Renamed "atoms" to "particles"

olla/include/kernels.h

@@ -200,7 +200,7 @@ 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.
      */
@@ -331,7 +331,7 @@ public:
 };
 
 /**
- * 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 ApplyAndersenThermostatKernel : public KernelImpl {
 public:

openmmapi/include/CMMotionRemover.h

@@ -40,7 +40,7 @@ namespace OpenMM {
 
 /**
  * This class prevents the center of mass of a System from drifting.  At each time step, it calculates the
- * center of mass momentum, then adjusts the individual atom velocities to make it zero.
+ * center of mass momentum, then adjusts the individual particle velocities to make it zero.
  */
 
 class OPENMM_EXPORT CMMotionRemover : public Force {

openmmapi/include/Force.h

@@ -39,15 +39,15 @@ namespace OpenMM {
 class ForceImpl;
 
 /**
- * Force objects apply forces to the atoms in a System, or alter their behavior in other
+ * Force objects apply forces to the particles in a System, or alter their behavior in other
  * ways.  This is an abstract class.  Subclasses define particular forces.
  * 
  * More specifically, a Force object can do any or all of the following:
  * 
  * <ul>
- * <li>Add a contribution to the force on each atom</li>
+ * <li>Add a contribution to the force on each particle</li>
  * <li>Add a contribution to the potential energy of the System</li>
- * <li>Modify the positions and velocities of atoms at the start of each time step</li>
+ * <li>Modify the positions and velocities of particles at the start of each time step</li>
  * <li>Define parameters which are stored in the OpenMMContext and can be modified by the user</li>
  * <li>Change the values of parameters defined by other Force objects at the start of each time step</li>
  * </ul>

openmmapi/include/GBSAOBCForceField.h

@@ -47,33 +47,33 @@ public:
     /*
      * Create a GBSAOBCForceField.
      * 
-     * @param numAtoms    the number of atoms in the system
+     * @param numParticles    the number of particles in the system
      */
-    GBSAOBCForceField(int numAtoms);
+    GBSAOBCForceField(int numParticles);
     /**
-     * Get the number of atoms in the system.
+     * Get the number of particles in the system.
      */
-    int getNumAtoms() const {
-        return atoms.size();
+    int getNumParticles() const {
+        return particles.size();
     }
     /**
-     * Get the force field parameters for an atom.
+     * Get the force field parameters for a particle.
      * 
-     * @param index          the index of the atom for which to get parameters
-     * @param charge         the charge of the atom, measured in units of the proton charge
-     * @param radius         the GBSA radius of the atom, measured in nm
-     * @param scalingFactor  the OBC scaling factor for the atom
+     * @param index          the index of the particle for which to get parameters
+     * @param charge         the charge of the particle, measured in units of the proton charge
+     * @param radius         the GBSA radius of the particle, measured in nm
+     * @param scalingFactor  the OBC scaling factor for the particle
      */
-    void getAtomParameters(int index, double& charge, double& radius, double& scalingFactor) const;
+    void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
     /**
-     * Set the force field parameters for an atom.
+     * Set the force field parameters for a particle.
      * 
-     * @param index          the index of the atom for which to set parameters
-     * @param charge         the charge of the atom, measured in units of the proton charge
-     * @param radius         the GBSA radius of the atom, measured in nm
-     * @param scalingFactor  the OBC scaling factor for the atom
+     * @param index          the index of the particle for which to set parameters
+     * @param charge         the charge of the particle, measured in units of the proton charge
+     * @param radius         the GBSA radius of the particle, measured in nm
+     * @param scalingFactor  the OBC scaling factor for the particle
      */
-    void setAtomParameters(int index, double charge, double radius, double scalingFactor);
+    void setParticleParameters(int index, double charge, double radius, double scalingFactor);
     /**
      * Get the dielectric constant for the solvent.
      */
@@ -101,7 +101,7 @@ public:
 protected:
     ForceImpl* createImpl();
 private:
-    class AtomInfo;
+    class ParticleInfo;
     double solventDielectric, soluteDielectric;
 
 // Retarded visual studio compiler complains about being unable to 
@@ -112,7 +112,7 @@ private:
 #pragma warning(disable:4251)
 #endif
 
-    std::vector<AtomInfo> atoms;
+    std::vector<ParticleInfo> particles;
 
 #if defined(_MSC_VER)
 #pragma warning(pop)
@@ -120,10 +120,10 @@ private:
 
 };
 
