles);
-    vector<int> atom3(numAngles);
+    vector<int> particle1(numAngles);
+    vector<int> particle2(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> atom2(numTorsions);
-    vector<int> atom3(numTorsions);
-    vector<int> atom4(numTorsions);
+    vector<int> particle1(numTorsions);
+    vector<int> particle2(numTorsions);
+    vector<int> particle3(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> atom2(numTorsions);
-    vector<int> atom3(numTorsions);
-    vector<int> atom4(numTorsions);
+    vector<int> particle1(numTorsions);
+    vector<int> particle2(numTorsions);
+    vector<int> particle3(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<float> c6(numAtoms);
-        vector<float> c12(numAtoms);
-        vector<float> q(numAtoms);
+        vector<int> particle(numParticles);
+        vector<float> c6(numParticles);
+        vector<float> c12(numParticles);
+        vector<float> q(numParticles);
         vector<char> symbol;
-        vector<vector<int> > exclusionList(numAtoms);
-        for (int i = 0; i < numAtoms; i++) {
+        vector<vector<int> > exclusionList(numParticles);
+        for (int i = 0; i < numParticles; i++) {
             double charge, radius, depth;
-            force.getAtomParameters(i, charge, radius, depth);
-            atom[i] = i;
+            force.getParticleParameters(i, charge, radius, depth);
+            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> atom2(num14);
+        vector<int> particle1(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<float> radius(numAtoms);
-    vector<float> scale(numAtoms);
-    for (int i = 0; i < numAtoms; i++) {
-        double charge, atomRadius, scalingFactor;
-        force.getAtomParameters(i, charge, atomRadius, scalingFactor);
-        atom[i] = i;
-        radius[i] = (float) atomRadius;
+    vector<int> particle(numParticles);
+    vector<float> radius(numParticles);
+    vector<float> scale(numParticles);
+    for (int i = 0; i < numParticles; i++) {
+        double charge, particleRadius, scalingFactor;
+        force.getParticleParameters(i, charge, particleRadius, scalingFactor);
+        particle[i] = i;
+        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();
-    vector<float> mass(numAtoms);
-    for (int i = 0; i < numAtoms; i++)
-        mass[i] = (float) system.getAtomMass(i);
+    int numParticles = system.getNumParticles();
+    vector<float> mass(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        mass[i] = (float) system.getParticleMass(i);
     gpuSetMass(gpu, mass);
     
     // Set constraints.
     
     int numConstraints = system.getNumConstraints();
-    vector<int> atom1(numConstraints);
-    vector<int> atom2(numConstraints);
+    vector<int> particle1(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);
-        atom1[i] = atom1Index;
-        atom2[i] = atom2Index;
+        system.getConstraintParameters(i, particle1Index, particle2Index, constraintDistance);
+        particle1[i] = particle1Index;
+        particle2[i] = particle2Index;
         distance[i] = (float) constraintDistance;
-        invMass1[i] = 1.0f/mass[atom1Index];
-        invMass2[i] = 1.0f/mass[atom2Index];
+        invMass1[i] = 1.0f/mass[particle1Index];
+        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();
-    masses.resize(numAtoms);
-    for (size_t i = 0; i < numAtoms; ++i)
-        masses[i] = system.getAtomMass(i);
+    int numParticles = system.getNumParticles();
+    masses.resize(numParticles);
+    for (size_t i = 0; i < numParticles; ++i)
+        masses[i] = system.getParticleMass(i);
 }
 
 double CudaCalcKineticEnergyKernel::execute(OpenMMContextImpl& context) {

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

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();
-    _gpuContext* gpu = (_gpuContext*) gpuInit(numAtoms);
+    int numParticles = context.getSystem().getNumParticles();
+    _gpuContext* gpu = (_gpuContext*) gpuInit(numParticles);
     context.setPlatformData(new PlatformData(gpu));
 }
 

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);

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) {
-        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;
     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);
-    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/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);
-    standard->setAtomParameters(0, 0.5, 1, 0);
+    forceField->setParticleParameters(0, 0.5, 0.15, 1);
+    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;
-    System system(numAtoms, 0);
+    const int numParticles = 10;
+    System system(numParticles, 0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForceField* forceField = new GBSAOBCForceField(numAtoms);
-    NonbondedForce* standard = new NonbondedForce(numAtoms, 0);
-    for (int i = 0; i < numAtoms; ++i) {
+    GBSAOBCForceField* forceField = new GBSAOBCForceField(numParticles);
+    NonbondedForce* standard = new NonbondedForce(numParticles, 0);
+    for (int i = 0; i < numParticles; ++i) {
         double charge = i%2 == 0 ? -1 : 1;
-        forceField->setAtomParameters(i, charge, 0.15, 1);
-        standard->setAtomParameters(i, charge, 1, 0);
+        forceField->setParticleParameters(i, charge, 0.15, 1);
+        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) {

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.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;
     CudaPlatform 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);
     
@@ -125,30 +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);
-    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 < 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> 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);
     }
@@ -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);
-            Vec3 p1 = state.getPositions()[atom1];
-            Vec3 p2 = state.getPositions()[atom2];
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            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);
         }

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->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);
     LangevinIntegrator integrator(0.0, 0.1, 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);
@@ -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->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);
@@ -142,8 +142,8 @@ 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);
         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->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);
@@ -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->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();
@@ -255,8 +255,8 @@ 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();
@@ -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->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/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

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);
-    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);
     AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
     system.addForce(thermstat);
     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);
     
@@ -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));
 }