Improvements to Doxygen comments

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -73,6 +73,12 @@ namespace OpenMM {
  * force->addPerParticleParameter("epsilon");
  * </pre></tt>
  *
+ * The expression <i>must</i> be symmetric with respect to the two particles.  It typically will only be evaluated once
+ * for each pair of particles, and no guarantee is made about which particle will be identified as "particle 1".  In the
+ * above example, the energy only depends on the products sigma1*sigma2 and epsilon1*epsilon2, both of which are unchanged
+ * if the labels 1 and 2 are reversed.  In contrast, if it depended on the difference sigma1-sigma2, the results would
+ * be undefined, because reversing the labels 1 and 2 would change the energy.
+ * 
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
  * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, step, delta.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.  The names of per-particle parameters

openmmapi/include/openmm/PeriodicTorsionForce.h

@@ -64,7 +64,7 @@ public:
      * @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 particle4    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
@@ -78,7 +78,7 @@ public:
      * @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 particle4    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
@@ -91,7 +91,7 @@ public:
      * @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 particle4    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

openmmapi/include/openmm/RBTorsionForce.h

@@ -64,7 +64,7 @@ public:
      * @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 particle4    the index of the fourth particle forming the torsion
      * @param c0           the coefficient of the constant term, measured in kJ/mol
      * @param c1           the coefficient of the 1st order term, measured in kJ/mol
      * @param c2           the coefficient of the 2nd order term, measured in kJ/mol
@@ -81,7 +81,7 @@ public:
      * @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 particle4    the index of the fourth particle forming the torsion
      * @param c0           the coefficient of the constant term, measured in kJ/mol
      * @param c1           the coefficient of the 1st order term, measured in kJ/mol
      * @param c2           the coefficient of the 2nd order term, measured in kJ/mol
@@ -97,7 +97,7 @@ public:
      * @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 particle4    the index of the fourth particle forming the torsion
      * @param c0           the coefficient of the constant term, measured in kJ/mol
      * @param c1           the coefficient of the 1st order term, measured in kJ/mol
      * @param c2           the coefficient of the 2nd order term, measured in kJ/mol