Jason's fixes to documentation

docs-source/usersguide/theory.rst

@@ -131,7 +131,7 @@ Each torsion is represented by an energy term of the form
 
 
 where :math:`\theta` is the dihedral angle formed by the four particles, :math:`\theta_0`
-is the equilibrium angle, *n* is the periodicity, and *k* is
+is the phase offset, *n* is the periodicity, and *k* is
 the force constant.
 
 RBTorsionForce
@@ -205,7 +205,7 @@ second derivatives at both ends
 
 When an exception has been added for a pair of particles, :math:`\sigma` and :math:`\epsilon`
 are the parameters specified by the exception.  Otherwise they are determined
-from the parameters of the individual particles using the Lorentz-Bertelot
+from the parameters of the individual particles using the Lorentz-Berthelot
 combining rule:
 
 .. math::
@@ -458,14 +458,14 @@ between particles *i* and *j*\ .  :math:`f_\text{GB}(d_{ij}, R_i, R_j)` is defin
 
 
 .. math::
-   {f}_{\text{GB}}\left({d}_{ij},{R}_{i},{R}_{j}\right)={\left[{d}_{{ij}^{2}}+{R}_{i}{R}_{j}\text{exp}\left(\frac{-{d}_{ij}}{{4R}_{i}{R}_{j}}\right)\right]}^{1/2}
+   {f}_{\text{GB}}\left({d}_{ij},{R}_{i},{R}_{j}\right)={\left[{d}_{ij}^2+{R}_{i}{R}_{j}\text{exp}\left(\frac{-{d}_{ij}^2}{{4R}_{i}{R}_{j}}\right)\right]}^{1/2}
 
 
 :math:`R_i` is the Born radius of particle *i*\ , which calculated as
 
 
 .. math::
-   R_i=\frac{1}{\rho_i^{-1}-r_i^{-1}\text{tanh}\left(\alpha \Psi_{i}-{\beta \Psi}_{{i}^{2}}+{\gamma \Psi}_{{i}^{3}}\right)}
+   R_i=\frac{1}{\rho_i^{-1}-r_i^{-1}\text{tanh}\left(\alpha \Psi_{i}-{\beta \Psi}_i^2+{\gamma \Psi}_i^3\right)}
 
 
 where :math:`\alpha`, :math:`\beta`, and :math:`\gamma` are the GB\ :sup:`OBC`\ II parameters :math:`\alpha` = 1, :math:`\beta` = 0.8, and :math:`\gamma` =
@@ -622,7 +622,7 @@ weight function
 
 
 where :math:`\Delta E` is the change in potential energy resulting from the step,
-\ *P* is the system pressure, *N* is the number of molecules in the
+\ *P* is the pressure being applied to the system, *N* is the number of molecules in the
 system, :math:`k_B` is Boltzmann’s constant, and *T* is the system
 temperature.  In particular, if :math:`\Delta W\le 0` the step is always accepted.
 If :math:`\Delta W > 0`\ , the step is accepted with probability

openmmapi/include/openmm/NonbondedForce.h

@@ -46,7 +46,7 @@ namespace OpenMM {
  * This class implements nonbonded interactions between particles, including a Coulomb force to represent
  * electrostatics and a Lennard-Jones force to represent van der Waals interactions.  It optionally supports
  * periodic boundary conditions and cutoffs for long range interactions.  Lennard-Jones interactions are
- * calculated with the Lorentz-Bertelot combining rule: it uses the arithmetic mean of the sigmas and the
+ * calculated with the Lorentz-Berthelot combining rule: it uses the arithmetic mean of the sigmas and the
  * geometric mean of the epsilons for the two interacting particles.
  *
  * To use this class, create a NonbondedForce object, then call addParticle() once for each particle in the
@@ -221,7 +221,7 @@ public:
      * Add the nonbonded force parameters for a particle.  This should be called once for each particle
      * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
      * For calculating the Lennard-Jones interaction between two particles, the arithmetic mean of the sigmas
-     * and the geometric mean of the epsilons for the two interacting particles is used (the Lorentz-Bertelot
+     * and the geometric mean of the epsilons for the two interacting particles is used (the Lorentz-Berthelot
      * combining rule).
      *
      * @param charge    the charge of the particle, measured in units of the proton charge
@@ -242,7 +242,7 @@ public:
     /**
      * Set the nonbonded force parameters for a particle.  When calculating the Lennard-Jones interaction between two particles,
      * it uses the arithmetic mean of the sigmas and the geometric mean of the epsilons for the two interacting particles
-     * (the Lorentz-Bertelot combining rule).
+     * (the Lorentz-Berthelot combining rule).
      *
      * @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