[Avida-SVN] r2026 - in development/source: cpu main

barrick at myxo.css.msu.edu barrick at myxo.css.msu.edu
Wed Aug 29 10:13:13 PDT 2007


Author: barrick
Date: 2007-08-29 13:13:13 -0400 (Wed, 29 Aug 2007)
New Revision: 2026

Modified:
   development/source/cpu/cHardwareCPU.cc
   development/source/cpu/cHardwareCPU.h
   development/source/cpu/cTestCPU.cc
   development/source/main/cAvidaConfig.h
   development/source/main/cOrganism.cc
   development/source/main/cOrganism.h
Log:
* New logic promoter model
Seems to be working correctly, but not yet thoroughly tested. I've seen some crazy phenotypic plasticity where the orgs use a "random" input number to regulate their promoters in some preliminary runs.

*Test CPU, Die Already...
Also fixed a bug where calling organism->Die() would not halt Test CPU execution.



Modified: development/source/cpu/cHardwareCPU.cc
===================================================================
--- development/source/cpu/cHardwareCPU.cc	2007-08-29 13:09:27 UTC (rev 2025)
+++ development/source/cpu/cHardwareCPU.cc	2007-08-29 17:13:13 UTC (rev 2026)
@@ -352,9 +352,10 @@
     tInstLibEntry<tMethod>("time", &cHardwareCPU::Inst_GetUpdate),
     
     // Promoter Model
+    tInstLibEntry<tMethod>("promoter", &cHardwareCPU::Inst_Promoter),
     tInstLibEntry<tMethod>("terminate", &cHardwareCPU::Inst_Terminate),
-    tInstLibEntry<tMethod>("promoter", &cHardwareCPU::Inst_Promoter),
     tInstLibEntry<tMethod>("regulate", &cHardwareCPU::Inst_Regulate),
+    tInstLibEntry<tMethod>("numberate", &cHardwareCPU::Inst_Numberate),
     
     // Energy usage
     tInstLibEntry<tMethod>("double-energy-usage", &cHardwareCPU::Inst_DoubleEnergyUsage),
@@ -463,20 +464,22 @@
   }
 #endif   
 
+  // Promoter model
   if (m_world->GetConfig().PROMOTERS_ENABLED.Get())
   {
     // Ideally, this shouldn't be hard-coded
     cInstruction promoter_inst = m_world->GetHardwareManager().GetInstSet().GetInst(cStringUtil::Stringf("promoter"));
-    promoter_search_pos = 0;
-    promoter_inst_executed = 0;
-    promoter_pos.Resize(0);
-    promoter_active.Resize(0);
+
+    m_promoter_index = -1; // Meaning the last promoter was nothing
+    m_promoter_offset = 0;
+    m_promoter_regulation = 0;
+    m_promoters.Resize(0);
     for (int i=0; i<GetMemory().GetSize(); i++)
     {
       if ( (GetMemory())[i] == promoter_inst)
       {
-        promoter_pos.Push(i);
-        promoter_active.Push(true);
+        int code = Numberate(i-1, -1);
+        m_promoters.Push( cPromoter(i,code) );
       }
     }
   }
@@ -502,20 +505,20 @@
   cur_head = nHardware::HEAD_IP;
   read_label.Clear();
   next_label.Clear();
+  
+  // Promoter model
+  m_promoter_inst_executed = 0;
 }
 
-
-
 // This function processes the very next command in the genome, and is made
 // to be as optimized as possible.  This is the heart of avida.
 
 void cHardwareCPU::SingleProcess(cAvidaContext& ctx)
 {
   int last_IP_pos = IP().GetPosition();
-
+  
   // Mark this organism as running...
   organism->SetRunning(true);
-  
   cPhenotype & phenotype = organism->GetPhenotype();
   
   if (m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1) {
@@ -523,6 +526,7 @@
     if (phenotype.GetCPUCyclesUsed() == 0) Inst_Terminate(m_world->GetDefaultContext());
   }
   
