[Avida-SVN] r1849 - branches/dkdev/source/main

[dknoester at myxo.css.msu.edu]

Author: dknoester
Date: 2007-07-25 13:25:04 -0400 (Wed, 25 Jul 2007)
New Revision: 1849

Modified:
   branches/dkdev/source/main/cAvidaConfig.h
   branches/dkdev/source/main/cBirthChamber.cc
   branches/dkdev/source/main/cPopulation.cc
   branches/dkdev/source/main/cStats.cc
   branches/dkdev/source/main/cStats.h
Log:
New clustering merit.

Modified: branches/dkdev/source/main/cAvidaConfig.h
===================================================================
--- branches/dkdev/source/main/cAvidaConfig.h	2007-07-25 02:06:13 UTC (rev 1848)
+++ branches/dkdev/source/main/cAvidaConfig.h	2007-07-25 17:25:04 UTC (rev 1849)
@@ -168,6 +168,7 @@
   CONFIG_ADD_VAR(GERMLINE_REPLACES_SOURCE, int, 0, "Whether the source germline is updated on replication; 0=no.");
   CONFIG_ADD_VAR(GERMLINE_RANDOM_PLACEMENT, int, 0, "Whether the seed for a germline is placed randomly within the deme; 0=no.");
   CONFIG_ADD_VAR(MAX_DEME_AGE, int, 500, "The maximum age of a deme (in updates) to be used for age-based replication (default=500).");
+  CONFIG_ADD_VAR(TRACK_GENOTYPES, int, 0, "Whether genotypes are tracked graphically.");
   CONFIG_ADD_VAR(RANDOM_SEED, int, 0, "Random number seed (0 for based on time)");
   CONFIG_ADD_VAR(HARDWARE_TYPE, int, 0, "0 = Original CPUs\n1 = New SMT CPUs\n2 = Transitional SMT");
   

Modified: branches/dkdev/source/main/cBirthChamber.cc
===================================================================
--- branches/dkdev/source/main/cBirthChamber.cc	2007-07-25 02:06:13 UTC (rev 1848)
+++ branches/dkdev/source/main/cBirthChamber.cc	2007-07-25 17:25:04 UTC (rev 1849)
@@ -149,6 +149,10 @@
   parent.GetGenotype()->SetBreedStats(*child_genotype);
     
   child_genotype->IncDeferAdjust();
+  
+  if(m_world->GetConfig().TRACK_GENOTYPES.Get()) {
+    m_world->GetStats().TrackGenotypes(child_genotype, parent.GetGenotype());
+  }
 
   return true;
 }

Modified: branches/dkdev/source/main/cPopulation.cc
===================================================================
--- branches/dkdev/source/main/cPopulation.cc	2007-07-25 02:06:13 UTC (rev 1848)
+++ branches/dkdev/source/main/cPopulation.cc	2007-07-25 17:25:04 UTC (rev 1849)
@@ -1034,7 +1034,11 @@
         //double target_clustering_coeff=50.0;
         double target_clustering_coeff=25.0;
         
-        source_germline_merit = pow(target_clustering_coeff - abs(target_clustering_coeff-clustering_coeff) + 1, 2);
+        // What we need here is an exponentially-decreasing function of target to both
+        // low and high-range limits.
+        clustering_coeff = std::min(100.0, clustering_coeff);
+        clustering_coeff = std::max(0.0, clustering_coeff);
+        source_germline_merit = pow(100.0-abs(clustering_coeff-target_clustering_coeff)+1, 2);
         break;
       }
       case 11: {

Modified: branches/dkdev/source/main/cStats.cc
===================================================================
--- branches/dkdev/source/main/cStats.cc	2007-07-25 02:06:13 UTC (rev 1848)
+++ branches/dkdev/source/main/cStats.cc	2007-07-25 17:25:04 UTC (rev 1849)
@@ -18,6 +18,7 @@
 #include "cWorldDriver.h"
 #include "cGenome.h"
 #include "cPopulation.h"
+#include "cGenotype.h"
 
 #include <float.h>
 #include <math.h>
@@ -1048,3 +1049,14 @@
   df.Write(cell_ids_collected.Average(), "mean cell ids collected (per deme)");
   df.Endl();
 }
+
+
+void cStats::TrackGenotypes(cGenotype* child, cGenotype* parent) {
+  typedef GenotypeNetwork::edge_descriptor edge_descriptor;
+
+  std::pair<edge_descriptor, bool> i=boost::add_edge(child->GetID(), parent->GetID(), _genotype_net);
+  if(!i.second) {
+    // Edge already exists; increment its count.
+    ++boost::get(boost::edge_bundle, _genotype_net)[i.first];
+  }
+}

Modified: branches/dkdev/source/main/cStats.h
===================================================================
--- branches/dkdev/source/main/cStats.h	2007-07-25 02:06:13 UTC (rev 1848)
+++ branches/dkdev/source/main/cStats.h	2007-07-25 17:25:04 UTC (rev 1849)
@@ -14,6 +14,7 @@
 #include <assert.h>
 #include <fstream>
 #include <iostream>
+#include <boost/graph/adjacency_list.hpp>
 
 #include "defs.h"
 #include "cDoubleSum.h"
@@ -578,6 +579,29 @@
   
   // Satellite
   void PrintCollectionData(const cString& filename);
+  
+  // Attractor
+public:
+  struct edge_properties {
+    edge_properties() : _count(1) { }
+    edge_properties& operator++() { ++_count; return *this; }
+    unsigned int _count;
+  };
+  
+  //! An ease-of-use typedef to support the distributed construction of a network.
+  typedef boost::adjacency_list<
+    boost::setS, // out-edge list
+    boost::vecS, // vertex list
+    boost::directedS, // directed graph
+    boost::no_property, // no vertex properties
+    edge_properties // edge properties
+    > GenotypeNetwork;
+  
+  void TrackGenotypes(cGenotype* child, cGenotype* parent);
+  
+private:
+  GenotypeNetwork _genotype_net;
+
 };