Update docs and manual

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME = "Understanding Breakthrough Curves"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER = "v0.2"
+PROJECT_NUMBER = "v0.3"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

README.md

@@ -1,9 +1,9 @@
 # Overview
 
-The purpose of this code and data is to enable reproduction
+The purpose of this code and data is to enable reproduction (see [Reproducing the manuscript](#reproducing-the-manuscript))
 and facilitate extension of the computational
-results associated with Ref. [1],
-as found in [Citing This Work](#citing-this-work).
+results associated with Ref. [1]
+(see [Citing This Work](#citing-this-work)).
 
 
 # Installation of dependencies

src/isotherms.py

@@ -26,7 +26,7 @@ def F(self, c):
  """!
  @return \f$L(c; k) = (1 + \kappa)c/(1 + \kappa c)\f$
  """
- return (1. + self.kappa)*c/(1 + self.kappa*c)
+ return (1. + self.k)*c/(1 + self.k*c)
 
  def F_prime(self, c):
  """!
@@ -52,12 +52,17 @@ def get_c_rarefaction(self, x, t):
  return 0.
 
  return 1./self.k*(sqrt((1 + self.k)* x / (t - x)) - 1.)
+
+ def shock_lambda(self):
+ """! speed of shock wave
+ @return float representing speed of shock wave"""
+ return 0.5
 
  def get_c_shock(self, x, t):
  """!
  @return concentration \f$c(x,t)\f$ associated with rarefaction wave
  """
- lamda = 0.5
+ lamda = self.shock_lambda()
  if x <= lamda*t:
  return 1.