[Avida-SVN] r3547 - in development/source: actions main

[connel42 at myxo.css.msu.edu]

Author: connel42
Date: 2009-12-07 10:18:55 -0500 (Mon, 07 Dec 2009)
New Revision: 3547

Modified:
   development/source/actions/PopulationActions.cc
   development/source/main/cStats.cc
   development/source/main/cStats.h
Log:
Added additional output to orgs_killed data file and expanded kill event to include a kill density parameter

Modified: development/source/actions/PopulationActions.cc
===================================================================
--- development/source/actions/PopulationActions.cc	2009-12-05 17:58:06 UTC (rev 3546)
+++ development/source/actions/PopulationActions.cc	2009-12-07 15:18:55 UTC (rev 3547)
@@ -4013,6 +4013,7 @@
  - The radius of the kill zone (default: 0)
  - The name of the resource
  - The amount of resource below which to execute the kill (default: 0)
+ - The fraction of orgs in the region to kill (1=all, 0.5 leave half) (default: 1) -- useful for controlling density with biofilms
  */
 
 class cActionKillWithinRadiusBelowResourceThreshold : public cAction
@@ -4022,17 +4023,19 @@
     int m_radius;
     cString m_resname;
     double m_threshold;
+    double m_kill_density;
   public:
-    cActionKillWithinRadiusBelowResourceThreshold(cWorld* world, const cString& args) : cAction(world, args), m_numradii(0), m_radius(0), m_threshold(0.0)
+    cActionKillWithinRadiusBelowResourceThreshold(cWorld* world, const cString& args) : cAction(world, args), m_numradii(0), m_radius(0), m_threshold(0.0), m_kill_density(1.0)
     {
       cString largs(args);
       if (largs.GetSize()) m_numradii = largs.PopWord().AsInt();
       if (largs.GetSize()) m_radius = largs.PopWord().AsInt();
       if (largs.GetSize()) m_resname = largs.PopWord();
       if (largs.GetSize()) m_threshold = largs.PopWord().AsDouble();
+      if (largs.GetSize()) m_kill_density = largs.PopWord().AsDouble();
      }
     
-    static const cString GetDescription() { return "Arguments: [int numradii=0, int radius=0, string resource name, double threshold=0]"; }
+    static const cString GetDescription() { return "Arguments: [int numradii=0, int radius=0, string resource name, double threshold=0, double killdensity=1]"; }
     
     void Process(cAvidaContext& ctx)
     {
@@ -4045,6 +4048,8 @@
       assert(m_radius <= world_x);
       assert(m_radius <= world_y);
       assert(m_threshold >= 0.0);
+      assert(m_kill_density >= 0.0);
+      assert(m_kill_density <= 1.0);
       assert(geometry == nGeometry::GRID || geometry == nGeometry::TORUS);
       
       cPopulation& pop = m_world->GetPopulation();
@@ -4081,7 +4086,9 @@
               
               int current_cell = (world_x * row_adj) + col_adj;
 							cPopulationCell& cell = pop.GetCell(current_cell);
-							if (cell.IsOccupied()) {
+              m_world->GetStats().IncNumCellsScannedAtKill();
+
+							if( (cell.IsOccupied()) && (ctx.GetRandom().P(m_kill_density)) ) {
 								pop.KillOrganism(cell);
 								m_world->GetStats().IncNumOrgsKilled();
 							} else {

Modified: development/source/main/cStats.cc
===================================================================
--- development/source/main/cStats.cc	2009-12-05 17:58:06 UTC (rev 3546)
+++ development/source/main/cStats.cc	2009-12-07 15:18:55 UTC (rev 3547)
@@ -136,6 +136,7 @@
   , m_spec_waste(0)
   , num_orgs_killed(0)
 	, num_unoccupied_cell_kill_attempts(0)
+  , num_cells_scanned_at_kill(0)
   , num_migrations(0)
   , m_deme_num_repls(0)
 	, m_deme_num_repls_treatable(0)
@@ -581,6 +582,7 @@
   
   num_orgs_killed = 0;
 	num_unoccupied_cell_kill_attempts = 0;
+  num_cells_scanned_at_kill = 0;
   num_migrations = 0;
 }
 
@@ -2483,6 +2485,7 @@
   df.Write(m_update,   "Update");
   df.Write(num_orgs_killed, "Num Orgs Killed");
   df.Write(num_unoccupied_cell_kill_attempts, "Num Unoccupied Cell Kill Attempts");
+  df.Write(num_cells_scanned_at_kill, "Num Cells Scanned By Kill Event");
   df.Endl();
 } //End PrintNumOrgsKilledData()
 

Modified: development/source/main/cStats.h
===================================================================
--- development/source/main/cStats.h	2009-12-05 17:58:06 UTC (rev 3546)
+++ development/source/main/cStats.h	2009-12-07 15:18:55 UTC (rev 3547)
@@ -343,6 +343,7 @@
   // Number of organisms killed by kill actions
   int num_orgs_killed;
 	int num_unoccupied_cell_kill_attempts;
+  int num_cells_scanned_at_kill;
   
   // Number of migrations that have been made
   int num_migrations;
@@ -577,6 +578,7 @@
   
   void IncNumOrgsKilled() { num_orgs_killed++; }
 	void IncNumUnoccupiedCellAttemptedToKill() { num_unoccupied_cell_kill_attempts++; }
+  void IncNumCellsScannedAtKill() { num_cells_scanned_at_kill++; }
   void IncNumMigrations() { num_migrations++; }
 
   void AddCurTask(int task_num) { task_cur_count[task_num]++; }
@@ -753,6 +755,7 @@
   int GetSpeculativeWaste() const { return m_spec_waste; }
   
   int GetNumOrgsKilled() const { return num_orgs_killed; }
+  int GetNumCellsScannedAtKill() const { return num_cells_scanned_at_kill; }
   int GetNumMigrations() const { return num_migrations; }
 
   // this value gets recorded when a creature with the particular