+  // Count the cpu cycles used
   phenotype.IncCPUCyclesUsed();
   if (!m_world->GetConfig().NO_CPU_CYCLE_TIME.Get()) phenotype.IncTimeUsed();
 
@@ -554,6 +558,14 @@
     // Test if costs have been paid and it is okay to execute this now...
     bool exec = SingleProcess_PayCosts(ctx, cur_inst);
 
+    // If there are no active promoters and a certain mode is set, then don't execute any further instructions
+    if ((m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1) 
+      && (m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 2) 
+      && (m_promoter_index == -1) ) 
+    { 
+      exec = false;
+    }
+    
     // Now execute the instruction...
     if (exec == true) {
       // NOTE: This call based on the cur_inst must occur prior to instruction
@@ -568,7 +580,7 @@
       
       //Add to the promoter inst executed count before executing the inst (in case it is a terminator)
       if (m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1) {
-        promoter_inst_executed++;
+        m_threads[m_cur_thread].IncPromoterInstExecuted();
       }
 
       if (exec == true) SingleProcess_ExecuteInst(ctx, cur_inst);
@@ -579,29 +591,19 @@
       
       // Pay the time cost of the instruction now
       phenotype.IncTimeUsed(time_cost);
-      
-      // In the promoter model, there may be a chance of termination
-      // that causes execution to start at a new instruction (per instruction executed)
-      if ( m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1 ) {
-        const double processivity = m_world->GetConfig().PROMOTER_PROCESSIVITY_INST.Get();
-        if ( ctx.GetRandom().P(1-processivity) ) Inst_Terminate(ctx);
+            
+      // In the promoter model, we may force termination after a certain number of inst have been executed
+      if ( m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1 )
+      {
+        const double processivity = m_world->GetConfig().PROMOTER_PROCESSIVITY.Get();
+        if ( ctx.GetRandom().P(1-processivity) ) 
+          Inst_Terminate(ctx);
+        if ( m_world->GetConfig().PROMOTER_INST_MAX.Get() && (m_threads[m_cur_thread].GetPromoterInstExecuted() >= m_world->GetConfig().PROMOTER_INST_MAX.Get()) ) 
+          Inst_Terminate(ctx);
       }
-      
+
     } // if exec
-    
-    // In the promoter model, there may be a chance of termination
-    // that causes execution to start at a new instruction (per cpu cycle executed)
-    // @JEB - since processivities usually v. close to 1 it doesn't
-    // improve speed much to combine with "per instruction" block
-    if ( m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1 )
-    {
-      const double processivity = m_world->GetConfig().PROMOTER_PROCESSIVITY.Get();
-      if ( ctx.GetRandom().P(1-processivity) ) 
-        Inst_Terminate(ctx);
-      if ( m_world->GetConfig().PROMOTER_MAX_INST.Get() && (promoter_inst_executed >= m_world->GetConfig().PROMOTER_MAX_INST.Get()) ) 
-        Inst_Terminate(ctx);
-    }
-    
+        
   } // Previous was executed once for each thread...
   
   // Kill creatures who have reached their max num of instructions executed
@@ -720,13 +722,16 @@
       
   if (m_world->GetConfig().PROMOTERS_ENABLED.Get())
   {
-    fp << "Promoters:";
-    for (int i=0; i<promoter_pos.GetSize(); i++)
+    fp << "Promoters: index=" << m_promoter_index << " offset=" << m_promoter_offset;
+    fp << " exe_inst=" << m_threads[m_cur_thread].GetPromoterInstExecuted();
+    fp << " regulation=0x" << setbase(16) << setfill('0') << setw(8) << m_promoter_regulation << endl;
+    for (int i=0; i<m_promoters.GetSize(); i++)
     {
-      fp << " " << promoter_pos[i] << "-" << (promoter_active[i] ? "on" : "off"); 
+      fp << setfill(' ') << setbase(10) << i << "(" << m_promoters[i].m_pos << "):";
+      fp << "Ox" << setbase(16) << setfill('0') << setw(8) << (m_promoters[i].m_bit_code ^ m_promoter_regulation) << " "; 
     }
-    fp << endl;
-    fp << "Instructions executed past promoter: " << promoter_inst_executed << endl;
+    fp << endl;    
+    fp << setfill(' ') << setbase(10) << endl;
   }    
   fp.flush();
 }
@@ -4242,56 +4247,188 @@
   return true;
 }
 
