[avida-cvs] avida CVS commits: /current/source/cpu hardware_cpu.cc /current/source/main config.cc config.hh phenotype.hh

[mercere99]

mercere99		Fri Jun  6 12:46:23 2003 EDT

  Modified files:              
    /avida/current/source/cpu	hardware_cpu.cc 
    /avida/current/source/main	config.cc config.hh phenotype.hh 
  Log:
  Fixed "sterilize" genesis options.  They no longer require test CPUs
  (they work right inside the population) and seem to finally actually
  be preventing any evolution from occuring.
  
  
Index: avida/current/source/cpu/hardware_cpu.cc
diff -u avida/current/source/cpu/hardware_cpu.cc:1.49 avida/current/source/cpu/hardware_cpu.cc:1.50
--- avida/current/source/cpu/hardware_cpu.cc:1.49	Tue May 27 18:08:18 2003
+++ avida/current/source/cpu/hardware_cpu.cc	Fri Jun  6 12:46:22 2003
@@ -1721,8 +1721,47 @@
   }
 
   // Save the information we collected here...
-  organism->GetPhenotype().SetLinesExecuted(executed_size);
-  organism->GetPhenotype().SetLinesCopied(copied_size);
+  cPhenotype & phenotype = organism->GetPhenotype();
+  phenotype.SetLinesExecuted(executed_size);
+  phenotype.SetLinesCopied(copied_size);
+
+  // Determine the fitness of this organism as compared to its parent...
+  if (cConfig::GetTestSterilize() == true &&
+      phenotype.IsInjected() == false) {
+    const int merit_base =
+      cPhenotype::CalcSizeMerit(genome_size, copied_size, executed_size);
+    const double cur_fitness =
+      merit_base * phenotype.GetCurBonus() / phenotype.GetTimeUsed();
+    const double fitness_ratio = cur_fitness / phenotype.GetLastFitness();
+
+
+    //  const double neut_min = parent_fitness * FITNESS_NEUTRAL_MIN;
+    //  const double neut_max = parent_fitness * FITNESS_NEUTRAL_MAX;
+  
+    bool sterilize = false;
+  
+    if (fitness_ratio < FITNESS_NEUTRAL_MIN) {
+      if (g_random.P(organism->GetSterilizeNeg())) sterilize = true;
+    } else if (fitness_ratio <= FITNESS_NEUTRAL_MAX) {
+      if (g_random.P(organism->GetSterilizeNeut())) sterilize = true;
+    } else {
+      if (g_random.P(organism->GetSterilizePos())) sterilize = true;
+    }
+  
+//     cout << "[ min(" << genome_size
+// 	 << "," << copied_size
+// 	 << "," << executed_size
+// 	 << ") * " << phenotype.GetCurBonus()
+// 	 << " / " << phenotype.GetTimeUsed()
+// 	 << "] / " << phenotype.GetLastFitness()
+// 	 << " == " << fitness_ratio;
+
+    if (sterilize == true) {
+      //Don't let this organism have this or any more children!
+      phenotype.IsFertile() = false;
+      return false;
+    }    
+  }
 
   return true; // (divide succeeds!)
 }
Index: avida/current/source/main/config.cc
diff -u avida/current/source/main/config.cc:1.57 avida/current/source/main/config.cc:1.58
--- avida/current/source/main/config.cc:1.57	Mon May 26 00:53:37 2003
+++ avida/current/source/main/config.cc	Fri Jun  6 12:46:23 2003
@@ -70,6 +70,7 @@
 double cConfig::min_exe_lines;
 int cConfig::require_allocate;
 bool cConfig::test_on_divide;
+bool cConfig::test_sterilize;
 double cConfig::revert_fatal;
 double cConfig::revert_neg;
 double cConfig::revert_neut;
@@ -330,9 +331,17 @@
 
   // Determine if any variables were set that require test CPUs to be run
   // at every divide.
-  test_on_divide = (revert_fatal > 0.0) || (revert_neg > 0.0) ||
-    (revert_neut > 0.0) || (revert_pos > 0.0) || (sterilize_fatal > 0.0) ||
-    (sterilize_neg > 0.0) || (sterilize_neut > 0.0) || (sterilize_pos > 0.0);
+  test_on_divide = false;
+  if ((revert_fatal > 0.0) || (revert_neg > 0.0) || (revert_neut > 0.0) ||
+      (revert_pos > 0.0) || (fail_implicit > 0)) {
+    test_on_divide = true;
+  }
+
+  test_sterilize = false;
+  if ((sterilize_fatal > 0.0) || (sterilize_neg > 0.0) ||
+      (sterilize_neut > 0.0) || (sterilize_pos > 0.0)) {
+    test_sterilize = true;
+  }
 
   // Determine if we are only logging threshold genotypes...
   log_threshold_only = false;
Index: avida/current/source/main/config.hh
diff -u avida/current/source/main/config.hh:1.50 avida/current/source/main/config.hh:1.51
--- avida/current/source/main/config.hh:1.50	Tue May 27 14:30:11 2003
+++ avida/current/source/main/config.hh	Fri Jun  6 12:46:23 2003
@@ -221,6 +221,7 @@
 
   // For specialized experiments -- mutation reversion.
   static bool test_on_divide;
+  static bool test_sterilize;
   static double revert_fatal;
   static double revert_neg;
   static double revert_neut;
@@ -336,6 +337,7 @@
   static int GetRequireAllocate() { return require_allocate; }
 
   static bool GetTestOnDivide() { return test_on_divide; }
+  static bool GetTestSterilize() { return test_sterilize; }
   static double GetRevertFatal() { return revert_fatal; }
   static double GetRevertNeg() { return revert_neg; }
   static double GetRevertNeut() { return revert_neut; }
Index: avida/current/source/main/phenotype.hh
diff -u avida/current/source/main/phenotype.hh:1.34 avida/current/source/main/phenotype.hh:1.35
--- avida/current/source/main/phenotype.hh:1.34	Sat May 17 12:33:53 2003
+++ avida/current/source/main/phenotype.hh	Fri Jun  6 12:46:23 2003
@@ -98,9 +98,6 @@
   bool last_child_fertile;  // Was the child being born to be fertile?
   int child_copied_size; // Instruction copied into child.
 
-private:
-  static int CalcSizeMerit(int full_size, int copied_size, int exe_size);
-
 public:
   cPhenotype(const cEnvironment & environment);
   ~cPhenotype();
@@ -129,6 +126,14 @@
   bool LoadState(std::ifstream & fp);
   void PrintStatus(std::ostream & fp);
 
+  // Some useful methods...
+  static int CalcSizeMerit(int full_size, int copied_size, int exe_size);
+  double CalcFitnessRatio() {
+    const int merit_base =
+      CalcSizeMerit(genome_length,copied_size,executed_size);
+    const double cur_fitness = merit_base * cur_bonus / time_used;
+    return cur_fitness / last_fitness;
+  }
 
   /////////////////////  Accessors -- Retrieving  ////////////////////
   const cEnvironment & GetEnvironment() const { return environment; };