[Avida-SVN] r2968 - in development/source: actions main

[mmcgill at myxo.css.msu.edu]

Author: mmcgill
Date: 2008-11-24 14:43:19 -0500 (Mon, 24 Nov 2008)
New Revision: 2968

Modified:
   development/source/actions/PopulationActions.cc
   development/source/main/cDeme.cc
   development/source/main/cDeme.h
Log:
added new cCompeteDemes subclass, and fixed a bug in cDeme::CalculateTotalEnergy() that incorrectly caused energy resource in a cell to be cleared

Modified: development/source/actions/PopulationActions.cc
===================================================================
--- development/source/actions/PopulationActions.cc	2008-11-24 19:35:55 UTC (rev 2967)
+++ development/source/actions/PopulationActions.cc	2008-11-24 19:43:19 UTC (rev 2968)
@@ -1562,7 +1562,50 @@
 	}
 };
 
+class cActionCompeteDemesByTaskCountAndEfficiency : public cAbstractCompeteDemes {
+private:
+  double _initial_deme_energy;
+	int _task_num;	// the task num to use when calculating fitness,
+						// defaults to 0 (the first task)
+public:
+	cActionCompeteDemesByTaskCountAndEfficiency(cWorld* world, const cString& args) 
+			: cAbstractCompeteDemes(world, args) {
+  	cString largs(args);
+    if (largs.GetSize() == 0) {
+      cerr << "CompeteDemesByTaskCountAndEfficiency must be given an initial deme energy amount" << endl;
+      exit(1);
+    }
 
+    _initial_deme_energy = largs.PopWord().AsDouble();
+    cout << "initial deme energy = " << _initial_deme_energy << endl;
+    assert(_initial_deme_energy > 0);
+
+		if (largs.GetSize() > 1) {
+			_task_num = largs.PopWord().AsInt();
+			assert(_task_num >= 0);
+			assert(_task_num < m_world->GetEnvironment().GetNumTasks());
+		} else {
+			_task_num = 0;
+		}
+	}
+	~cActionCompeteDemesByTaskCountAndEfficiency() {}
+
+	static const cString GetDescription() { 
+		return "Competes demes according to the number of times a given task has been completed within that deme and the efficiency with which it was done"; 
+	}
+
+	virtual double Fitness(const cDeme& deme) {
+    double energy_used = _initial_deme_energy - deme.CalculateTotalEnergy();
+		double fitness = 
+      pow(deme.GetCurTaskExeCount()[_task_num] * (_initial_deme_energy/energy_used),2);
+    if (fitness == 0.0) fitness = 0.1;
+    cout  << "Deme " << deme.GetID() << ": used " << energy_used << " energy" 
+          << " fitness=" << fitness << endl;
+    return fitness;
+	}
+};
+
+
 /*! Send an artificial flash to a single organism in each deme in the population
  at a specified period.
  
@@ -2445,6 +2488,7 @@
   action_lib->Register<cActionSwapCells>("SwapCells");
 
   action_lib->Register<cActionCompeteDemesByTaskCount>("CompeteDemesByTaskCount");
+  action_lib->Register<cActionCompeteDemesByTaskCountAndEfficiency>("CompeteDemesByTaskCountAndEfficiency");
 
   // @DMB - The following actions are DEPRECATED aliases - These will be removed in 2.7.
   action_lib->Register<cActionInject>("inject");

Modified: development/source/main/cDeme.cc
===================================================================
--- development/source/main/cDeme.cc	2008-11-24 19:35:55 UTC (rev 2967)
+++ development/source/main/cDeme.cc	2008-11-24 19:43:19 UTC (rev 2968)
@@ -446,6 +446,25 @@
   }
 }
 
+double cDeme::GetCellEnergy(int absolute_cell_id) const {
+  assert(cell_ids[0] <= absolute_cell_id);
+  assert(absolute_cell_id <= cell_ids[cell_ids.GetSize()-1]);
+
+  double total_energy = 0.0;
+  int relative_cell_id = GetRelativeCellID(absolute_cell_id);
+  tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
+  
+  // sum all energy resources
+  for(int i = 0; i < energy_res_ids.GetSize(); i++) {
+    if(cell_resources[energy_res_ids[i]] > 0.0) {
+      total_energy += cell_resources[energy_res_ids[i]];
+      cell_resources[energy_res_ids[i]] *= -1.0;
+    }
+  }
+
+  return total_energy;
+}
+
 double cDeme::GetAndClearCellEnergy(int absolute_cell_id) {
   assert(cell_ids[0] <= absolute_cell_id);
   assert(absolute_cell_id <= cell_ids[cell_ids.GetSize()-1]);
@@ -577,7 +596,7 @@
       cPhenotype& phenotype = organism->GetPhenotype();
       energy_sum += phenotype.GetStoredEnergy();
     } else {
-      double energy_in_cell = cell.UptakeCellEnergy(1.0);
+      double energy_in_cell = GetCellEnergy(cellid);
       energy_sum += energy_in_cell * m_world->GetConfig().FRAC_ENERGY_TRANSFER.Get();
     }
   }

Modified: development/source/main/cDeme.h
===================================================================
--- development/source/main/cDeme.h	2008-11-24 19:35:55 UTC (rev 2967)
+++ development/source/main/cDeme.h	2008-11-24 19:43:19 UTC (rev 2968)
@@ -234,6 +234,7 @@
   void SetDemeResourceCount(const cResourceCount in_res) { deme_resource_count = in_res; }
   void ResizeSpatialGrids(const int in_x, const int in_y) { deme_resource_count.ResizeSpatialGrids(in_x, in_y); }
   void ModifyDemeResCount(const tArray<double> & res_change, const int absolute_cell_id);
+  double GetCellEnergy(int absolute_cell_id) const;
   double GetAndClearCellEnergy(int absolute_cell_id);
   void GiveBackCellEnergy(int absolute_cell_id, double value);
   void SetupDemeRes(int id, cResource * res, int verbosity);