[Avida-SVN] r2648 - in development/source: actions cpu main
beckma24 at myxo.css.msu.edu
beckma24 at myxo.css.msu.edu
Mon Jun 16 08:40:37 PDT 2008
Author: beckma24
Date: 2008-06-16 11:40:36 -0400 (Mon, 16 Jun 2008)
New Revision: 2648
Modified:
development/source/actions/EnvironmentActions.cc
development/source/actions/PopulationActions.cc
development/source/actions/PrintActions.cc
development/source/cpu/cHardwareBase.cc
development/source/cpu/cHardwareBase.h
development/source/cpu/cHardwareCPU.cc
development/source/cpu/cHardwareCPU.h
development/source/cpu/cHardwareGX.h
development/source/cpu/cTestCPUInterface.cc
development/source/cpu/cTestCPUInterface.h
development/source/main/cAvidaConfig.h
development/source/main/cDeme.cc
development/source/main/cDeme.h
development/source/main/cDemeCellEvent.cc
development/source/main/cDemeCellEvent.h
development/source/main/cOrgInterface.h
development/source/main/cOrgMovementPredicate.h
development/source/main/cOrganism.cc
development/source/main/cOrganism.h
development/source/main/cPhenotype.cc
development/source/main/cPhenotype.h
development/source/main/cPopulation.cc
development/source/main/cPopulation.h
development/source/main/cPopulationInterface.cc
development/source/main/cPopulationInterface.h
development/source/main/cResourceCount.cc
development/source/main/cResourceCount.h
development/source/main/cStats.cc
development/source/main/cStats.h
development/source/main/cTaskLib.cc
development/source/main/cTaskLib.h
Log:
Added alarm messages, deme testament, cell attacks, attack removal, etc. This commit breaks one of my consistency test which I will be replacing shortly
Modified: development/source/actions/EnvironmentActions.cc
===================================================================
--- development/source/actions/EnvironmentActions.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/actions/EnvironmentActions.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -734,11 +734,20 @@
int m_delay; // deme age when event occurs
int m_duration; // length of event; subverted when deme is reset
bool m_static_pos;
- int m_time_to_live; // update when event no longer exists
- int m_id;
+ int m_total_events; // total number of unique event to create; they may overlab
+ bool m_static_position;
public:
- cActionDelayedDemeEvent(cWorld* world, const cString& args) : cAction(world, args), m_x1(-1), m_y1(-1), m_x2(-1), m_y2(-1), m_delay(-1), m_duration(-1), m_static_pos(1), m_time_to_live(-1), m_id(-1)
+ cActionDelayedDemeEvent(cWorld* world, const cString& args) :
+ cAction(world, args)
+ , m_x1(-1)
+ , m_y1(-1)
+ , m_x2(-1)
+ , m_y2(-1)
+ , m_delay(-1)
+ , m_duration(-1)
+ , m_total_events(1)
+ , m_static_position(true)
{
cString largs(args);
if (largs.GetSize()) m_x1 = largs.PopWord().AsInt();
@@ -747,26 +756,79 @@
if (largs.GetSize()) m_y2 = largs.PopWord().AsInt();
if (largs.GetSize()) m_delay = largs.PopWord().AsInt();
if (largs.GetSize()) m_duration = largs.PopWord().AsInt();
- if (largs.GetSize()) m_static_pos = largs.PopWord().AsInt();
- if (largs.GetSize()) m_time_to_live = largs.PopWord().AsInt();
- if (largs.GetSize()) m_id = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_static_position = static_cast<bool>(largs.PopWord().AsInt());
+ if (largs.GetSize()) m_total_events = largs.PopWord().AsInt();
}
- static const cString GetDescription() { return "Arguments: <int x1> <int y1> <int x2> <int y2> <int delay> <int duraion> <int static_position> <int time_to_live> <event ID>"; }
+ static const cString GetDescription() { return "Arguments: <int x1> <int y1> <int x2> <int y2> <int delay> <int duraion> <bool static_position> <int total_events>"; }
void Process(cAvidaContext& ctx)
{
cPopulation& pop = m_world->GetPopulation();
int numDemes = pop.GetNumDemes();
for(int i = 0; i < numDemes; i++) {
- pop.GetDeme(i).SetCellEvent(m_x1, m_y1, m_x2, m_y2, m_delay, m_duration, m_static_pos, m_time_to_live, m_id);
+ pop.GetDeme(i).SetCellEvent(m_x1, m_y1, m_x2, m_y2, m_delay, m_duration, m_static_position, m_total_events);
}
}
};
+class cActionDelayedDemeEventsPerSlots : public cAction
+{
+private:
+ int m_x1, m_y1, m_x2, m_y2; // bounding box of event in deme
+ int m_delay; // deme age when event occurs
+ int m_duration; // length of event; subverted when deme is reset
+ int m_total_slots; // total number of slots
+ int m_total_events_per_slot_max; // maximum number of unique event to create per slot; they may overlab
+ int m_total_events_per_slot_min; // minimum number of unique event to create per slot; they may overlab
+ int m_tolal_event_flow_levels; // total number of evenly spaced event flow levels; not all flow levels will be represented in a single deme
+ bool m_static_position;
+
+public:
+ cActionDelayedDemeEventsPerSlots(cWorld* world, const cString& args) :
+ cAction(world, args)
+ , m_x1(-1)
+ , m_y1(-1)
+ , m_x2(-1)
+ , m_y2(-1)
+ , m_delay(-1)
+ , m_duration(-1)
+ , m_total_slots(1)
+ , m_total_events_per_slot_max(1)
+ , m_total_events_per_slot_min(1)
+ , m_tolal_event_flow_levels(1)
+ , m_static_position(true)
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_x1 = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_y1 = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_x2 = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_y2 = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_delay = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_duration = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_static_position = static_cast<bool>(largs.PopWord().AsInt());
+ if (largs.GetSize()) m_total_slots = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_total_events_per_slot_max = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_total_events_per_slot_min = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_tolal_event_flow_levels = largs.PopWord().AsInt();
+ }
+
+ static const cString GetDescription() { return "Arguments: <int x1> <int y1> <int x2> <int y2> <int delay> <int duraion> <bool static_position> <int total_slots_per_deme> <int total_events_per_slot_max> <int total_events_per_slot_min> <int tolal_event_flow_levels>"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ cPopulation& pop = m_world->GetPopulation();
+ int numDemes = pop.GetNumDemes();
+ for(int i = 0; i < numDemes; i++) {
+ pop.GetDeme(i).SetCellEventSlots(m_x1, m_y1, m_x2, m_y2, m_delay, m_duration, m_static_position, m_total_slots, m_total_events_per_slot_max, m_total_events_per_slot_min, m_tolal_event_flow_levels);
+ }
+ }
+};
+
void RegisterEnvironmentActions(cActionLibrary* action_lib)
{
action_lib->Register<cActionDelayedDemeEvent>("DelayedDemeEvent");
+ action_lib->Register<cActionDelayedDemeEventsPerSlots>("DelayedDemeEventsPerSlots");
action_lib->Register<cActionInjectResource>("InjectResource");
action_lib->Register<cActionInjectScaledResource>("InjectScaledResource");
action_lib->Register<cActionOutflowScaledResource>("OutflowScaledResource");
Modified: development/source/actions/PopulationActions.cc
===================================================================
--- development/source/actions/PopulationActions.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/actions/PopulationActions.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -1267,7 +1267,11 @@
'corners' - ...demes with upper left and lower right corners filled.