-class GBSAOBCForceField::AtomInfo {
+class GBSAOBCForceField::ParticleInfo {
 public:
     double charge, radius, scalingFactor;
-    AtomInfo() {
+    ParticleInfo() {
         charge = radius = scalingFactor = 0.0;
     }
 };

openmmapi/include/HarmonicAngleForce.h

@@ -41,7 +41,7 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between groups of three atoms that varies harmonically with the angle
+ * This class implements an interaction between groups of three particles that varies harmonically with the angle
  * between them.  When creating a HarmonicAngleForce, you specify the number of angle as an argument to the
  * constructor, then loop over them and call setAngleParameters() to set the force field parameters for each one.
  */
@@ -64,24 +64,24 @@ public:
      * Get the force field parameters for an angle term.
      * 
      * @param index     the index of the angle for which to get parameters
-     * @param atom1     the index of the first atom forming the angle
-     * @param atom2     the index of the second atom forming the angle
-     * @param atom3     the index of the third atom forming the angle
+     * @param particle1 the index of the first particle forming the angle
+     * @param particle2 the index of the second particle forming the angle
+     * @param particle3 the index of the third particle forming the angle
      * @param length    the equilibrium angle, measured in radians
      * @param k         the harmonic force constant for the angle
      */
-    void getAngleParameters(int index, int& atom1, int& atom2, int& atom3, double& angle, double& k) const;
+    void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& angle, double& k) const;
     /**
      * Set the force field parameters for an angle term.
      * 
      * @param index     the index of the angle for which to set parameters
-     * @param atom1     the index of the first atom forming the angle
-     * @param atom2     the index of the second atom forming the angle
-     * @param atom3     the index of the third atom forming the angle
+     * @param particle1 the index of the first particle forming the angle
+     * @param particle2 the index of the second particle forming the angle
+     * @param particle3 the index of the third particle forming the angle
      * @param length    the equilibrium angle, measured in radians
      * @param k         the harmonic force constant for the angle
      */
-    void setAngleParameters(int index, int atom1, int atom2, int atom3, double angle, double k);
+    void setAngleParameters(int index, int particle1, int particle2, int particle3, double angle, double k);
 protected:
     ForceImpl* createImpl();
 private:
@@ -103,10 +103,10 @@ private:
 
 class HarmonicAngleForce::AngleInfo {
 public:
-    int atom1, atom2, atom3;
+    int particle1, particle2, particle3;
     double angle, k;
     AngleInfo() {
-        atom1 = atom2 = atom3 = -1;
+        particle1 = particle2 = particle3 = -1;
         angle = k = 0.0;
     }
 };

openmmapi/include/HarmonicBondForce.h

@@ -41,7 +41,7 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between pairs of atoms that varies harmonically with the distance
+ * This class implements an interaction between pairs of particles that varies harmonically with the distance
  * between them.  When creating a HarmonicBondForce, you specify the number of bonds as an argument to the
  * constructor, then loop over them and call setBondParameters() to set the force field parameters for each one.
  */
@@ -64,22 +64,22 @@ public:
      * Get the force field parameters for a bond term.
      * 
      * @param index     the index of the bond for which to get parameters
-     * @param atom1     the index of the first atom connected by the bond
-     * @param atom2     the index of the second atom connected by the bond
+     * @param particle1 the index of the first particle connected by the bond
+     * @param particle2 the index of the second particle connected by the bond
      * @param length    the equilibrium length of the bond, measured in nm
      * @param k         the harmonic force constant for the bond
      */
-    void getBondParameters(int index, int& atom1, int& atom2, double& length, double& k) const;
+    void getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const;
     /**
      * Set the force field parameters for a bond term.
      * 
      * @param index     the index of the bond for which to set parameters
-     * @param atom1     the index of the first atom connected by the bond
-     * @param atom2     the index of the second atom connected by the bond
+     * @param particle1 the index of the first particle connected by the bond
+     * @param particle2 the index of the second particle connected by the bond
      * @param length    the equilibrium length of the bond, measured in nm
      * @param k         the harmonic force constant for the bond
      */
-    void setBondParameters(int index, int atom1, int atom2, double length, double k);
+    void setBondParameters(int index, int particle1, int particle2, double length, double k);
 protected:
     ForceImpl* createImpl();
 private:
@@ -101,10 +101,10 @@ private:
 
 class HarmonicBondForce::BondInfo {
 public:
-    int atom1, atom2;
+    int particle1, particle2;
     double length, k;
     BondInfo() {
-        atom1 = atom2 = -1;
+        particle1 = particle2 = -1;
         length = k = 0.0;
     }
 };