-// Move execution to a new promoter
+// Move the instruction ptr to the next active promoter
 bool cHardwareCPU::Inst_Terminate(cAvidaContext& ctx)
 {
-  // Reset the CPU, clearing everything except R/W head positions.
-  const int write_head_pos = GetHead(nHardware::HEAD_WRITE).GetPosition();
-  const int read_head_pos = GetHead(nHardware::HEAD_READ).GetPosition();
-  m_threads[m_cur_thread].Reset(this, m_threads[m_cur_thread].GetID());
-  GetHead(nHardware::HEAD_WRITE).Set(write_head_pos);
-  GetHead(nHardware::HEAD_READ).Set(read_head_pos);
+  // Optionally,
+  // Reset the thread.
+  if (m_world->GetConfig().TERMINATION_RESETS.Get())
+  {
+    //const int write_head_pos = GetHead(nHardware::HEAD_WRITE).GetPosition();
+    //const int read_head_pos = GetHead(nHardware::HEAD_READ).GetPosition();
+    m_threads[m_cur_thread].Reset(this, m_threads[m_cur_thread].GetID());
+    //GetHead(nHardware::HEAD_WRITE).Set(write_head_pos);
+    //GetHead(nHardware::HEAD_READ).Set(read_head_pos);
+    
+    //Setting this makes it harder to do things. You have to be modular.
+    organism->GetOrgInterface().ResetInputs(ctx);   // Re-randomize the inputs this organism sees
+    organism->ClearInput();                         // Also clear their input buffers, or they can still claim
+                                                    // rewards for numbers no longer in their environment!
+  }
+  
+  // Reset our count
+  m_threads[m_cur_thread].ResetPromoterInstExecuted();
+  m_advance_ip = false;
+  const int reg_used = REG_BX; // register to put chosen promoter code in, for now always BX
 
-  // We want to execute the promoter that we land on.
-  promoter_inst_executed = 0;
-  m_advance_ip = false;
+  // Search for an active promoter  
+  int start_offset = m_promoter_offset;
+  int start_index  = m_promoter_index;
   
-  //Setting this makes it harder to do things. You have to be modular.
-  organism->GetOrgInterface().ResetInputs(ctx);   // Re-randomize the inputs this organism sees
-  organism->ClearInput();                         // Also clear their input buffers, or they can still claim
-                                                  // rewards for numbers no longer in their environment!
-  
-  // Find the next active promoter
-  int started_search_pos = promoter_search_pos;
-  
-  while (promoter_pos.GetSize() > 0) // conditional infinite loop, breaks out
+  bool no_promoter_found = true;
+  if ( m_promoters.GetSize() > 0 ) 
   {
-    promoter_search_pos++;
-    promoter_search_pos %= promoter_active.GetSize();
-    if (promoter_active[promoter_search_pos]) break;
-    if (started_search_pos == promoter_search_pos) break;
-  } 
+    while( true )
+    {
+      // If the next promoter is active, then break out
+      NextPromoter();
+      if (IsActivePromoter()) 
+      {
+        no_promoter_found = false;
+        break;
+      }
+      
+      // If we just checked the promoter that we were originally on, then there
+      // are no active promoters.
+      if ( (start_offset == m_promoter_offset) && (start_index == m_promoter_index) ) break;
+
+      // If we originally were not on a promoter, then stop once we check the
+      // first promoter and an offset of zero
+      if (start_index == -1)
+      {
+          start_index = 0;
+      }
+    } 
+  }
   