'deme-age' - ...demes that are a certain age
'birth-count' ...demes that have had a certain number of births.
+<<<<<<< .working
'sat-mov-pred' - ...demes whose movement predicate was previously satisfied
+=======
+ 'events-killed' ...demes that have killed a certian number of events
+>>>>>>> .merge-right.r2644
*/
class cActionReplicateDemes : public cAction
@@ -1287,6 +1291,7 @@
else if (in_trigger == "deme-age") m_rep_trigger = 3;
else if (in_trigger == "birth-count") m_rep_trigger = 4;
else if (in_trigger == "sat-mov-pred") m_rep_trigger = 5;
+ else if (in_trigger == "events-killed") m_rep_trigger = 6;
else {
cString err("Unknown replication trigger '");
err += in_trigger;
Modified: development/source/actions/PrintActions.cc
===================================================================
--- development/source/actions/PrintActions.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/actions/PrintActions.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -110,6 +110,7 @@
STATS_OUT_FILE(PrintPerDemeGenPerFounderData, deme_gen_between_founders.dat );
// @WRE: Added output event for collected visit counts
STATS_OUT_FILE(PrintCellVisitsData, visits.dat );
+STATS_OUT_FILE(PrintFlowRateTuples, flow_rate_tuples.dat);
#define POP_OUT_FILE(METHOD, DEFAULT) /* 1 */ \
@@ -128,6 +129,7 @@
POP_OUT_FILE(PrintPhenotypeData, phenotype_count.dat );
POP_OUT_FILE(PrintPhenotypeStatus, phenotype_status.dat);
+POP_OUT_FILE(PrintDemeTestamentStats, deme_testament.dat );
class cActionPrintData : public cAction
@@ -2649,6 +2651,7 @@
// Stats Out Files
action_lib->Register<cActionPrintAverageData>("PrintAverageData");
action_lib->Register<cActionPrintDemeAverageData>("PrintDemeAverageData");
+ action_lib->Register<cActionPrintFlowRateTuples>("PrintFlowRateTuples");
action_lib->Register<cActionPrintErrorData>("PrintErrorData");
action_lib->Register<cActionPrintVarianceData>("PrintVarianceData");
action_lib->Register<cActionPrintDominantData>("PrintDominantData");
@@ -2681,6 +2684,8 @@
action_lib->Register<cActionPrintPhenotypeData>("PrintPhenotypeData");
action_lib->Register<cActionPrintPhenotypeStatus>("PrintPhenotypeStatus");
+ action_lib->Register<cActionPrintDemeTestamentStats>("PrintDemeTestamentStats");
+
// deme output files
action_lib->Register<cActionPrintDemeAllStats>("PrintDemeAllStats");
action_lib->Register<cActionPrintDemeAllStats>("PrintDemeStats"); //duplicate of previous
@@ -2707,9 +2712,8 @@
//Coalescence Clade Actions
action_lib->Register<cActionPrintCCladeCounts>("PrintCCladeCounts");
action_lib->Register<cActionPrintCCladeFitnessHistogram>("PrintCCladeFitnessHistogram");
- action_lib->Register<cActionPrintCCladeRelativeFitnessHistogram>("PrintCCladeRelativeFitnessHistogram");
+ action_lib->Register<cActionPrintCCladeRelativeFitnessHistogram>("PrintCCladeRelativeFitnessHistogram");
-
// Processed Data
action_lib->Register<cActionPrintData>("PrintData");
action_lib->Register<cActionPrintInstructionAbundanceHistogram>("PrintInstructionAbundanceHistogram");
Modified: development/source/cpu/cHardwareBase.cc
===================================================================
--- development/source/cpu/cHardwareBase.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/cpu/cHardwareBase.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -806,18 +806,30 @@
}
bool cHardwareBase::Inst_DoubleEnergyUsage(cAvidaContext& ctx) {
- double energy_req = inst_energy_cost[IP().GetNextInst().GetOp()]
+/* double energy_req = inst_energy_cost[IP().GetNextInst().GetOp()]
* cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio() * 2.0, m_world)
/ 100.0; //compensate by factor of 100
-
- return organism->GetPhenotype().DoubleEnergyUsage(energy_req);
+*/
+ organism->GetPhenotype().DoubleEnergyUsage();
+ double newOrgMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio(), m_world);
+ organism->UpdateMerit(newOrgMerit);
+ return true;
}
bool cHardwareBase::Inst_HalfEnergyUsage(cAvidaContext& ctx) {
organism->GetPhenotype().HalfEnergyUsage();
+ double newOrgMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio(), m_world);
+ organism->UpdateMerit(newOrgMerit);
return true;
}
+bool cHardwareBase::Inst_DefaultEnergyUsage(cAvidaContext& ctx) {
+ organism->GetPhenotype().DefaultEnergyUsage();
+ double newOrgMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio(), m_world);
+ organism->UpdateMerit(newOrgMerit);
+ return true;
+}
+
// This method will test to see if all costs have been paid associated
// with executing an instruction and only return true when that instruction
// should proceed.
@@ -845,8 +857,8 @@
if(m_world->GetConfig().LOG_SLEEP_TIMES.Get() == 1) {
pop.AddBeginSleep(cellID,m_world->GetStats().GetUpdate());
}
- pop.GetCell(cellID).GetOrganism()->SetSleeping(true);
- m_world->GetStats().incNumAsleep(pop.GetCell(cellID).GetDemeID());
+ organism->SetSleeping(true);
+ organism->GetOrgInterface().GetDeme()->IncSleepingCount();
}
} else {
organism->GetPhenotype().SetToDie();
Modified: development/source/cpu/cHardwareBase.h
===================================================================
--- development/source/cpu/cHardwareBase.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/cpu/cHardwareBase.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -189,6 +189,9 @@
// -------- State Transfer --------
virtual void InheritState(cHardwareBase& in_hardware){ ; }
+ //alarm
+ virtual bool Jump_To_Alarm_Label(int jump_label) { return false; }
+
protected:
// -------- No-Operation Instruction --------
bool Inst_Nop(cAvidaContext& ctx); // A no-operation instruction that does nothing!