openmmapi/include/NonbondedForce.h

@@ -51,8 +51,8 @@ namespace OpenMM {
  * for those separated by three bonds (known as "1-4 interactions").  This class lets you provide a list of
  * 1-4 interactions to include in the potential, along with the parameters to use for each one.
  * 
- * When creating a NonbondedForce, you specify the number of atoms and the number of 1-4 interactions as
- * arguments to the constructor.  You then loop over them and call setAtomParameters() for each atom and
+ * When creating a NonbondedForce, you specify the number of particles and the number of 1-4 interactions as
+ * arguments to the constructor.  You then loop over them and call setParticleParameters() for each particle and
  * setNonbond14Parameters() for each 1-4 interaction.
  */
 
@@ -73,8 +73,8 @@ public:
          */
         CutoffNonPeriodic = 1,
         /**
-         * Periodic boundary conditions are used, so that each atom interacts only with the nearest periodic copy of
-         * each other atom.  Interactions beyond the cutoff distance are ignored.  Coulomb interactions closer than the
+         * Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
+         * each other particle.  Interactions beyond the cutoff distance are ignored.  Coulomb interactions closer than the
          * cutoff distance are modified using the reaction field method.
          */
         CutoffPeriodic = 2
@@ -82,15 +82,15 @@ public:
     /**
      * Create a NonbondedForce.
      * 
-     * @param numAtoms            the number of atoms in the system
+     * @param numParticles            the number of particles in the system
      * @param numNonbonded14      the number of nonbonded 1-4 terms in the potential function
      */
-    NonbondedForce(int numAtoms, int numNonbonded14);
+    NonbondedForce(int numParticles, int numNonbonded14);
     /**
-     * Get the number of atoms in the system.
+     * Get the number of particles in the system.
      */
-    int getNumAtoms() const {
-        return atoms.size();
+    int getNumParticles() const {
+        return particles.size();
     }
     /**
      * Get the number of nonbonded 1-4 terms in the potential function
@@ -141,49 +141,49 @@ public:
      */
     void setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c);
     /**
-     * Get the nonbonded force parameters for an atom.
+     * Get the nonbonded force parameters for a particle.
      * 
-     * @param index     the index of the atom for which to get parameters
-     * @param charge    the charge of the atom, measured in units of the proton charge
-     * @param radius    the van der Waals radius of the atom, measured in nm
+     * @param index     the index of the particle for which to get parameters
+     * @param charge    the charge of the particle, measured in units of the proton charge
+     * @param radius    the van der Waals radius of the particle, measured in nm
      * @param depth     the well depth of the van der Waals interaction, measured in kJ/mol
      */
-    void getAtomParameters(int index, double& charge, double& radius, double& depth) const;
+    void getParticleParameters(int index, double& charge, double& radius, double& depth) const;
     /**
-     * Set the nonbonded force parameters for an atom.
+     * Set the nonbonded force parameters for a particle.
      * 
-     * @param index     the index of the atom for which to set parameters
-     * @param charge    the charge of the atom, measured in units of the proton charge
-     * @param radius    the van der Waals radius of the atom (sigma in the Lennard Jones potential), measured in nm
+     * @param index     the index of the particle for which to set parameters
+     * @param charge    the charge of the particle, measured in units of the proton charge
+     * @param radius    the van der Waals radius of the particle (sigma in the Lennard Jones potential), measured in nm
      * @param depth     the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
      */
-    void setAtomParameters(int index, double charge, double radius, double depth);
+    void setParticleParameters(int index, double charge, double radius, double depth);
     /**
      * Get the force field parameters for a nonbonded 1-4 term.
      * 
      * @param index     the index of the interaction for which to get parameters
-     * @param atom1     the index of the first atom involved in the interaction
-     * @param atom2     the index of the second atom involved in the interaction
+     * @param particle1 the index of the first particle involved in the interaction
+     * @param particle2 the index of the second particle involved in the interaction
      * @param charge    the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge
-     * @param radius    the van der Waals radius of the atom (sigma in the Lennard Jones potential), measured in nm
+     * @param radius    the van der Waals radius of the particle (sigma in the Lennard Jones potential), measured in nm
      * @param depth     the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
      */
-    void getNonbonded14Parameters(int index, int& atom1, int& atom2, double& charge, double& radius, double& depth) const;
+    void getNonbonded14Parameters(int index, int& particle1, int& particle2, double& charge, double& radius, double& depth) const;
     /**
      * Set the force field parameters for a nonbonded 1-4 term.
      * 
      * @param index     the index of the interaction for which to get parameters
-     * @param atom1     the index of the first atom involved in the interaction
-     * @param atom2     the index of the second atom involved in the interaction
+     * @param particle1 the index of the first particle involved in the interaction
+     * @param particle2 the index of the second particle involved in the interaction
      * @param charge    the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge
-     * @param radius    the van der Waals radius of the atom (sigma in the Lennard Jones potential), measured in nm
+     * @param radius    the van der Waals radius of the particle (sigma in the Lennard Jones potential), measured in nm
      * @param depth     the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
      */
-    void setNonbonded14Parameters(int index, int atom1, int atom2, double charge, double radius, double depth);
+    void setNonbonded14Parameters(int index, int particle1, int particle2, double charge, double radius, double depth);
 protected:
     ForceImpl* createImpl();
 private:
-    class AtomInfo;
+    class ParticleInfo;
     class NB14Info;
     NonbondedMethod nonbondedMethod;
     double cutoffDistance;
@@ -196,7 +196,7 @@ private:
 #pragma warning(push)
 #pragma warning(disable:4251)
 #endif
-    std::vector<AtomInfo> atoms;
+    std::vector<ParticleInfo> particles;
     std::vector<NB14Info> nb14s;
 #if defined(_MSC_VER)
 #pragma warning(pop)
@@ -204,20 +204,20 @@ private:
 
