Implement, test demes parasite memory

avida-core/source/actions/PopulationActions.cc

@@ -1187,6 +1187,47 @@ class cActionKillProb : public cAction
   }
 };
 
+class cActionClearParasites : public cAction
+{
+private:
+  int m_cell_start;
+  int m_cell_end;
+
+public:
+  cActionClearParasites(cWorld *world, const cString &args, Feedback &) : cAction(world, args), m_cell_start(0), m_cell_end(-1)
+  {
+    cString largs(args);
+    if (largs.GetSize())
+      m_cell_start = largs.PopWord().AsInt();
+    if (largs.GetSize())
+      m_cell_end = largs.PopWord().AsInt();
+
+    if (m_cell_end == -1)
+      m_cell_end = m_cell_start + 1;
+  }
+
+  static const cString GetDescription() { return "Arguments: [int cell_start=0] [int cell_end=-1]"; }
+
+  void Process(cAvidaContext &ctx)
+  {
+    if (m_cell_start < 0 || m_cell_end > m_world->GetPopulation().GetSize() || m_cell_start >= m_cell_end)
+    {
+      ctx.Driver().Feedback().Warning("ClearParasites has invalid range!");
+    }
+    else
+    {
+      cUserFeedback feedback;
+      const cInstSet &is = m_world->GetHardwareManager().GetDefaultInstSet();
+      for (int i = m_cell_start; i < m_cell_end; i++)
+      {
+        auto &cell = m_world->GetPopulation().GetCell(i);
+        if (cell.IsOccupied()) cell.GetOrganism()->ClearParasites();
+      }
+      m_world->GetPopulation().SetSyncEvents(true);
+    }
+  }
+};
+
 /*                                                                                                 
  Applies a fixed population bottleneck to the current population.                                  
  Parameters:                                                                                       
@@ -3970,6 +4011,38 @@ class cActionDecayPoints : public cAction
   }
 };
 
+
+class cActionUpdateDemeParasiteMemoryScores : public cAction
+{
+private:
+  double m_decay_rate;
+  bool m_verbose;
+
+public:
+  cActionUpdateDemeParasiteMemoryScores(cWorld* world, const cString& args, Feedback&) : cAction(world, args), m_decay_rate(0.99), m_verbose(false)
+  {
+    cString largs(args);
+    m_decay_rate = largs.PopWord().AsDouble();
+    m_verbose = largs.PopWord().AsInt();
+  }
+
+  static const cString GetDescription() { return "Arguments: <double decay_rate>"; }
+
+  void Process(cAvidaContext& ctx)
+  {
+    auto& pop = m_world->GetPopulation();
+    const int numDemes = pop.GetNumDemes();
+    for (int deme_id = 0; deme_id < numDemes; deme_id++)
+    {
+      auto &deme = pop.GetDeme(deme_id);
+      deme.UpdateParasiteMemoryScore(m_decay_rate);
+      if (m_verbose) std::cout << deme.GetParasiteMemoryScore() << " ";
+    }
+    if (m_verbose) std::cout << std::endl;
+  }
+};
+
+
 class cActionCompeteOrganisms : public cAction
 {
 private:
@@ -5826,6 +5899,7 @@ void RegisterPopulationActions(cActionLibrary* action_lib)
   action_lib->Register<cActionKillInstLimit>("KillInstLimit");
   action_lib->Register<cActionKillInstPair>("KillInstPair");
   action_lib->Register<cActionKillProb>("KillProb");
+  action_lib->Register<cActionClearParasites>("ClearParasites");
   action_lib->Register<cActionApplyBottleneck>("ApplyBottleneck");
   action_lib->Register<cActionKillDominantGenotype>("KillDominantGenotype");
   action_lib->Register<cActionProbKillSequence>("KillProbSequence");
@@ -5859,6 +5933,7 @@ void RegisterPopulationActions(cActionLibrary* action_lib)
   action_lib->Register<cActionMixPopulation>("MixPopulation");
 
   action_lib->Register<cActionDecayPoints>("DecayPoints");
+  action_lib->Register<cActionUpdateDemeParasiteMemoryScores>("UpdateDemeParasiteMemoryScores");
 
   action_lib->Register<cActionFlash>("Flash");
 