@@ -200,6 +203,7 @@
// -------- Execution Speed Instruction --------
bool Inst_DoubleEnergyUsage(cAvidaContext& ctx);
bool Inst_HalfEnergyUsage(cAvidaContext& ctx);
+ bool Inst_DefaultEnergyUsage(cAvidaContext& ctx);
};
Modified: development/source/cpu/cHardwareCPU.cc
===================================================================
--- development/source/cpu/cHardwareCPU.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/cpu/cHardwareCPU.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -211,6 +211,9 @@
tInstLibEntry<tMethod>("if-resources", &cHardwareCPU::Inst_IfResources, nInstFlag::STALL),
// Data collection
tInstLibEntry<tMethod>("collect-cell-data", &cHardwareCPU::Inst_CollectCellData, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("kill-cell-event", &cHardwareCPU::Inst_KillCellEvent, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("kill-faced-cell-event", &cHardwareCPU::Inst_KillFacedCellEvent, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("collect-cell-data-and-kill-event", &cHardwareCPU::Inst_CollectCellDataAndKillEvent, nInstFlag::STALL),
tInstLibEntry<tMethod>("donate-rnd", &cHardwareCPU::Inst_DonateRandom, nInstFlag::STALL),
tInstLibEntry<tMethod>("donate-kin", &cHardwareCPU::Inst_DonateKin, nInstFlag::STALL),
@@ -230,16 +233,25 @@
tInstLibEntry<tMethod>("rotate-left-one", &cHardwareCPU::Inst_RotateLeftOne, nInstFlag::STALL),
tInstLibEntry<tMethod>("rotate-right-one", &cHardwareCPU::Inst_RotateRightOne, nInstFlag::STALL),
tInstLibEntry<tMethod>("rotate-label", &cHardwareCPU::Inst_RotateLabel, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("rotate-to-unoccupied-cell", &cHardwareCPU::Inst_RotateUnoccupiedCell, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("rotate-to-occupied-cell", &cHardwareCPU::Inst_RotateOccupiedCell, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("rotate-to-event-cell", &cHardwareCPU::Inst_RotateEventCell, nInstFlag::STALL),
+
tInstLibEntry<tMethod>("set-cmut", &cHardwareCPU::Inst_SetCopyMut),
tInstLibEntry<tMethod>("mod-cmut", &cHardwareCPU::Inst_ModCopyMut),
tInstLibEntry<tMethod>("get-cell-xy", &cHardwareCPU::Inst_GetCellPosition),
tInstLibEntry<tMethod>("get-cell-x", &cHardwareCPU::Inst_GetCellPositionX),
tInstLibEntry<tMethod>("get-cell-y", &cHardwareCPU::Inst_GetCellPositionY),
tInstLibEntry<tMethod>("dist-from-diag", &cHardwareCPU::Inst_GetDistanceFromDiagonal),
+
// @WRE additions for movement
tInstLibEntry<tMethod>("tumble", &cHardwareCPU::Inst_Tumble, nInstFlag::STALL),
tInstLibEntry<tMethod>("move", &cHardwareCPU::Inst_Move, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("move-to-event", &cHardwareCPU::Inst_MoveToEvent, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("if-event-in-unoccupied-neighbor-cell", &cHardwareCPU::Inst_IfNeighborEventInUnoccupiedCell),
+ tInstLibEntry<tMethod>("if-event-in-faced-cell", &cHardwareCPU::Inst_IfFacingEventCell),
+ tInstLibEntry<tMethod>("if-event-in-current-cell", &cHardwareCPU::Inst_IfEventInCell),
// Threading instructions
tInstLibEntry<tMethod>("fork-th", &cHardwareCPU::Inst_ForkThread),
@@ -355,7 +367,11 @@
tInstLibEntry<tMethod>("kazi", &cHardwareCPU::Inst_Kazi, nInstFlag::STALL),
tInstLibEntry<tMethod>("kazi5", &cHardwareCPU::Inst_Kazi5, nInstFlag::STALL),
tInstLibEntry<tMethod>("die", &cHardwareCPU::Inst_Die, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("relinquishEnergyToFutureDeme", &cHardwareCPU::Inst_RelinquishEnergyToFutureDeme, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("relinquishEnergyToNeighborOrganisms", &cHardwareCPU::Inst_RelinquishEnergyToNeighborOrganisms, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("relinquishEnergyToOrganismsInDeme", &cHardwareCPU::Inst_RelinquishEnergyToOrganismsInDeme, nInstFlag::STALL),
+
// Sleep and time
tInstLibEntry<tMethod>("sleep", &cHardwareCPU::Inst_Sleep, nInstFlag::STALL),
tInstLibEntry<tMethod>("sleep1", &cHardwareCPU::Inst_Sleep, nInstFlag::STALL),
@@ -386,11 +402,21 @@
// Energy usage
tInstLibEntry<tMethod>("double-energy-usage", &cHardwareCPU::Inst_DoubleEnergyUsage, nInstFlag::STALL),
tInstLibEntry<tMethod>("half-energy-usage", &cHardwareCPU::Inst_HalfEnergyUsage, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("default-energy-usage", &cHardwareCPU::Inst_DefaultEnergyUsage, nInstFlag::STALL),
// Messaging
tInstLibEntry<tMethod>("send-msg", &cHardwareCPU::Inst_SendMessage, nInstFlag::STALL),
tInstLibEntry<tMethod>("retrieve-msg", &cHardwareCPU::Inst_RetrieveMessage, nInstFlag::STALL),
-
+
+ // Alarms
+ tInstLibEntry<tMethod>("send-alarm-msg-local", &cHardwareCPU::Inst_Alarm_MSG_local, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("send-alarm-msg-multihop", &cHardwareCPU::Inst_Alarm_MSG_multihop, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("send-alarm-msg-bit-cons24-local", &cHardwareCPU::Inst_Alarm_MSG_Bit_Cons24_local, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("send-alarm-msg-bit-cons24-multihop", &cHardwareCPU::Inst_Alarm_MSG_Bit_Cons24_multihop, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("alarm-label-high", &cHardwareCPU::Inst_Alarm_Label),
+ tInstLibEntry<tMethod>("alarm-label-low", &cHardwareCPU::Inst_Alarm_Label),
+
+
// Placebo instructions
tInstLibEntry<tMethod>("skip", &cHardwareCPU::Inst_Skip),
@@ -1676,7 +1702,6 @@
void cHardwareCPU::InheritState(cHardwareBase& in_hardware)
{
m_epigenetic_state = true;
-
cHardwareCPU& in_h = (cHardwareCPU&)in_hardware;
const cLocalThread& thread = in_h.GetThread(in_h.GetCurThread());
for (int i=0; i<NUM_REGISTERS; i++) {
@@ -1687,8 +1712,6 @@
m_threads[m_cur_thread].stack = m_epigenetic_saved_stack;
}
-
-
//////////////////////////
// And the instructions...