 };
 
-class NonbondedForce::AtomInfo {
+class NonbondedForce::ParticleInfo {
 public:
     double charge, radius, depth;
-    AtomInfo() {
+    ParticleInfo() {
         charge = radius = depth = 0.0;
     }
 };
 
 class NonbondedForce::NB14Info {
 public:
-    int atom1, atom2;
+    int particle1, particle2;
     double charge, radius, depth;
     NB14Info() {
-        atom1 = atom2 = -1;
+        particle1 = particle2 = -1;
         charge = radius = depth = 0.0;
     }
 };

openmmapi/include/OpenMMContext.h

@@ -50,15 +50,15 @@ class Platform;
  * 
  * <ul>
  * <li>The current time</li>
- * <li>The position of each atom</li>
- * <li>The velocity of each atom</li>
+ * <li>The position of each particle</li>
+ * <li>The velocity of each particle</li>
  * <li>The values of configurable parameters defined by Force objects in the System</li>
  * </ul>
  * 
  * You can retrieve a snapshot of the current state at any time by calling getState().  This
  * allows you to record the state of the simulation at various points, either for analysis
  * or for checkpointing.  getState() can also be used to retrieve the current forces on each
- * atom and the current energy of the System.
+ * particle and the current energy of the System.
  */
 
 class OPENMM_EXPORT OpenMMContext {
@@ -112,17 +112,17 @@ public:
      */
     void setTime(double time);
     /**
-     * Set the positions of all atoms in the System (measured in nm).
+     * Set the positions of all particles in the System (measured in nm).
      * 
-     * @param a vector whose length equals the number of atoms in the System.  The i'th element
-     * contains the position of the i'th atom.
+     * @param positions   a vector whose length equals the number of particles in the System.  The i'th element
+     * contains the position of the i'th particle.
      */
     void setPositions(const std::vector<Vec3>& positions);
     /**
-     * Set the velocities of all atoms in the System (measured in nm/picosecond).
+     * Set the velocities of all particles in the System (measured in nm/picosecond).
      * 
-     * @param a vector whose length equals the number of atoms in the System.  The i'th element
-     * contains the velocity of the i'th atom.
+     * @param velocities  a vector whose length equals the number of particles in the System.  The i'th element
+     * contains the velocity of the i'th particle.
      */
     void setVelocities(const std::vector<Vec3>& velocities);
     /**