-  //Can't find a promoter -- start at the beginning of the genome (or die! or sleep!)
-  if ((promoter_pos.GetSize() == 0) || ((promoter_search_pos == started_search_pos) && (!promoter_active[promoter_search_pos])))
+  if (no_promoter_found)
   {
-    IP().Set(0);
+    if ((m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 0) || (m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 2))
+    {
+      // Set defaults for when no active promoter is found
+      m_promoter_index = -1;
+      IP().Set(0);
+      GetRegister(reg_used) = 0;
+      
+      // @JEB HACK! -- All kinds of bad stuff happens if execution length is zero. For now:
+      if (m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 2) GetMemory().SetFlagExecuted(0);
+    }
+    // Death to organisms that refuse to use promoters!
+    else if (m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 1)
+    {
+      organism->Die();
+    }
+    else
+    {
+      cout << "Unrecognized NO_ACTIVE_PROMOTER_EFFECT setting: " << m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() << endl;
+    }
   }
   else
   {
-    IP().Set(promoter_pos[promoter_search_pos]);
+    // We found an active match, offset to just after it.
+    // and put its bit code in BX for the organism to have
+      // cHeadCPU will do the mod genome size for us
+    IP().Set(m_promoters[m_promoter_index].m_pos + 1);
+    GetRegister(reg_used) = m_promoters[m_promoter_index].m_bit_code;
   }
-  
   return true;
 }
 
-// To be implemented...
+// Get a new regulation code (which is XOR'ed with promoter codes).
 bool cHardwareCPU::Inst_Regulate(cAvidaContext& ctx)
 {
+  const int reg_used = FindModifiedRegister(REG_BX);
+  m_promoter_regulation = GetRegister(reg_used);
   return true;
 }
 
+// Create a number from inst bit codes
+bool cHardwareCPU::Inst_Numberate(cAvidaContext& ctx)
+{
+  const int reg_used = FindModifiedRegister(REG_BX);
+  
+  // advance the IP now, so that it rests on the beginning of our number
+  IP().Advance();
+  m_advance_ip = false;
+  
+  int num = Numberate(IP().GetPosition(), +1);
+  GetRegister(reg_used) = num;
+  return true;
+}
 