//////////////////////////
@@ -2632,6 +2655,10 @@
// const bool viable = Divide_CheckViable(ctx, div_point, child_size);
// these checks should be done, but currently they make some assumptions
// that crash when evaluating this kind of organism -- JEB
+
+ // check if repro can replace an existing organism
+ if(m_world->GetConfig().REPRO_METHOD.Get() == 0 && organism->IsNeighborCellOccupied())
+ return false;
if (organism->GetPhenotype().GetCurBonus() < m_world->GetConfig().REQUIRED_BONUS.Get()) return false;
@@ -2749,9 +2776,60 @@
bool cHardwareCPU::Inst_Die(cAvidaContext& ctx)
{
organism->Die();
- return true;
+ return true;
}
+bool cHardwareCPU::Inst_RelinquishEnergyToFutureDeme(cAvidaContext& ctx)
+{
+ double stored_energy = organism->GetPhenotype().GetStoredEnergy() * m_world->GetConfig().FRAC_ENERGY_RELINQUISH.Get();
+ // put stored energy into testament pool for offspring deme
+ cDeme* deme = organism->GetOrgInterface().GetDeme();
+ if(deme == NULL)
+ return false; // in test CPU
+ deme->IncreaseTotalEnergyTestament(stored_energy);
+ m_world->GetStats().SumEnergyTestamentToFutureDeme().Add(stored_energy);
+ organism->Die();
+ return true;
+}
+
+bool cHardwareCPU::Inst_RelinquishEnergyToNeighborOrganisms(cAvidaContext& ctx)
+{
+ double stored_energy = organism->GetPhenotype().GetStoredEnergy() * m_world->GetConfig().FRAC_ENERGY_RELINQUISH.Get();
+ // put stored energy into toBeApplied energy pool of neighbor organisms
+ int numOcuppiedNeighbors(0);
+ int orginalFacing = organism->GetFacing();
+ for(int i = 0; i < organism->GetNeighborhoodSize(); i++) {
+ if(organism->IsNeighborCellOccupied()) {
+ // count neighboring organisms
+ numOcuppiedNeighbors++;
+ }
+ organism->Rotate(1);
+ }
+ assert(organism->GetFacing() == orginalFacing);
+
+ for(int i = 0; i < organism->GetNeighborhoodSize(); i++) {
+ if(organism->IsNeighborCellOccupied()) {
+ // give energy testament to neighboring organisms
+ organism->GetNeighbor()->GetPhenotype().EnergyTestament(stored_energy/numOcuppiedNeighbors);
+ }
+ organism->Rotate(1);
+ }
+ assert(organism->GetFacing() == orginalFacing);
+ m_world->GetStats().SumEnergyTestamentToNeighborOrganisms().Add(stored_energy);
+ organism->Die();
+ return true;
+}
+
+bool cHardwareCPU::Inst_RelinquishEnergyToOrganismsInDeme(cAvidaContext& ctx) {
+ double stored_energy = organism->GetPhenotype().GetStoredEnergy() * m_world->GetConfig().FRAC_ENERGY_RELINQUISH.Get();
+ // put stored energy into toBeApplied energy pool of neighbor organisms
+
+ organism->DivideOrgTestamentAmongDeme(stored_energy);
+ m_world->GetStats().SumEnergyTestamentToDemeOrganisms().Add(stored_energy);
+ organism->Die();
+ return true;
+}
+
// The inject instruction can be used instead of a divide command, paired
// with an allocate. Note that for an inject to work, one needs to have a
// broad range for sizes allowed to be allocated.
@@ -3215,12 +3293,50 @@
bool cHardwareCPU::Inst_CollectCellData(cAvidaContext& ctx) {
- int cellID = organism->GetCellID();
const int out_reg = FindModifiedRegister(REG_BX);
- GetRegister(out_reg) = m_world->GetPopulation().GetCell(cellID).GetCellData();
+ GetRegister(out_reg) = organism->GetCellData();
return true;
}
+bool cHardwareCPU::Inst_KillCellEvent(cAvidaContext& ctx) {
+ // Fail if we're running in the test CPU.
+ if((organism->GetOrgInterface().GetDemeID() < 0) || (organism->GetCellID() < 0))
+ return false;
+
+ const int reg = FindModifiedRegister(REG_BX);
+ int eventID = organism->GetCellData();
+ GetRegister(reg) = organism->GetOrgInterface().GetDeme()->KillCellEvent(eventID);
+ return true;
+}
+
+bool cHardwareCPU::Inst_KillFacedCellEvent(cAvidaContext& ctx) {
+ // Fail if we're running in the test CPU.
+ if((organism->GetOrgInterface().GetDemeID() < 0) || (organism->GetCellID() < 0))
+ return false;
+
+ const int reg = FindModifiedRegister(REG_BX);
+ int eventID = organism->GetNeighborCellContents();
+ GetRegister(reg) = organism->GetOrgInterface().GetDeme()->KillCellEvent(eventID);
+
+ if(GetRegister(reg))
+ organism->SetEventKilled();
+
+ return true;
+}
+
+bool cHardwareCPU::Inst_CollectCellDataAndKillEvent(cAvidaContext& ctx) {
+ // Fail if we're running in the test CPU.
+ if((organism->GetOrgInterface().GetDemeID() < 0) || (organism->GetCellID() < 0))
+ return false;
+
+ const int out_reg = FindModifiedRegister(REG_BX);
+ int eventID = organism->GetCellData();
+ GetRegister(out_reg) = eventID;
+
+ organism->GetOrgInterface().GetDeme()->KillCellEvent(eventID);
+ return true;
+}
+
void cHardwareCPU::DoDonate(cOrganism* to_org)
{
assert(to_org != NULL);
@@ -3891,6 +4007,50 @@
return true;
}
+bool cHardwareCPU::Inst_RotateUnoccupiedCell(cAvidaContext& ctx) {
+ const int reg_used = FindModifiedRegister(REG_BX);
+
+ for(int i = 0; i < organism->GetNeighborhoodSize(); i++) {
+ if(!organism->IsNeighborCellOccupied()) // faced cell is unoccupied
+ {
+ GetRegister(reg_used) = 1;
+ return true;
+ }
+ organism->Rotate(1); // continue to rotate
+ }
+ GetRegister(reg_used) = 0;
+ return true;
+}
+
+bool cHardwareCPU::Inst_RotateOccupiedCell(cAvidaContext& ctx) {
+ const int reg_used = FindModifiedRegister(REG_BX);
+
+ for(int i = 0; i < organism->GetNeighborhoodSize(); i++) {
+ if(organism->IsNeighborCellOccupied()) { // faced cell is occupied
+ GetRegister(reg_used) = 1;
+ return true;
+ }
+ organism->Rotate(1); // continue to rotate
+ }
+ GetRegister(reg_used) = 0;
+ return true;
+}
+
+
+bool cHardwareCPU::Inst_RotateEventCell(cAvidaContext& ctx) {
+ const int reg_used = FindModifiedRegister(REG_BX);
+
+ for(int i = 0; i < organism->GetNeighborhoodSize(); i++) {
+ if(organism->GetCellData() > 0) { // event in faced cell
+ GetRegister(reg_used) = 1;
+ return true;
+ }
+ organism->Rotate(1); // continue to rotate
+ }
+ GetRegister(reg_used) = 0;
+ return true;
+}
+
bool cHardwareCPU::Inst_SetCopyMut(cAvidaContext& ctx)
{
const int reg_used = FindModifiedRegister(REG_BX);
@@ -4031,8 +4191,55 @@
}
}
+bool cHardwareCPU::Inst_MoveToEvent(cAvidaContext& ctx) {
+ const int reg_used = FindModifiedRegister(REG_BX);
+ int orginalFacing = organism->GetFacing();
+
+ for(int i = 0; i < organism->GetNeighborhoodSize(); i++) {
+ if(organism->GetNeighborCellContents() > 0) {
+ Inst_Move(ctx);
+ GetRegister(reg_used) = 1;
+ return true;
+ }
+ organism->Rotate(1);
+ }
+ assert(organism->GetFacing() == orginalFacing);
+ Inst_Move(ctx);
+ GetRegister(reg_used) = 0;
+ return true;
+}
+
+bool cHardwareCPU::Inst_IfNeighborEventInUnoccupiedCell(cAvidaContext& ctx) {
+ int orginalFacing = organism->GetFacing();
+
+ for(int i = 0; i < organism->GetNeighborhoodSize(); i++) {
+ if(organism->GetNeighborCellContents() > 0 && !organism->IsNeighborCellOccupied()) {
+ return true;
+ }
+ organism->Rotate(1);
+ }
+ assert(organism->GetFacing() == orginalFacing);
+ IP().Advance();
+ return true;
+}
+
+bool cHardwareCPU::Inst_IfFacingEventCell(cAvidaContext& ctx) {
+ if(organism->GetNeighborCellContents() > 0) {
+ return true;
+ }
+ IP().Advance();
+ return true;
+}
+
+bool cHardwareCPU::Inst_IfEventInCell(cAvidaContext& ctx) {
+ if(organism->GetCellData() > 0) {
+ return true;
+ }
+ IP().Advance();
+ return true;
+}
+
// Multi-threading.