openmmapi/include/PeriodicTorsionForce.h

@@ -41,7 +41,7 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between groups of four atoms that varies periodically with the torsion angle
+ * This class implements an interaction between groups of four particles that varies periodically with the torsion angle
  * between them.  When creating a PeriodicTorsionForce, you specify the number of torsions as an argument to the
  * constructor, then loop over them and call setTorsionParameters() to set the force field parameters for each one.
  */
@@ -64,43 +64,28 @@ public:
      * Get the force field parameters for a periodic torsion term.
      * 
      * @param index        the index of the torsion for which to get parameters
-     * @param atom1        the index of the first atom forming the torsion
-     * @param atom2        the index of the second atom forming the torsion
-     * @param atom3        the index of the third atom forming the torsion
-     * @param atom3        the index of the fourth atom forming the torsion
+     * @param particle1    the index of the first particle forming the torsion
+     * @param particle2    the index of the second particle forming the torsion
+     * @param particle3    the index of the third particle forming the torsion
+     * @param particle3    the index of the fourth particle forming the torsion
      * @param periodicity  the periodicity of the torsion
      * @param phase        the phase offset of the torsion, measured in radians
      * @param k            the force constant for the torsion
      */
-    void getTorsionParameters(int index, int& atom1, int& atom2, int& atom3, int& atom4, int& periodicity, double& phase, double& k) const;
+    void getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, int& periodicity, double& phase, double& k) const;
     /**
      * Set the force field parameters for a periodic torsion term.
      * 
      * @param index        the index of the torsion for which to set parameters
-     * @param atom1        the index of the first atom forming the torsion
-     * @param atom2        the index of the second atom forming the torsion
-     * @param atom3        the index of the third atom forming the torsion
-     * @param atom3        the index of the fourth atom forming the torsion
+     * @param particle1    the index of the first particle forming the torsion
+     * @param particle2    the index of the second particle forming the torsion
+     * @param particle3    the index of the third particle forming the torsion
+     * @param particle3    the index of the fourth particle forming the torsion
      * @param periodicity  the periodicity of the torsion
      * @param phase        the phase offset of the torsion, measured in radians
      * @param k            the force constant for the torsion
      */
-    void setTorsionParameters(int index, int atom1, int atom2, int atom3, int atom4, int periodicity, double phase, double k);
-    /**
-     * Get the force field parameters for a Ryckaert-Bellemans torsion term.
-     * 
-     * @param index        the index of the torsion for which to get parameters
-     * @param atom1        the index of the first atom forming the torsion
-     * @param atom2        the index of the second atom forming the torsion
-     * @param atom3        the index of the third atom forming the torsion
-     * @param atom3        the index of the fourth atom forming the torsion
-     * @param c0           the coefficient of the constant term
-     * @param c1           the coefficient of the 1st order term
-     * @param c2           the coefficient of the 2nd order term
-     * @param c3           the coefficient of the 3rd order term
-     * @param c4           the coefficient of the 4th order term
-     * @param c5           the coefficient of the 5th order term
-     */
+    void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k);
 protected:
     ForceImpl* createImpl();
 private:
@@ -122,10 +107,10 @@ private:
 
 class PeriodicTorsionForce::PeriodicTorsionInfo {
 public:
-    int atom1, atom2, atom3, atom4, periodicity;
+    int particle1, particle2, particle3, particle4, periodicity;
     double phase, k;
     PeriodicTorsionInfo() {
-        atom1 = atom2 = atom3 = atom4 = -1;
+        particle1 = particle2 = particle3 = particle4 = -1;
         periodicity = 1;
         phase = k = 0.0;
     }

openmmapi/include/RBTorsionForce.h

@@ -41,7 +41,7 @@
 namespace OpenMM {
 
 /**
- * This class implements an interaction between groups of four atoms that varies with the torsion angle between them
+ * This class implements an interaction between groups of four particles that varies with the torsion angle between them
  * according to the Ryckaert-Bellemans potential.  When creating an RBTorsionForce, you specify the number of torsions
  * as an argument to the constructor, then loop over them and call setTorsionParameters() to set the force field
  * parameters for each one.
@@ -65,10 +65,10 @@ public:
      * Get the force field parameters for a Ryckaert-Bellemans torsion term.
      * 
      * @param index        the index of the torsion for which to get parameters
-     * @param atom1        the index of the first atom forming the torsion
-     * @param atom2        the index of the second atom forming the torsion
-     * @param atom3        the index of the third atom forming the torsion
-     * @param atom3        the index of the fourth atom forming the torsion
+     * @param particle1    the index of the first particle forming the torsion
+     * @param particle2    the index of the second particle forming the torsion
+     * @param particle3    the index of the third particle forming the torsion
+     * @param particle3    the index of the fourth particle forming the torsion
      * @param c0           the coefficient of the constant term
      * @param c1           the coefficient of the 1st order term
      * @param c2           the coefficient of the 2nd order term
@@ -76,15 +76,15 @@ public:
      * @param c4           the coefficient of the 4th order term
      * @param c5           the coefficient of the 5th order term
      */
-    void 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 getTorsionParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4, double& c0, double& c1, double& c2, double& c3, double& c4, double& c5) const;
     /**
      * Set the force field parameters for a Ryckaert-Bellemans torsion term.
      * 
      * @param index        the index of the torsion for which to set parameters
-     * @param atom1        the index of the first atom forming the torsion
-     * @param atom2        the index of the second atom forming the torsion
-     * @param atom3        the index of the third atom forming the torsion
-     * @param atom3        the index of the fourth atom forming the torsion
+     * @param particle1    the index of the first particle forming the torsion
+     * @param particle2    the index of the second particle forming the torsion
+     * @param particle3    the index of the third particle forming the torsion
+     * @param particle3    the index of the fourth particle forming the torsion
      * @param c0           the coefficient of the constant term
      * @param c1           the coefficient of the 1st order term
      * @param c2           the coefficient of the 2nd order term
@@ -92,7 +92,7 @@ public:
      * @param c4           the coefficient of the 4th order term
      * @param c5           the coefficient of the 5th order term
      */
-    void setTorsionParameters(int index, int atom1, int atom2, int atom3, int atom4, double c0, double c1, double c2, double c3, double c4, double c5);
+    void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5);
 protected:
     ForceImpl* createImpl();
 private:
@@ -114,10 +114,10 @@ private:
 
