diff --git a/Pv_mod/Source.cpp b/Pv_mod/Source.cpp
index 3e5c6725943263e04cab595041ef9e4457e3521f..76cd0ff6ea1567a6c643bcd470f4326587fa80de 100644
--- a/Pv_mod/Source.cpp
+++ b/Pv_mod/Source.cpp
@@ -7,7 +7,7 @@
/// Institut Pasteur ///
/// michael.white@pasteur.fr ///
/// ///
-/// With contributions from Dr Thomas Obadia ///
+/// With contributions from Dr Thomas Obadia and Diggory Hardy ///
/// ///
/// Please feel free to use and modify if you wish. However, ///
/// please provide appropriate acknowledgement and get in touch ///
@@ -16,44 +16,49 @@
/// ///
/// There is a prize of a pint for reporting any serious bugs or ///
/// finding something new that results in >20% speed up. ///
+/// First prize to this goes to Diggory who achieved >80% speeed up, ///
+/// which will earn him 4 pints or his chosen equivalent. ///
/// ///
+/// Model code is split up into multiple files as follows: ///
/// ///
-/// The code below is structured as follows: ///
+/// 1.1. Source.cpp ///
+/// This file ///
/// ///
-/// 0. SETTING UP STRUCTURES AND CLASSES ///
-/// All parameter values are stored in a structure called params. ///
-/// A class is created which stores all the information of a ///
-/// single individual. ///
-/// A structure called population stores all individuals. ///
-/// The time-dependent output of the model is stored in a ///
-/// structure called simulation. ///
+/// 2.1. Params.h ///
+/// 2.2. Params.cpp ///
+/// The Params structure stores input parameters and has ///
+/// associated code for reading parameters from input files. ///
/// ///
-/// 1. MAIN - SIMULATION ///
-/// Here we read in parameters from files (model parameters, ///
-/// mosquito parameters, intervention parameters). ///
-/// A population of individuals is created at equilibrium and ///
-/// then simulated. ///
+/// 3.1. Intervention.h ///
+/// 3.2. Intervention.cpp ///
+/// The Intervention struct stores intervention parameters. ///
/// ///
-/// 2. FUNCTIONS ///
-/// Useful functions needed for model simulations. ///
-/// Mosquitoes are simulated using a deterministic ODE solver. ///
-/// The functions for simulating a population of individuals are ///
-/// provided here - note that the model itself appears in Section 4. ///
+/// 4.1. Individual.h ///
+/// 4.2 Individual.cpp ///
+/// A class is created which stores all the information of a ///
+/// single individual. ///
+/// Details of the stochastic individual-based model for each ///
+/// person. Transitions occur with a fixed time step according to ///
+/// compting hazards ///
/// ///
-/// 3. EQUILIBRIUM SETUP ///
-/// This set of functions calculates the equilibrium set up of the ///
-/// population. It is only called once while the population is ///
-/// being initialised. ///
+/// 5.1. Population.h ///
+/// 5.2. Population.cpp ///
+/// A structure called Population stores all individuals. ///
+/// This set of functions calculates the equilibrium set up of the ///
+/// population. It is only called once while the population is ///
+/// being initialised. ///
/// ///
-/// 4. INDIVIDUAL-BASED MODEL ///
-/// Details of the stochastic individual-based model for each ///
-/// person. Transitions occur with a fixed time step according to ///
-/// compting hazards ///
+/// 6.1. Mosquito.cpp ///
+/// Mosquitoes are simulated using a deterministic ODE solver. ///
/// ///
+/// 7.1. Simulation.h ///
+/// 7.2. Simulation.cpp ///
+/// Creation of class for storing simulation output, running ///
+/// and writing output ///
+/// ///
/////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////
-
#include "Simulation.h"
#include <iostream>
@@ -62,6 +67,11 @@
#include "randlib.h"
+////////////////////////////////////////////
+// //
+// 1.1.1. Initiate main object //
+// //
+////////////////////////////////////////////
int main(int argc, char** argv)
{
@@ -73,7 +83,7 @@ int main(int argc, char** argv)
////////////////////////////////////////////
// //
- // 1.1 Read in file names //
+ // 1.1.2. Read in file names //
// //
////////////////////////////////////////////
@@ -98,21 +108,20 @@ int main(int argc, char** argv)
////////////////////////////////////////////
// //
- // 1.2. Initialise objects //
+ // 1.1.2. Initialise objects //
// //
////////////////////////////////////////////
Population PNG_pop;
Params Pv_mod_par;
-
-
- ////////////////////////////////////////////
- // //
- // 1.3. Read in model parameters //
- // //
- ////////////////////////////////////////////
+ ///////////////////////////////////////////////
+ // //
+ // 1.1.3. Read in model parameters //
+ // and create an intervention object //
+ // //
+ ///////////////////////////////////////////////
SimTimes times = Pv_mod_par.read(parameter_File, mosquito_File);
PNG_pop.N_pop = Pv_mod_par.N_pop;
@@ -122,9 +131,9 @@ int main(int argc, char** argv)
///////////////////////////////////////////////////////////////////////////
// //
- // 1.8. Initialise Population of individuals //
- // Note that they begin with exponential age distribution //
- // and susceptible without immunity //
+ // 1.1.4. Initialise Population of individuals //
+ // Note that they begin with exponential age distribution //
+ // and susceptible without immunity //
// //
///////////////////////////////////////////////////////////////////////////
@@ -139,7 +148,7 @@ int main(int argc, char** argv)
/////////////////////////////////////////////////////////////////////////
// //
- // 1.9. Create simulation object //
+ // 1.1.5. Create Simulation object //
// //
/////////////////////////////////////////////////////////////////////////
@@ -148,7 +157,7 @@ int main(int argc, char** argv)
//////////////////////////////////////////////////////
// //
- // 1.10. Begin stochastic simulations //
+ // 1.1.6. Begin stochastic simulations //
// //
//////////////////////////////////////////////////////
@@ -162,7 +171,7 @@ int main(int argc, char** argv)
//////////////////////////////////////////////////////
// //
- // 1.11. Output to file //
+ // 1.1.7. Output to file //
// //
//////////////////////////////////////////////////////