-
bool cHardwareCPU::Inst_ForkThread(cAvidaContext& ctx)
{
IP().Advance();
@@ -4440,7 +4647,7 @@
pop.AddEndSleep(cellID, m_world->GetStats().GetUpdate());
}
organism->SetSleeping(false); //this instruction get executed at the end of a sleep cycle
- m_world->GetStats().decNumAsleep(pop.GetCell(cellID).GetDemeID());
+ GetOrganism()->GetOrgInterface().GetDeme()->DecSleepingCount();
if(m_world->GetConfig().APPLY_ENERGY_METHOD.Get() == 2) {
organism->GetPhenotype().RefreshEnergy();
organism->GetPhenotype().ApplyToEnergyStore();
@@ -4878,7 +5085,65 @@
return true;
}
+bool cHardwareCPU::Inst_Alarm_MSG_multihop(cAvidaContext& ctx) {
+ const int reg_used = FindModifiedRegister(REG_BX);
+ return organism->BcastAlarmMSG(ctx, abs(GetRegister(reg_used)%2), m_world->GetConfig().BCAST_HOPS.Get()); // jump to Alarm-label- odd=high even=low
+}
+bool cHardwareCPU::Inst_Alarm_MSG_Bit_Cons24_multihop(cAvidaContext& ctx) {
+ const int reg_used = FindModifiedRegister(REG_BX);
+ return organism->BcastAlarmMSG(ctx, (BitCount(GetRegister(reg_used) & MASK24) >= CONSENSUS24) ? 1 : 0, m_world->GetConfig().BCAST_HOPS.Get());// jump to Alarm-label-high OR Alarm-label-low
+}
+
+bool cHardwareCPU::Inst_Alarm_MSG_local(cAvidaContext& ctx) {
+ const int reg_used = FindModifiedRegister(REG_BX);
+ return organism->BcastAlarmMSG(ctx, abs(GetRegister(reg_used)%2), 1); // jump to Alarm-label- odd=high even=low
+}
+
+bool cHardwareCPU::Inst_Alarm_MSG_Bit_Cons24_local(cAvidaContext& ctx) {
+ const int reg_used = FindModifiedRegister(REG_BX);
+ return organism->BcastAlarmMSG(ctx, (BitCount(GetRegister(reg_used) & MASK24) >= CONSENSUS24) ? 1 : 0, 1);// jump to Alarm-label-high OR Alarm-label-low
+}
+
+
+bool cHardwareCPU::Inst_Alarm_Label(cAvidaContext& ctx) {
+ return true;
+}
+
+bool cHardwareCPU::Jump_To_Alarm_Label(int jump_label) {
+ if(organism->IsSleeping()) {
+ return false;
+ }
+
+ cString channel;
+
+ if(jump_label == 1) {
+ channel = "high";
+ } else if(jump_label == 0) {
+ channel = "low";
+ } else {
+ assert(false);
+ }
+
+ cInstruction label_inst = GetInstSet().GetInst(cStringUtil::Stringf("alarm-label-")+channel);
+
+ cHeadCPU search_head(IP());
+ int start_pos = search_head.GetPosition();
+ search_head++;
+
+ while (start_pos != search_head.GetPosition()) {
+ if (search_head.GetInst() == label_inst) {
+ // move IP to here
+ IP().Set(search_head.GetPosition());
+ m_advance_ip = false; // Don't automatically move the IP
+ return true;
+ }
+ search_head++;
+ }
+ return false;
+}
+
+
//// Placebo insts ////
bool cHardwareCPU::Inst_Skip(cAvidaContext& ctx)
{
@@ -5142,7 +5407,7 @@
cPopulationCell& mycell = pop.GetCell(cellid);
cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
cResourceCount deme_resource_count = deme.GetDemeResourceCount();
- int relative_cell_id = deme.GetRelativeCellID(cellid);
+// int relative_cell_id = deme.GetRelativeCellID(cellid);
//tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
tArray<double> cell_resources;
@@ -5280,7 +5545,7 @@
cPopulationCell& mycell = pop.GetCell(cellid);
cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
cResourceCount deme_resource_count = deme.GetDemeResourceCount();
- int relative_cell_id = deme.GetRelativeCellID(cellid);
+// int relative_cell_id = deme.GetRelativeCellID(cellid);
//tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
tArray<double> cell_resources;
@@ -5424,7 +5689,7 @@
cPopulationCell& mycell = pop.GetCell(cellid);
cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
cResourceCount deme_resource_count = deme.GetDemeResourceCount();
- int relative_cell_id = deme.GetRelativeCellID(cellid);
+// int relative_cell_id = deme.GetRelativeCellID(cellid);
//tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
tArray<double> cell_resources;
@@ -5548,7 +5813,7 @@
bool cHardwareCPU::Inst_Explore(cAvidaContext& ctx)
{
- int num_rotations = 0;
+// int num_rotations = 0;
cPopulation& pop = m_world->GetPopulation();
int cellid = organism->GetCellID();
@@ -5557,12 +5822,12 @@
return true;
}
- cPopulationCell& mycell = pop.GetCell(cellid);
+// cPopulationCell& mycell = pop.GetCell(cellid);
cDeme &deme = pop.GetDeme(pop.GetCell(cellid).GetDemeID());
cResourceCount deme_resource_count = deme.GetDemeResourceCount();
int fromcellID, destcellID;
- int cell_data;
+// int cell_data;
// Pheromone drop stuff
double pher_amount = 0;
@@ -5680,7 +5945,7 @@
double pher_amount = 0; // this is used in logging
int drop_mode = -1;
-int smc = mycell.ConnectionList().GetSize();
+//int smc = mycell.ConnectionList().GetSize();
//SingleProcess shows decent-looking cellids until the end. maybe this is a deme replication problem (probably)
cPopulationCell faced = mycell.GetCellFaced();
@@ -5695,7 +5960,7 @@
mycell.ConnectionList().CircNext();
}
- assert(faced == pop.GetCell(fromcellID).GetCellFaced());
+// assert(faced == pop.GetCell(fromcellID).GetCellFaced());
// Rotate until we face the neighbor with a target.
// If there was no winner, just move forward.
@@ -5828,7 +6093,7 @@
mycell.ConnectionList().CircNext();
}
- assert(faced == pop.GetCell(fromcellID).GetCellFaced());
+// assert(faced == pop.GetCell(fromcellID).GetCellFaced());
// Rotate until we face the neighbor with a target.
// If there was no winner, just move forward.
@@ -5960,7 +6225,7 @@
mycell.ConnectionList().CircNext();
}
- assert(faced == pop.GetCell(fromcellID).GetCellFaced());
+// assert(faced == pop.GetCell(fromcellID).GetCellFaced());
// Rotate until we face the neighbor with a target.
// If there was no winner, just move forward.