 class RBTorsionForce::RBTorsionInfo {
 public:
-    int atom1, atom2, atom3, atom4;
+    int particle1, particle2, particle3, particle4;
     double c[6];
     RBTorsionInfo() {
-        atom1 = atom2 = atom3 = atom4 = -1;
+        particle1 = particle2 = particle3 = particle4 = -1;
         c[0] = c[1] = c[2] = c[3] = c[4] = c[5] = 0.0;
     }
 };

openmmapi/include/State.h

@@ -62,15 +62,15 @@ public:
      */
     double getTime() const;
     /**
-     * Get the position of each atom.  If this State does not contain positions, this will throw an exception.
+     * Get the position of each particle.  If this State does not contain positions, this will throw an exception.
      */
     const std::vector<Vec3>& getPositions() const;
     /**
-     * Get the velocity of each atom.  If this State does not contain velocities, this will throw an exception.
+     * Get the velocity of each particle.  If this State does not contain velocities, this will throw an exception.
      */
     const std::vector<Vec3>& getVelocities() const;
     /**
-     * Get the force acting on each atom.  If this State does not contain forces, this will throw an exception.
+     * Get the force acting on each particle.  If this State does not contain forces, this will throw an exception.
      */
     const std::vector<Vec3>& getForces() const;
     /**
@@ -87,7 +87,7 @@ public:
     const std::map<std::string, double>& getParameters() const;
 private:
     friend class OpenMMContext;
-    State(double time, int numAtoms, DataType types);
+    State(double time, int numParticles, DataType types);
 
 // Retarded visual studio compiler complains about being unable to 
 // export private stl class members.

openmmapi/include/System.h

@@ -44,14 +44,14 @@ class OPENMM_EXPORT Force;
  * three elements:
  * 
  * <ol>
- * <li>The set of atoms in the system</li>
+ * <li>The set of particles in the system</li>
  * <li>The forces acting on them</li>
- * <li>Pairs of atoms whose separation should be connstrained to a fixed value</li>
+ * <li>Pairs of particles whose separation should be connstrained to a fixed value</li>
  * </ol>
  * 
- * The atoms and constraints are defined directly by the System object.
+ * The particles and constraints are defined directly by the System object.
  * The forces are defined by objects that extend the Force class.  The System
- * stores a list of Force objects that determine the motion of the atoms.
+ * stores a list of Force objects that determine the motion of the particles.
  */
 
