added more doxygen documentation to infrastructure files

src/cosmology_parameters.cc

@@ -17,6 +17,10 @@
 
 #include <cosmology_parameters.hh>
 
+/**
+ * @brief namespace encapsulating all things cosmology
+ * 
+ */
 namespace cosmology{
 
 //! we store here the preset cosmological paramters
@@ -100,7 +104,10 @@ parameters::defaultmmap_t parameters::default_pmaps_
     {"Tcmb",        2.7255}}}
 };
 
-
+/**
+ * @brief Output all sets of cosmological parameters that we store internally
+ * 
+ */
 void print_ParameterSets( void ){
   music::ilog << "Available cosmology parameter sets:" << std::endl;
   cosmology::parameters p;

src/ic_generator.cc

@@ -27,19 +27,39 @@
 
 #include <unistd.h> // for unlink
 
+
+/**
+ * @brief the possible species of fluids
+ *  
+ */
 std::map<cosmo_species,std::string> cosmo_species_name = 
 {
   {cosmo_species::dm,"Dark matter"},
   {cosmo_species::baryon,"Baryons"},
-  {cosmo_species::neutrino,"Neutrinos"}
+  {cosmo_species::neutrino,"Neutrinos"} // not implemented yet
 };
 
+/**
+ * @brief the namespace encapsulating the main IC generation routines
+ * 
+ */
 namespace ic_generator{
 
+//! global RNG object
 std::unique_ptr<RNG_plugin> the_random_number_generator;
+
+//! global output object
 std::unique_ptr<output_plugin> the_output_plugin;
+
+//! global cosmology object (calculates all things cosmological)
 std::unique_ptr<cosmology::calculator>  the_cosmo_calc;
 
+/**
+ * @brief Initialises all global objects
+ * 
+ * @param the_config reference to config_file object
+ * @return int 0 if successful
+ */
 int initialise( config_file& the_config )
 {
     the_random_number_generator = std::move(select_RNG_plugin(the_config));
@@ -49,12 +69,23 @@ int initialise( config_file& the_config )
     return 0;
 }
 
+/**
+ * @brief Reset all global objects
+ * 
+ */
 void reset () {
     the_random_number_generator.reset();
     the_output_plugin.reset();
     the_cosmo_calc.reset();
 }
 
+
+/**
+ * @brief Main driver routine for IC generation, everything interesting happens here
+ * 
+ * @param the_config reference to the config_file object
+ * @return int 0 if successful
+ */
 int run( config_file& the_config )
 {
     //--------------------------------------------------------------------------------------------------------

src/main.cc

@@ -60,6 +60,13 @@ void handle_eptr(std::exception_ptr eptr) // passing by value is ok
     }
 }
 
+/**
+ * @brief the main routine of MUSIC2-monofonIC
+ * 
+ * @param argc 
+ * @param argv 
+ * @return int 
+ */
 int main( int argc, char** argv )
 {
 

src/output_plugin.cc

@@ -17,13 +17,21 @@
 
 #include "output_plugin.hh"
 
-
+/**
+ * @brief Get the output plugin map object
+ * 
+ * @return std::map< std::string, output_plugin_creator *>& 
+ */
 std::map< std::string, output_plugin_creator *>& get_output_plugin_map()
 {
 	static std::map< std::string, output_plugin_creator* > output_plugin_map;
 	return output_plugin_map;
 }
 
+/**
+ * @brief Print out the names of all output plugins compiled in
+ * 
+ */
 void print_output_plugins()
 {
 	std::map< std::string, output_plugin_creator *>& m = get_output_plugin_map();
@@ -40,6 +48,15 @@ void print_output_plugins()
 	music::ilog << std::endl;
 }
 
+/**
+ * @brief Return a pointer to the desired output plugin as given in the config file
+ * 
+ * Implements the abstract factory pattern (https://en.wikipedia.org/wiki/Abstract_factory_pattern)
+ * 
+ * @param cf reference to config_file object
+ * @param pcc reference to cosmology::calculator object
+ * @return std::unique_ptr<output_plugin> 
+ */
 std::unique_ptr<output_plugin> select_output_plugin( config_file& cf, std::unique_ptr<cosmology::calculator>& pcc )
 {
 	std::string formatname = cf.get_value<std::string>( "output", "format" );

src/random_plugin.cc

@@ -18,6 +18,11 @@
 #include <general.hh>
 #include <random_plugin.hh>
 
+/**
+ * @brief Get the RNG plugin map object
+ * 
+ * @return std::map<std::string, RNG_plugin_creator *>& 
+ */
 std::map<std::string, RNG_plugin_creator *> &
 get_RNG_plugin_map()
 {
@@ -25,6 +30,10 @@ get_RNG_plugin_map()
     return RNG_plugin_map;
 }
 
+/**
+ * @brief Print out the names of all RNG plugins compiled in
+ * 
+ */
 void print_RNG_plugins()
 {
     std::map<std::string, RNG_plugin_creator *> &m = get_RNG_plugin_map();
@@ -41,6 +50,15 @@ void print_RNG_plugins()
     music::ilog << std::endl;
 }
 
+
+/**
+ * @brief Return a pointer to the desired random number generator plugin as given in the config file
+ * 
+ * Implements the abstract factory pattern (https://en.wikipedia.org/wiki/Abstract_factory_pattern)
+ * 
+ * @param cf reference to config_file object
+ * @return std::unique_ptr<RNG_plugin> unique pointer to plugin
+ */
 std::unique_ptr<RNG_plugin> select_RNG_plugin(config_file &cf)
 {
     std::string rngname = cf.get_value<std::string>("random", "generator");

src/transfer_function_plugin.cc

@@ -17,6 +17,11 @@
 
 #include <transfer_function_plugin.hh>
 
+/**
+ * @brief Get the TransferFunction plugin map object
+ * 
+ * @return std::map<std::string, TransferFunction_plugin_creator *>& 
+ */
 std::map<std::string, TransferFunction_plugin_creator *> &
 get_TransferFunction_plugin_map()
 {
@@ -24,6 +29,10 @@ get_TransferFunction_plugin_map()
     return TransferFunction_plugin_map;
 }
 
+/**
+ * @brief Print out the names of all transfer function plugins compiled in
+ * 
+ */
 void print_TransferFunction_plugins()
 {
     std::map<std::string, TransferFunction_plugin_creator *> &m = get_TransferFunction_plugin_map();
@@ -39,6 +48,15 @@ void print_TransferFunction_plugins()
     music::ilog << std::endl;
 }
 
+/**
+ * @brief Return a pointer to the desired transfer function plugin as given in the config file
+ * 
+ * Implements the abstract factory pattern (https://en.wikipedia.org/wiki/Abstract_factory_pattern)
+ * 
+ * @param cf  reference to config_file object
+ * @param cosmo_param reference to cosmology::parameters object holding cosmological parameter values
+ * @return std::unique_ptr<TransferFunction_plugin> 
+ */
 std::unique_ptr<TransferFunction_plugin> select_TransferFunction_plugin(config_file &cf, const cosmology::parameters& cosmo_param)
 {
     std::string tfname = cf.get_value<std::string>("cosmology", "transfer");