Modified: development/source/cpu/cHardwareCPU.h
===================================================================
--- development/source/cpu/cHardwareCPU.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/cpu/cHardwareCPU.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -440,6 +440,9 @@
bool Inst_Kazi(cAvidaContext& ctx);
bool Inst_Kazi5(cAvidaContext& ctx);
bool Inst_Die(cAvidaContext& ctx);
+ bool Inst_RelinquishEnergyToFutureDeme(cAvidaContext& ctx);
+ bool Inst_RelinquishEnergyToNeighborOrganisms(cAvidaContext& ctx);
+ bool Inst_RelinquishEnergyToOrganismsInDeme(cAvidaContext& ctx);
// I/O and Sensory
bool Inst_TaskGet(cAvidaContext& ctx);
@@ -464,6 +467,9 @@
//! Execute the following instruction if all resources are above their min level.
bool Inst_IfResources(cAvidaContext& ctx);
bool Inst_CollectCellData(cAvidaContext& ctx);
+ bool Inst_KillCellEvent(cAvidaContext& ctx);
+ bool Inst_KillFacedCellEvent(cAvidaContext& ctx);
+ bool Inst_CollectCellDataAndKillEvent(cAvidaContext& ctx);
void DoDonate(cOrganism * to_org);
void DoEnergyDonate(cOrganism* to_org);
@@ -491,6 +497,9 @@
bool Inst_RotateLeftOne(cAvidaContext& ctx);
bool Inst_RotateRightOne(cAvidaContext& ctx);
bool Inst_RotateLabel(cAvidaContext& ctx);
+ bool Inst_RotateOccupiedCell(cAvidaContext& ctx);
+ bool Inst_RotateUnoccupiedCell(cAvidaContext& ctx);
+ bool Inst_RotateEventCell(cAvidaContext& ctx);
bool Inst_SetCopyMut(cAvidaContext& ctx);
bool Inst_ModCopyMut(cAvidaContext& ctx);
bool Inst_GetCellPosition(cAvidaContext& ctx);
@@ -501,6 +510,10 @@
// @WRE additions for movement
bool Inst_Tumble(cAvidaContext& ctx);
bool Inst_Move(cAvidaContext& ctx);
+ bool Inst_MoveToEvent(cAvidaContext& ctx);
+ bool Inst_IfNeighborEventInUnoccupiedCell(cAvidaContext& ctx);
+ bool Inst_IfFacingEventCell(cAvidaContext& ctx);
+ bool Inst_IfEventInCell(cAvidaContext& ctx);
// Multi-threading...
@@ -601,6 +614,15 @@
bool Inst_SendMessage(cAvidaContext& ctx);
bool Inst_RetrieveMessage(cAvidaContext& ctx);
+ //// Alarm ////
+ bool Inst_Alarm_MSG_local(cAvidaContext& ctx);
+ bool Inst_Alarm_MSG_multihop(cAvidaContext& ctx);
+ bool Inst_Alarm_MSG_Bit_Cons24_local(cAvidaContext& ctx);
+ bool Inst_Alarm_MSG_Bit_Cons24_multihop(cAvidaContext& ctx);
+ bool Inst_Alarm_Label(cAvidaContext& ctx);
+ bool Jump_To_Alarm_Label(int jump_label);
+
+
//// Placebo ////
bool Inst_Skip(cAvidaContext& ctx);
Modified: development/source/cpu/cHardwareGX.h
===================================================================
--- development/source/cpu/cHardwareGX.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/cpu/cHardwareGX.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -370,6 +370,7 @@
// -------- Parasite Stuff --------
bool InjectHost(const cCodeLabel& in_label, const cGenome& injection);
+
// -------- Input/Output Buffers --------
virtual tBuffer<int>& GetInputBuf() { return m_current->GetInputBuf(); }
virtual tBuffer<int>& GetOutputBuf() { return m_current->GetOutputBuf(); }
Modified: development/source/cpu/cTestCPUInterface.cc
===================================================================
--- development/source/cpu/cTestCPUInterface.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/cpu/cTestCPUInterface.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -41,6 +41,10 @@
return NULL;
}
+bool cTestCPUInterface::IsNeighborCellOccupied() {
+ return false;
+}
+
int cTestCPUInterface::GetNumNeighbors()
{
return 0;
Modified: development/source/cpu/cTestCPUInterface.h
===================================================================
--- development/source/cpu/cTestCPUInterface.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/cpu/cTestCPUInterface.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -49,6 +49,9 @@
cDeme* GetDeme() { return 0; }
void SetCellID(int in_id) { ; }
void SetDemeID(int in_id) { ; }
+
+ int GetCellData() { return -1; }
+ void SetCellData(const int newData) { ; }
int GetPrevSeenCellID() { return 0; }
int GetPrevTaskCellID() { return 0; }
@@ -59,7 +62,9 @@
bool Divide(cAvidaContext& ctx, cOrganism* parent, cGenome& child_genome);
cOrganism* GetNeighbor();
+ bool IsNeighborCellOccupied();
int GetNumNeighbors();
+ int GetNeighborCellContents() { return 0; }
void Rotate(int direction = 1);
void Breakpoint() { ; }
int GetInputAt(int& input_pointer);
@@ -84,6 +89,9 @@
int GetFacing() { return 0; }
bool SendMessage(cOrgMessage& msg) { return false; }
+ bool BcastAlarm(int jump_label, int bcast_range) { return false; }
+
+ void DivideOrgTestamentAmongDeme(double value) {;}
};
Modified: development/source/main/cAvidaConfig.h
===================================================================
--- development/source/main/cAvidaConfig.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cAvidaConfig.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -283,6 +283,8 @@
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\n3 = Experimental CPU\n4 = Gene Expression CPU");
CONFIG_ADD_VAR(SPECULATIVE, bool, 1, "Enable speculative execution");
+ CONFIG_ADD_VAR(BCAST_HOPS, int, 1, "Number of hops to broadcast an alarm");
+ CONFIG_ADD_VAR(ALARM_SELF, bool, 0, "Does sending an alarm move sender IP to alarm label?\n0=no\n1=yes");
CONFIG_ADD_GROUP(CONFIG_FILE_GROUP, "Configuration Files");
CONFIG_ADD_VAR(DATA_DIR, cString, "data", "Directory in which config files are found");
@@ -296,7 +298,7 @@
CONFIG_ADD_GROUP(DEME_GROUP, "Demes and Germlines");
CONFIG_ADD_VAR(NUM_DEMES, int, 1, "Number of independent groups in the\npopulation (default=1).");
CONFIG_ADD_VAR(DEMES_USE_GERMLINE, int, 0, "Whether demes use a distinct germline (default=0).");
- CONFIG_ADD_VAR(DEMES_PREVENT_STERILE, int, 0, "Whether to prevent sterile demes from\nreplicating (default=0).");
+ CONFIG_ADD_VAR(DEMES_PREVENT_STERILE, int, 0, "Whether to prevent sterile demes from\nreplicating (default=0 or no).");
CONFIG_ADD_VAR(DEMES_RESET_RESOURCES, int, 0, "Reset resources in demes on replication. \n0 = reset both demes \n1 = reset target deme \n2 = deme resources remain unchanged\n");
CONFIG_ADD_VAR(DEMES_REPLICATE_SIZE, int, 1, "Number of identical organisms to create or copy from the\nsource deme to the target deme (default=1).");
CONFIG_ADD_VAR(DEMES_PROB_ORG_TRANSFER, double, 0.0, "Probablity of an organism being transferred from the\nsource deme to the target deme (default=0.0).");
