Documentation updates

doc/Doxyfile.in

@@ -759,7 +759,9 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @top_srcdir@ @top_srcdir@/src @top_srcdir@/src/hydro/Minimal @top_srcdir@/src/gravity/Default @top_srcdir@/riemann
+INPUT                  =  @top_srcdir@ @top_srcdir@/src @top_srcdir@/tests @top_srcdir@/examples
+INPUT		       += @top_srcdir@/src/hydro/Minimal @top_srcdir@/src/gravity/Default
+INPUT		       += @top_srcdir@/src/riemann 
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

src/riemann/riemann_exact.h

@@ -192,6 +192,8 @@ __attribute__((always_inline)) INLINE static GFLOAT riemann_guess_p(
  *
  * @param lower_limit Lower limit for the method (riemann_f(lower_limit) < 0)
  * @param upper_limit Upper limit for the method (riemann_f(upper_limit) > 0)
+ * @param lowf ??? Bert?
+ * @param upf  ??? Bert?
  * @param error_tol Tolerance used to decide if the solution is converged
  * @param WL Left state vector
  * @param WR Right state vector

tests/test27cells.c

@@ -32,14 +32,25 @@ enum velocity_types {
 };
 
 /**
- * @breif Returns a random number (uniformly distributed) in [a,b[
+ * @brief Returns a random number (uniformly distributed) in [a,b[
  */
 double random_uniform(double a, double b) {
   return (rand() / (double)RAND_MAX) * (b - a) + a;
 }
 
-/* n is both particles per axis and box size:
- * particles are generated on a mesh with unit spacing
+
+/**
+ * @brief Constructs a cell and all of its particle in a valid state prior to
+ * a DOPAIR or DOSELF calcuation.
+ *
+ * @param n The cube root of the number of particles.
+ * @param offset The position of the cell offset from (0,0,0).
+ * @param size The cell size.
+ * @param h The smoothing length of the particles in units of the inter-particle separation.
+ * @param density The density of the fluid.
+ * @param partId The running counter of IDs.
+ * @param pert The perturbation to apply to the particles in the cell in units of the inter-particle separation.
+ * @param vel The type of velocity field (0, random, divergent, rotating)
  */
 struct cell *make_cell(size_t n, double *offset, double size, double h,
                        double density, long long *partId, double pert,