 class OPENMM_EXPORT System {
@@ -59,32 +59,32 @@ public:
     /**
      * Create a new System.
      * 
-     * @param numAtoms       the number of atoms in the System
+     * @param numParticles   the number of particles in the System
      * @param numConstraints the number of distance constraints in the System.
      */
-    System(int numAtoms, int numConstraints);
+    System(int numParticles, int numConstraints);
     ~System();
     /**
-     * Get the number of atoms in this System.
+     * Get the number of particles in this System.
      */
-    int getNumAtoms() const {
+    int getNumParticles() const {
         return masses.size();
     }
     /**
-     * Get the mass (in atomic mass units) of an atom.
+     * Get the mass (in atomic mass units) of a particle.
      * 
-     * @param index the index of the atom for which to get the mass
+     * @param index the index of the particle for which to get the mass
      */
-    double getAtomMass(int index) const {
+    double getParticleMass(int index) const {
         return masses[index];
     }
     /**
-     * Set the mass (in atomic mass units) of an atom.
+     * Set the mass (in atomic mass units) of a particle.
      * 
-     * @param index  the index of the atom for which to set the mass
-     * @param mass   the mass of the atom
+     * @param index  the index of the particle for which to set the mass
+     * @param mass   the mass of the particle
      */
-    void setAtomMass(int index, double mass) {
+    void setParticleMass(int index, double mass) {
         masses[index] = mass;
     }
     /**
@@ -97,20 +97,20 @@ public:
      * Get the parameters defining a distance constraint.
      * 
      * @param index     the index of the constraint for which to get parameters
-     * @param atom1     the index of the first atom involved in the constraint
-     * @param atom2     the index of the second atom involved in the constraint
-     * @param distance  the required distance between the two atoms, measured in nm
+     * @param particle1 the index of the first particle involved in the constraint
+     * @param particle2 the index of the second particle involved in the constraint
+     * @param distance  the required distance between the two particles, measured in nm
      */
-    void getConstraintParameters(int index, int& atom1, int& atom2, double& distance) const;
+    void getConstraintParameters(int index, int& particle1, int& particle2, double& distance) const;
     /**
      * Set the parameters defining a distance constraint.
      * 
      * @param index     the index of the constraint for which to set parameters
-     * @param atom1     the index of the first atom involved in the constraint
-     * @param atom2     the index of the second atom involved in the constraint
-     * @param distance  the required distance between the two atoms, measured in nm
+     * @param particle1 the index of the first particle involved in the constraint
+     * @param particle2 the index of the second particle involved in the constraint
+     * @param distance  the required distance between the two particles, measured in nm
      */
-    void setConstraintParameters(int index, int atom1, int atom2, double distance);
+    void setConstraintParameters(int index, int particle1, int particle2, double distance);
     /**
      * Add a Force to the System.  The Force should have been created on the heap with the
      * "new" operator.  The System takes over ownership of it, and deletes the Force when the
@@ -156,10 +156,10 @@ private:
 
 class System::ConstraintInfo {
 public:
-    int atom1, atom2;
+    int particle1, particle2;
     double distance;
     ConstraintInfo() {
-        atom1 = atom2 = -1;
+        particle1 = particle2 = -1;
         distance = 0.0;
     }
 };

openmmapi/include/internal/AndersenThermostatImpl.h

@@ -52,7 +52,7 @@ public:
     }
     void updateContextState(OpenMMContextImpl& context);
     void calcForces(OpenMMContextImpl& context, Stream& forces) {
-        // This force doesn't apply forces to atoms.
+        // This force doesn't apply forces to particles.
     }
     double calcEnergy(OpenMMContextImpl& context) {
         return 0.0; // This force doesn't contribute to the potential energy.

openmmapi/include/internal/CMMotionRemoverImpl.h

@@ -51,7 +51,7 @@ public:
     }
     void updateContextState(OpenMMContextImpl& context);
     void calcForces(OpenMMContextImpl& context, Stream& forces) {
-        // This force doesn't apply forces to atoms.
+        // This force doesn't apply forces to particles.
     }
     double calcEnergy(OpenMMContextImpl& context) {
         return 0.0; // This force doesn't contribute to the potential energy.

openmmapi/include/internal/ForceImpl.h

@@ -74,7 +74,7 @@ public:
      */
     virtual void updateContextState(OpenMMContextImpl& context) = 0;
     /**
-     * Calculate the force on each atom generated by this ForceImpl.  The forces should be <i>added</i>
+     * Calculate the force on each particle generated by this ForceImpl.  The forces should be <i>added</i>
      * to the values already present in the array that is passed in.  If this ForceImpl does not generate
      * any new forces, it should simply return without modifying the array.
      * 

openmmapi/include/internal/NonbondedForceImpl.h

@@ -64,7 +64,7 @@ public:
     std::vector<std::string> getKernelNames();
 private:
     void findExclusions(const std::vector<std::vector<int> >& bondIndices, std::vector<std::set<int> >& exclusions, std::set<std::pair<int, int> >& bonded14Indices) const;
-    void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseAtom, int fromAtom, int currentLevel) const;
+    void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
     NonbondedForce& owner;
     Kernel kernel;
 };