@@ -305,6 +307,8 @@
CONFIG_ADD_VAR(DEMES_ORGANISM_FACING, int, 0, "How organisms are facing during deme replication.\n0=unchanged (default).\n1=northwest.\n2=random.");
CONFIG_ADD_VAR(DEMES_MAX_AGE, int, 500, "The maximum age of a deme (in updates) to be\nused for age-based replication (default=500).");
CONFIG_ADD_VAR(DEMES_MAX_BIRTHS, int, 100, "The maximum number of births that can occur\nwithin a deme; used with birth-count\nreplication (default=100).");
+ CONFIG_ADD_VAR(DEMES_MIM_EVENTS_KILLED_RATIO, double, 0.7, "Minimum ratio of events killed required for event period to be a success.");
+ CONFIG_ADD_VAR(DEMES_MIM_SUCCESSFUL_EVENT_PERIODS, int, 1, "Minimum number of consecutive event periods that must be a success.");
CONFIG_ADD_VAR(GERMLINE_COPY_MUT, double, 0.0075, "Prob. of copy mutations occuring during\ngermline replication (default=0.0075).");
CONFIG_ADD_VAR(GERMLINE_INS_MUT, double, 0.05, "Prob. of an insertion mutation occuring\nduring germline replication (default=0.05).");
CONFIG_ADD_VAR(GERMLINE_DEL_MUT, double, 0.05, "Prob. of a deletion mutation occuring\nduring germline replication (default=0.05).");
@@ -336,6 +340,7 @@
CONFIG_ADD_VAR(INJECT_METHOD, int, 0, "0 = Leaves the parasite thread state untouched.\n1 = Resets the calling thread state on inject");
CONFIG_ADD_VAR(GENERATION_INC_METHOD, int, 1, "0 = Only the generation of the child is\n increased on divide.\n1 = Both the generation of the mother and child are\n increased on divide (good with DIVIDE_METHOD 1).");
CONFIG_ADD_VAR(RESET_INPUTS_ON_DIVIDE, int, 0, "Reset environment inputs of parent upon successful divide.");
+ CONFIG_ADD_VAR(REPRO_METHOD, int, 1, "Replace existing organism: 1=yes");
CONFIG_ADD_GROUP(RECOMBINATION_GROUP, "Sexual Recombination and Modularity");
CONFIG_ADD_VAR(RECOMBINATION_PROB, double, 1.0, "probability of recombination in div-sex");
@@ -478,6 +483,10 @@
CONFIG_ADD_VAR(APPLY_ENERGY_METHOD, int, 0, "When should rewarded energy be applied to current energy?\n0 = on divide\n1 = on completion of task\n2 = on sleep");
CONFIG_ADD_VAR(FRAC_ENERGY_TRANSFER, double, 0.0, "Fraction of replaced organism's energy take by new resident");
CONFIG_ADD_VAR(LOG_SLEEP_TIMES, bool, 0, "Log sleep start and end times. 0/1 (off/on)\nWARNING: may use lots of memory.");
+ CONFIG_ADD_VAR(FRAC_ENERGY_RELINQUISH, double, 1.0, "Fraction of organisms energy to relinquish");
+ CONFIG_ADD_VAR(ENERGY_PASSED_ON_DEME_REPLICATION_METHOD, int, 0, "Who get energy passed from a parent deme\n0 = Energy divided among organisms injected to offspring deme\n1 = Energy divided among cells in offspring deme");
+ CONFIG_ADD_VAR(INHERIT_EXE_RATE, int, 0, "Inherit energy rate from parent? 0=no 1=yes");
+ CONFIG_ADD_VAR(ATTACK_DECAY_RATE, double, 0.0, "Percent of cell's energy decayed by attack");
CONFIG_ADD_GROUP(SECOND_PASS_GROUP, "Tracking metrics known after the running experiment previously");
CONFIG_ADD_VAR(TRACK_CCLADES, int, 0, "Enable tracking of coalescence clades");
Modified: development/source/main/cDeme.cc
===================================================================
--- development/source/main/cDeme.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cDeme.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -30,6 +30,7 @@
#include "cPopulation.h"
#include "cPopulationCell.h"
#include "cResource.h"
+#include "cStats.h"
#include "cWorld.h"
#include "cOrgMessagePredicate.h"
#include "cOrgMovementPredicate.h"
@@ -42,6 +43,7 @@
last_birth_count = 0;
cur_org_count = 0;
last_org_count = 0;
+ birth_count_perslot = 0;
m_world = world;
_current_merit = 1.0;
@@ -107,12 +109,51 @@
}
void cDeme::ProcessUpdate() {
+ energyUsage.Clear();
+
+ if(IsEmpty()) { // deme is not processed if no organisms are present
+ total_energy_testament = 0.0;
+ return;
+ }
+
+ for(int i = 0; i < GetSize(); i++) {
+ cPopulationCell& cell = GetCell(i);
+ if(cell.IsOccupied()) {
+ energyUsage.Add(cell.GetOrganism()->GetPhenotype().GetEnergyUsageRatio());
+ }
+ }
+
for(int i = 0; i < cell_events.Size(); i++) {
cDemeCellEvent& event = cell_events[i];
- if(event.GetDelay() == _age) {
- event.ActivateEvent(m_world); //start event
+
+ if(event.IsActive() && event.GetDelay() < _age && _age <= event.GetDelay()+event.GetDuration()) {
+ //remove energy from cells (should be done with outflow, but this will work for now)
int eventCell = event.GetNextEventCellID();
+ cResource* res = m_world->GetEnvironment().GetResourceLib().GetResource("CELL_ENERGY");
+
while(eventCell != -1) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(GetCellID(eventCell));
+ if(event.GetEventID() == cell.GetCellData()){
+ if(cell.IsOccupied()) {
+ // remove energy from organism
+ cPhenotype& orgPhenotype = cell.GetOrganism()->GetPhenotype();
+ orgPhenotype.ReduceEnergy(orgPhenotype.GetStoredEnergy()*m_world->GetConfig().ATTACK_DECAY_RATE.Get());
+ }
+ //remove energy from cell... organism might not takeup all of a cell's energy
+ tArray<double> cell_resources = deme_resource_count.GetCellResources(eventCell); // uses global cell_id; is this a problem
+ cell_resources[res->GetID()] *= m_world->GetConfig().ATTACK_DECAY_RATE.Get();
+ deme_resource_count.ModifyCell(cell_resources, eventCell);
+ }
+ eventCell = event.GetNextEventCellID();
+ }
+ }
+
+
+
+ if(!event.IsActive() && event.GetDelay() == _age) {
+ event.ActivateEvent(); //start event
+ int eventCell = event.GetNextEventCellID();
+ while(eventCell != -1) {
// place event ID in cells' data
if(event.IsDecayed()) {
m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(event.GetEventIDDecay(GetCellPosition(eventCell)));
@@ -124,44 +165,83 @@
std::pair<int, int> pos = GetCellPosition(eventCell);
m_world->GetStats().IncEventCount(pos.first, pos.second);
+
+ //TODO // increase outflow of energy from these cells if not event currently present
+
+
eventCell = event.GetNextEventCellID();
}
- } else if(event.GetDelay()+event.GetDuration() == _age) {
+ } else if(event.IsActive() && event.GetDelay()+event.GetDuration() == _age) {
int eventCell = event.GetNextEventCellID();
while(eventCell != -1) {
if(event.GetEventID() == m_world->GetPopulation().GetCell(GetCellID(eventCell)).GetCellData()) { // eventID == CellData
//set cell data to 0
m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(0);
- eventCell = event.GetNextEventCellID();
+