+// Move to the next promoter.
+void cHardwareCPU::NextPromoter()
+{
+  // Move promoter index, rolling over if necessary
+  m_promoter_index++;
+  if (m_promoter_index == m_promoters.GetSize())
+  {
+    m_promoter_index = 0;
+    
+    // Move offset, rolling over when there are not enough bits before we would have to wrap around left
+    m_promoter_offset+=m_world->GetConfig().PROMOTER_EXE_LENGTH.Get();
+    if (m_promoter_offset + m_world->GetConfig().PROMOTER_EXE_LENGTH.Get() >= cHardwareCPU::PROMOTER_CODE_SIZE)
+    {
+      m_promoter_offset = 0;
+    }
+  }
+}
+
+
+// Check whether the current promoter is active.
+bool cHardwareCPU::IsActivePromoter()
+{
+  assert( m_promoters.GetSize() != 0 );
+  int count = 0;
+  unsigned int code = m_promoters[m_promoter_index].m_bit_code ^ m_promoter_regulation;
+  for(int i=0; i<m_world->GetConfig().PROMOTER_EXE_LENGTH.Get(); i++)
+  {
+    int offset = m_promoter_offset + i;
+    offset %= cHardwareCPU::PROMOTER_CODE_SIZE;
+    int state = code >> offset;
+    count += (state & 1);
+  }
+
+  return (count >= m_world->GetConfig().PROMOTER_EXE_THRESHOLD.Get());
+}
+
+// Construct a promoter bit code from instruction bit codes
+int cHardwareCPU::Numberate(int _pos, int _dir)
+{  
+  int code_size = 0;
+  unsigned int code = 0;
+  int j = _pos;
+  j %= GetMemory().GetSize();
+  while (code_size < cHardwareCPU::PROMOTER_CODE_SIZE)
+  {
+    unsigned int inst_code = (unsigned int) GetInstSet().GetInstructionCode( (GetMemory())[j] );
+    // shift bits in, one by one ... excuse the counter pun
+    for (int code_on = 0; (code_size < cHardwareCPU::PROMOTER_CODE_SIZE) && (code_on < m_world->GetConfig().INST_CODE_LENGTH.Get()); code_on++)
+    {
+      if (_dir < 0)
+      {
+        code >>= 1; // shift first so we don't go one too far at the end
+        code += (1 << (cHardwareCPU::PROMOTER_CODE_SIZE - 1)) * (inst_code & 1);
+        inst_code >>= 1; 
+      }
+      else
+      {
+        code <<= 1; // shift first so we don't go one too far at the end;        
+        code += (inst_code >> (m_world->GetConfig().INST_CODE_LENGTH.Get() - 1)) & 1;
+        inst_code <<= 1; 
+      }
+      code_size++;
+    }
+    
+     // move back one inst
+    j += GetMemory().GetSize() + _dir;
+    j %= GetMemory().GetSize();
+
+  }
+  return code;
+}
+
+
 /*! Send a message to the organism that is currently faced by this cell,
 where the label field of sent message is from register ?BX?, and the data field
 is from register ~?BX?.
@@ -4307,7 +4444,6 @@
   return organism->SendMessage(ctx, msg);
 }
 
-
 /*! This method /attempts/ to retrieve a message -- It may not be possible, as in
 the case of an empty receive buffer.
 
@@ -4328,7 +4464,6 @@
   return true;
 }
 
-
 //// Placebo insts ////
 bool cHardwareCPU::Inst_Skip(cAvidaContext& ctx)
 {

Modified: development/source/cpu/cHardwareCPU.h
===================================================================
--- development/source/cpu/cHardwareCPU.h	2007-08-29 13:09:27 UTC (rev 2025)
+++ development/source/cpu/cHardwareCPU.h	2007-08-29 17:13:13 UTC (rev 2026)
@@ -89,13 +89,14 @@
   static const int NUM_HEADS = nHardware::NUM_HEADS >= NUM_REGISTERS ? nHardware::NUM_HEADS : NUM_REGISTERS;
   enum tRegisters { REG_AX = 0, REG_BX, REG_CX, REG_DX, REG_EX, REG_FX };
   static const int NUM_NOPS = 3;
+  static const int PROMOTER_CODE_SIZE = sizeof(int) * 8; // Number of bits in promoter codes
   
   // --------  Data Structures  --------
   struct cLocalThread
   {
   private:
     int m_id;
-    
+    int m_promoter_inst_executed;
   public:
     int reg[NUM_REGISTERS];
     cHeadCPU heads[NUM_HEADS];
@@ -115,6 +116,9 @@
     void Reset(cHardwareBase* in_hardware, int in_id);
     int GetID() const { return m_id; }
     void SetID(int in_id) { m_id = in_id; }
+    int GetPromoterInstExecuted() { return m_promoter_inst_executed; }
+    void IncPromoterInstExecuted() { m_promoter_inst_executed++; }
+    void ResetPromoterInstExecuted() { m_promoter_inst_executed = 0; }
   };
 
     
@@ -137,13 +141,24 @@
   bool m_mal_active;         // Has an allocate occured since last divide?
   bool m_advance_ip;         // Should the IP advance after this instruction?
   bool m_executedmatchstrings;	// Have we already executed the match strings instruction?
+
+  // <-- Promoter model
+  int m_promoter_index;       //site to begin looking for the next active promoter from
+  int m_promoter_offset;      //bit offset when testing whether a promoter is on
+  int m_promoter_regulation;  //bit code that modifies current execution, via an XOR
   