openmmapi/include/internal/OpenMMContextImpl.h

@@ -81,19 +81,19 @@ public:
         return *platform;
     }
     /**
-     * Get the Stream containing the current position of each atom.
+     * Get the Stream containing the current position of each particle.
      */
     Stream& getPositions() {
         return positions;
     }
     /**
-     * Get the Stream containing the current velocity of each atom.
+     * Get the Stream containing the current velocity of each particle.
      */
     Stream& getVelocities() {
         return velocities;
     }
     /**
-     * Get the Stream containing the force on each atom that was calculated by
+     * Get the Stream containing the force on each particle that was calculated by
      * the most recent call to calcForces().
      */
     Stream& getForces() {

openmmapi/src/BrownianIntegrator.cpp

@@ -49,17 +49,17 @@ void BrownianIntegrator::initialize(OpenMMContextImpl& contextRef) {
     context = &contextRef;
     kernel = context->getPlatform().createKernel(IntegrateBrownianStepKernel::Name(), contextRef);
     const System& system = context->getSystem();
-    vector<double> masses(system.getNumAtoms());
+    vector<double> masses(system.getNumParticles());
     vector<std::vector<int> > constraintIndices(system.getNumConstraints());
     vector<double> constraintLengths(system.getNumConstraints());
-    for (int i = 0; i < system.getNumAtoms(); ++i)
-        masses[i] = system.getAtomMass(i);
+    for (int i = 0; i < system.getNumParticles(); ++i)
+        masses[i] = system.getParticleMass(i);
     for (int i = 0; i < system.getNumConstraints(); ++i) {
-        int atom1, atom2;
+        int particle1, particle2;
         double distance;
-        system.getConstraintParameters(i, atom1, atom2, distance);
-        constraintIndices[i].push_back(atom1);
-        constraintIndices[i].push_back(atom2);
+        system.getConstraintParameters(i, particle1, particle2, distance);
+        constraintIndices[i].push_back(particle1);
+        constraintIndices[i].push_back(particle2);
         constraintLengths[i] = distance;
     }
     dynamic_cast<IntegrateBrownianStepKernel&>(kernel.getImpl()).initialize(system, *this);

openmmapi/src/GBSAOBCForceField.cpp

@@ -36,19 +36,19 @@
 
 using namespace OpenMM;
 
-GBSAOBCForceField::GBSAOBCForceField(int numAtoms) : atoms(numAtoms), solventDielectric(78.3), soluteDielectric(1.0) {
+GBSAOBCForceField::GBSAOBCForceField(int numParticles) : particles(numParticles), solventDielectric(78.3), soluteDielectric(1.0) {
 }
 
-void GBSAOBCForceField::getAtomParameters(int index, double& charge, double& radius, double& scalingFactor) const {
-    charge = atoms[index].charge;
-    radius = atoms[index].radius;
-    scalingFactor = atoms[index].scalingFactor;
+void GBSAOBCForceField::getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const {
+    charge = particles[index].charge;
+    radius = particles[index].radius;
+    scalingFactor = particles[index].scalingFactor;
 }
 
-void GBSAOBCForceField::setAtomParameters(int index, double charge, double radius, double scalingFactor) {
-    atoms[index].charge = charge;
-    atoms[index].radius = radius;
-    atoms[index].scalingFactor = scalingFactor;
+void GBSAOBCForceField::setParticleParameters(int index, double charge, double radius, double scalingFactor) {
+    particles[index].charge = charge;
+    particles[index].radius = radius;
+    particles[index].scalingFactor = scalingFactor;
 }
 
 ForceImpl* GBSAOBCForceField::createImpl() {

openmmapi/src/HarmonicAngleForce.cpp

@@ -39,18 +39,18 @@ using namespace OpenMM;
 HarmonicAngleForce::HarmonicAngleForce(int numAngles) : angles(numAngles) {
 }
 
-void HarmonicAngleForce::getAngleParameters(int index, int& atom1, int& atom2, int& atom3, double& angle, double& k) const {
-    atom1 = angles[index].atom1;
-    atom2 = angles[index].atom2;
-    atom3 = angles[index].atom3;
+void HarmonicAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& angle, double& k) const {
+    particle1 = angles[index].particle1;
+    particle2 = angles[index].particle2;
+    particle3 = angles[index].particle3;
     angle = angles[index].angle;
     k = angles[index].k;
 }
 
-void HarmonicAngleForce::setAngleParameters(int index, int atom1, int atom2, int atom3, double angle, double k) {
-    angles[index].atom1 = atom1;
-    angles[index].atom2 = atom2;
-    angles[index].atom3 = atom3;
+void HarmonicAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, double angle, double k) {
+    angles[index].particle1 = particle1;
+    angles[index].particle2 = particle2;
+    angles[index].particle3 = particle3;
     angles[index].angle = angle;
     angles[index].k = k;
 }