avida-core/source/main/cAvidaConfig.h

@@ -507,6 +507,7 @@ class cAvidaConfig {
   CONFIG_ADD_VAR(DEMES_PARASITE_MIGRATION_RATE, double, 0.0, "Probability of a parasite migrating to a different deme. Note: only works with DEMES_MIGRATION_METHOD 4.");
   CONFIG_ADD_VAR(DEMES_MIGRATION_METHOD, int, 0, "Which demes can an offspring land in when it migrates?\n0 = Any other deme\n1 = Eight neighboring demes\n2 = Two adjacent demes in list\n3 = Proportional based on the number of points\n4 = Use the weight matrix specified in MIGRATION_FILE");
   CONFIG_ADD_VAR(DEMES_PARASITE_MIGRATION_TARGET_SELECTION_METHOD, int, 0, "How should a target cell be chosen in the migrated-to deme?\n0 = Select a cell randomly, if it is not occupied infection fails\n1 = Select an occupied cell randomly");
+  CONFIG_ADD_VAR(DEMES_PARASITE_MIGRATION_MEMORY_SCORE_PROTECTIVE_THRESHOLD, double, 1.0, "Above what parasite memory score should hosts be protected from incoming parasite migration?");
   CONFIG_ADD_VAR(DEMES_NUM_X, int, 0, "Simulated number of demes in X dimension. Used only for migration. ");
   CONFIG_ADD_VAR(DEMES_PARTITION_INTERVAL, int, 0, "Restrict deme replication to within partitions of DEMES_PARTITION_INTERVAL consecutive deme ids. No restriction if 0. Partition size cannot be smaller than two. Does not affect migration.");
   CONFIG_ADD_VAR(DEMES_SEED_METHOD, int, 0, "Deme seeding method.\n0 = Maintain old consistency\n1 = New method using genotypes");

avida-core/source/main/cDeme.cc

@@ -56,6 +56,7 @@ cDeme::cDeme()
   , birth_count_perslot(0)
   , _age(0)
   , generation(0)
+  , parasite_memory_score(0.0)
   , total_org_energy(0.0)
   , time_used(0)
   , gestation_time(0)
@@ -117,6 +118,7 @@ cDeme& cDeme::operator=(const cDeme& in_deme)
   birth_count_perslot                 = in_deme.birth_count_perslot;
   _age                                = in_deme._age;
   generation                          = in_deme.generation;
+  parasite_memory_score               = in_deme.parasite_memory_score;
   total_org_energy                    = in_deme.total_org_energy;
   time_used                           = in_deme.time_used;
   gestation_time                      = in_deme.gestation_time;
@@ -202,6 +204,7 @@ void cDeme::Setup(int id, const Apto::Array<int> & in_cells, int in_width, cWorl
   last_org_count = 0;
   birth_count_perslot = 0;
   m_world = world;
+  parasite_memory_score = 0.0;
 
   replicateDeme = false;
 
@@ -513,6 +516,7 @@ void cDeme::Reset(cAvidaContext& ctx, bool resetResources, double deme_energy)
   time_used = 0;
   cur_birth_count = 0;
   cur_normalized_time_used = 0;
+  parasite_memory_score = 0.0;
   injected_count = 0;
   birth_count_perslot = 0;
   eventsTotal = 0;

avida-core/source/main/cDeme.h

@@ -70,6 +70,7 @@ class cDeme
   int birth_count_perslot;
   int _age; //!< Age of this deme, in updates.
   int generation; //!< Generation of this deme
+  double parasite_memory_score;
   double total_org_energy; //! amount of energy in organisms in this deme
   int time_used; //!< number of cpu cycles this deme has used
   int gestation_time; // Time used during last generation
@@ -188,7 +189,13 @@ class cDeme
   double GetParasiteLoad() const {
     return static_cast<double>(GetNumParasites()) / GetOrgCount();
   }
-
+
+  void UpdateParasiteMemoryScore(const double decay) {
+    parasite_memory_score += GetParasiteLoad();
+    parasite_memory_score *= decay;
+  }
+  double GetParasiteMemoryScore() const { return parasite_memory_score; }
+
   void IncOrgCount() { cur_org_count++; }
   void DecOrgCount() { cur_org_count--; }