-  // Promoter model
-  int promoter_search_pos;      //site to begin looking for the next active promoter from
-  int promoter_inst_executed;   //num inst executed since last termination
-  tArray<int> promoter_pos;     //positions with promoter instructions
-  tArray<bool> promoter_active; //whether each promoter is active (same size as promoter_pos)
-  
+  struct cPromoter 
+  {
+  public:
+    int m_pos;      //position within genome
+    int m_bit_code; //bit code of promoter
+  public:
+    cPromoter(int _pos = 0, int _bit_code = 0) { m_pos = _pos; m_bit_code = _bit_code; }
+    ~cPromoter() { ; }
+  };
+  tArray<cPromoter> m_promoters;
+  // Promoter Model -->
+
   bool SingleProcess_ExecuteInst(cAvidaContext& ctx, const cInstruction& cur_inst);
   
   // --------  Stack Manipulation...  --------
@@ -533,7 +548,13 @@
   bool Inst_Promoter(cAvidaContext& ctx);
   bool Inst_Terminate(cAvidaContext& ctx);
   bool Inst_Regulate(cAvidaContext& ctx);
+  bool Inst_Numberate(cAvidaContext& ctx);
 
+    // Helper functions //
+  bool IsActivePromoter();
+  void NextPromoter();
+  int Numberate(int _pos, int _dir);
+
   //// Messaging ////
   bool Inst_SendMessage(cAvidaContext& ctx);
   bool Inst_RetrieveMessage(cAvidaContext& ctx);

Modified: development/source/cpu/cTestCPU.cc
===================================================================
--- development/source/cpu/cTestCPU.cc	2007-08-29 13:09:27 UTC (rev 2025)
+++ development/source/cpu/cTestCPU.cc	2007-08-29 17:13:13 UTC (rev 2026)
@@ -221,7 +221,7 @@
   
   organism.GetHardware().SetTrace(tracer);
   while (time_used < time_allocated && organism.GetHardware().GetMemory().GetSize() &&
-         organism.GetPhenotype().GetNumDivides() == 0)
+         organism.GetPhenotype().GetNumDivides() == 0 && !organism.IsDead())
   {
     time_used++;
     

Modified: development/source/main/cAvidaConfig.h
===================================================================
--- development/source/main/cAvidaConfig.h	2007-08-29 13:09:27 UTC (rev 2025)
+++ development/source/main/cAvidaConfig.h	2007-08-29 17:13:13 UTC (rev 2026)
@@ -465,14 +465,15 @@
 
