improve documentation

include/aspect/adiabatic_conditions/interface.h

@@ -61,9 +61,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialization function. Because this function is called after
-         * initializing the SimulatorAccess, all of the necessary information
-         * is available to calculate the adiabatic profile.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual
         void

include/aspect/boundary_composition/box.h

@@ -77,7 +77,7 @@ namespace aspect
         parse_parameters (ParameterHandler &prm);
 
         /**
-         * It performs some basic
+         * This function performs some basic
          * sanity checks on the parameter values previously read from the
          * input file.
          */

include/aspect/boundary_composition/interface.h

@@ -57,7 +57,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialize function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual void initialize ();
 

include/aspect/boundary_temperature/interface.h

@@ -57,7 +57,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialize function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual void initialize ();
 

include/aspect/compositional_initial_conditions/interface.h

@@ -56,7 +56,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialization function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual
         void

include/aspect/geometry_model/interface.h

@@ -63,7 +63,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialize function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual void initialize ();
 

include/aspect/gravity_model/interface.h

@@ -54,7 +54,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialize function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual void initialize ();
 

include/aspect/heating_model/interface.h

@@ -55,7 +55,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialization function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual
         void

include/aspect/initial_conditions/interface.h

@@ -55,10 +55,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialization function. Take references to the geometry model, the
-         * object that describes the temperature boundary values, and the
-         * adiabatic conditions and store them so that derived classes can
-         * access them.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual
         void

include/aspect/material_model/interface.h

@@ -141,7 +141,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialization function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual
         void

include/aspect/mesh_refinement/interface.h

@@ -80,7 +80,9 @@ namespace aspect
         ~Interface ();
 
         /**
-         * Initialize function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual void initialize ();
 

include/aspect/termination_criteria/interface.h

@@ -73,7 +73,9 @@ namespace aspect
         ~Interface ();
 
         /**
-         * Initialize function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual void initialize ();
 

include/aspect/velocity_boundary_conditions/gplates.h

@@ -279,8 +279,7 @@ namespace aspect
 
         /**
          * Initialization function. This function is called once at the
-         * beginning of the program. Parses the user input and checks for
-         * valid geometry model.
+         * beginning of the program. Checks preconditions.
          */
         virtual
         void

include/aspect/velocity_boundary_conditions/interface.h

@@ -56,7 +56,9 @@ namespace aspect
         virtual ~Interface();
 
         /**
-         * Initialization function.
+         * Initialization function. This function is called once at the
+         * beginning of the program after parse_parameters is run and after the
+         * SimulatorAccess (if applicable) is initialized.
          */
         virtual
         void