   CONFIG_ADD_GROUP(PROMOTER_GROUP, "Promoters");
   CONFIG_ADD_VAR(PROMOTERS_ENABLED, int, 0, "Use the promoter/terminator execution scheme.\nCertain instructions must also be included.");
-  CONFIG_ADD_VAR(PROMOTER_MAX_INST, int, 20, "Maximum number of instructions to execute before terminating.");
+  CONFIG_ADD_VAR(PROMOTER_INST_MAX, int, 0, "Maximum number of instructions to execute before terminating. 0 = off");
   CONFIG_ADD_VAR(PROMOTER_PROCESSIVITY, double, 1.0, "Chance of not terminating after each cpu cycle.");
   CONFIG_ADD_VAR(PROMOTER_PROCESSIVITY_INST, double, 1.0, "Chance of not terminating after each instruction.");
-  CONFIG_ADD_VAR(PROMOTER_BG_STRENGTH, double, 0, "Probability of positions that are not promoter\ninstructions initiating execution (promoters are 1).");
-  CONFIG_ADD_VAR(REGULATION_STRENGTH, double, 1, "Strength added or subtracted to a promoter by regulation.");
-  CONFIG_ADD_VAR(REGULATION_DECAY_FRAC, double, 0.1, "Fraction of regulation that decays away. \nMax regulation = 2^(REGULATION_STRENGTH/REGULATION_DECAY_FRAC)");
+  CONFIG_ADD_VAR(TERMINATION_RESETS, int, 0, "Does termination reset the thread's state?");
+  CONFIG_ADD_VAR(NO_ACTIVE_PROMOTER_EFFECT, int, 0, "What happens when there are no active promoters?\n0 = Start execution at the beginning of the genome.\n1 = Kill the organism.\n2 = Stop the organism from executing any further instructions.");
+  CONFIG_ADD_VAR(PROMOTER_EXE_LENGTH, int, 4, "Length of promoter windows used to determine execution.");
+  CONFIG_ADD_VAR(PROMOTER_EXE_THRESHOLD, int, 3, "Minimum number of bits that must be set in a promoter window to allow execution.");
   CONFIG_ADD_VAR(INST_CODE_LENGTH, int, 4, "Instruction binary code length (number of bits)");
-  CONFIG_ADD_VAR(INST_CODE_DEFAULT_TYPE, int, 0, "Default value of instruction binary code value.\n0 = All zeros\n1 = Based of the instruction number");
+  CONFIG_ADD_VAR(INST_CODE_DEFAULT_TYPE, int, 0, "Default value of instruction binary code value.\n0 = All zeros\n1 = Based off the instruction number");
 
   CONFIG_ADD_GROUP(COLORS_GROUP, "Output colors for when data files are printed in HTML mode.\nThere are two sets of these; the first are for lineages,\nand the second are for mutation tests.");
   CONFIG_ADD_VAR(COLOR_DIFF, cString, "CCCCFF", "Color to flag stat that has changed since parent.");

Modified: development/source/main/cOrganism.cc
===================================================================
--- development/source/main/cOrganism.cc	2007-08-29 13:09:27 UTC (rev 2025)
+++ development/source/main/cOrganism.cc	2007-08-29 17:13:13 UTC (rev 2026)
@@ -69,6 +69,7 @@
   , m_max_executed(-1)
   , m_is_running(false)
   , m_is_sleeping(false)
+  , m_is_dead(false)
   , m_net(NULL)
   , m_msg(0)
 {

Modified: development/source/main/cOrganism.h
===================================================================
--- development/source/main/cOrganism.h	2007-08-29 13:09:27 UTC (rev 2025)
+++ development/source/main/cOrganism.h	2007-08-29 17:13:13 UTC (rev 2026)
@@ -121,6 +121,7 @@
   int m_max_executed;      // Max number of instruction executed before death.  
   bool m_is_running;       // Does this organism have the CPU?
   bool m_is_sleeping;      // Is this organisms sleeping?
+  bool m_is_dead;          // Is this organism dead?
   
   class cNetSupport
   {
@@ -181,6 +182,7 @@
   void SetSleeping(bool in_sleeping) { m_is_sleeping = in_sleeping; }
   bool IsSleeping() { return m_is_sleeping; }
   
+  bool IsDead() { return m_is_dead; }
   
   // --------  cOrgInterface Methods  --------
   cHardwareBase& GetHardware() { return *m_hardware; }
@@ -193,7 +195,7 @@
   int GetNextInput(int& in_input_pointer) { return m_interface->GetInputAt(in_input_pointer); } //@JEB alternate for GX
   tBuffer<int>& GetInputBuf() { return m_input_buf; }
   tBuffer<int>& GetOutputBuf() { return m_output_buf; }
-  void Die() { m_interface->Die(); }
+  void Die() { m_interface->Die(); m_is_dead = true; }
   void Kaboom(int dist) { m_interface->Kaboom(dist);}
   void SpawnDeme() { m_interface->SpawnDeme(); }
   int GetCellID() { return m_interface->GetCellID(); }




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