+ // TODO // remove energy outflow from these cells
+
}
+ eventCell = event.GetNextEventCellID();
}
event.DeactivateEvent(); //event over
}
}
+
+ for(vector<pair<int, int> >::iterator iter = event_slot_end_points.begin(); iter < event_slot_end_points.end(); iter++) {
+ if(_age == (*iter).first) {
+ // at end point
+ if(GetEventsKilledThisSlot() >= m_world->GetConfig().DEMES_MIM_EVENTS_KILLED_RATIO.Get() * (*iter).second)
+ consecutiveSuccessfulEventPeriods++;
+ else
+ consecutiveSuccessfulEventPeriods = 0;
+
+ // update stats.flow_rate_tuples
+ std::map<int, flow_rate_tuple>& flowRateTuples = m_world->GetStats().FlowRateTuples();
+
+ flowRateTuples[(*iter).second].orgCount.Add(GetOrgCount());
+ flowRateTuples[(*iter).second].eventsKilled.Add(GetEventsKilledThisSlot());
+ flowRateTuples[(*iter).second].attemptsToKillEvents.Add(GetEventKillAttemptsThisSlot());
+ flowRateTuples[(*iter).second].AvgEnergyUsageRatio.Add(energyUsage.Average());
+ flowRateTuples[(*iter).second].totalBirths.Add(birth_count_perslot);
+ flowRateTuples[(*iter).second].currentSleeping.Add(sleeping_count);
+ birth_count_perslot = 0;
+ eventsKilledThisSlot = 0;
+ eventKillAttemptsThisSlot = 0;
+ break;
+ }
+ }
++_age;
}
void cDeme::Reset(bool resetResources, double deme_energy)
{
+ double additional_resource = 0.0;
// Handle energy model
if (m_world->GetConfig().ENERGY_ENABLED.Get())
{
assert(cur_org_count>0);
- total_org_energy = deme_energy;
- if(total_org_energy < 0.0)
- total_org_energy = 0.0;
+ total_energy_testament = 0.0;
- // split deme energy evenly between organisms in deme
- for (int i=0; i<GetSize(); i++) {
- int cellid = GetCellID(i);
- cPopulationCell& cell = m_world->GetPopulation().GetCell(cellid);
- if(cell.IsOccupied()) {
- cOrganism* organism = cell.GetOrganism();
- cPhenotype& phenotype = organism->GetPhenotype();
- phenotype.SetEnergy(phenotype.GetStoredEnergy() + total_org_energy/static_cast<double>(cur_org_count));
- phenotype.SetMerit(cMerit(cMerit::EnergyToMerit(phenotype.GetStoredEnergy() * phenotype.GetEnergyUsageRatio(), m_world)));
+ if(m_world->GetConfig().ENERGY_PASSED_ON_DEME_REPLICATION_METHOD.Get() == 0) {
+ total_org_energy = deme_energy;
+ if(total_org_energy < 0.0)
+ total_org_energy = 0.0;
+
+ // split deme energy evenly between organisms in deme
+ for (int i=0; i<GetSize(); i++) {
+ int cellid = GetCellID(i);
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(cellid);
+ if(cell.IsOccupied()) {
+ cOrganism* organism = cell.GetOrganism();
+ cPhenotype& phenotype = organism->GetPhenotype();
+ phenotype.SetEnergy(phenotype.GetStoredEnergy() + total_org_energy/static_cast<double>(cur_org_count));
+ phenotype.SetMerit(cMerit(cMerit::EnergyToMerit(phenotype.GetStoredEnergy() * phenotype.GetEnergyUsageRatio(), m_world)));
+ }
}
+ } else if(m_world->GetConfig().ENERGY_PASSED_ON_DEME_REPLICATION_METHOD.Get() == 1) {
+ // split deme energy evenly between cell in deme
+ additional_resource = deme_energy; // spacial resource handles resource division
}
}
@@ -171,12 +251,18 @@
cur_birth_count = 0;
cur_normalized_time_used = 0;
injected_count = 0;
+ birth_count_perslot = 0;
+ eventsKilled = 0;
+ eventsKilledThisSlot = 0;
+ eventKillAttempts = 0;
+ eventKillAttemptsThisSlot = 0;
+ sleeping_count = 0;
+ consecutiveSuccessfulEventPeriods = 0;
+
cur_task_exe_count.SetAll(0);
cur_reaction_count.SetAll(0);
- if(resetResources) deme_resource_count.ReinitializeResources();
-
//reset remaining message predicates
for(int i = 0; i < message_pred_list.Size(); i++) {
(*message_pred_list[i]).Reset();
@@ -186,6 +272,8 @@
(*movement_pred_list[i]).Reset();
}
+ if(resetResources)
+ deme_resource_count.ReinitializeResources(additional_resource);
}
@@ -377,23 +465,89 @@
deme_resource_count.ModifyCell(cell_resources, relative_cell_id);
}
-void cDeme::SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live, int ID) {
- cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width, GetHeight(), static_pos, time_to_live, this);
- if(ID != -1)
- demeEvent.SetEventID(ID);
- cell_events.Add(demeEvent);
+void cDeme::SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, bool static_position, int total_events) {
+ for(int i = 0; i < total_events; i++) {
+ cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width, GetHeight(), static_position, this, m_world);
+ cell_events.Add(demeEvent);
+ }
}
-void cDeme::SetCellEventGradient(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live) {
+/*void cDeme::SetCellEventGradient(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live) {
cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width, GetHeight(), static_pos, time_to_live, this);
demeEvent.DecayEventIDFromCenter();
cell_events.Add(demeEvent);
-}
+}*/
int cDeme::GetNumEvents() {
return cell_events.Size();
}
+void cDeme::SetCellEventSlots(int x1, int y1, int x2, int y2, int delay, int duration,
+ bool static_position, int m_total_slots, int m_total_events_per_slot_max,
+ int m_total_events_per_slot_min, int m_tolal_event_flow_levels) {
+ assert(cell_events.Size() == 0); // not designed to be used with other cell events
+ assert(m_world->GetConfig().DEMES_MAX_AGE.Get() >= m_total_slots);
+
+ int flow_level_increment = (m_total_events_per_slot_max - m_total_events_per_slot_min) / (m_tolal_event_flow_levels-1);
+ int slot_length = m_world->GetConfig().DEMES_MAX_AGE.Get() / m_total_slots;
+
+ // setup stats tuples
+
+ for(int i = 0; i < m_total_slots; i++) {
+ int slot_flow_level = flow_level_increment * m_world->GetRandom().GetInt(m_tolal_event_flow_levels) + m_total_events_per_slot_min; // number of event during this slot
+ int slot_delay = i * slot_length;
+ event_slot_end_points.push_back(make_pair(slot_delay+slot_length, slot_flow_level)); // last slot is never reached it is == to MAX_AGE
+
+ for(int k = 0; k < slot_flow_level; k++) {
+ cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width, GetHeight(), static_position, this, m_world);
+ demeEvent.ConfineToTimeSlot(slot_delay, slot_delay+slot_length);
+ cell_events.Add(demeEvent);
+ }
+ }
+
+ // setup stats.flow_rate_tuples
+ std::map<int, flow_rate_tuple>& flowRateTuples = m_world->GetStats().FlowRateTuples();
+
+ for(int i = m_total_events_per_slot_min; i <= m_total_events_per_slot_max; i+=flow_level_increment) {
+ flowRateTuples[i].orgCount.Clear();
+ flowRateTuples[i].eventsKilled.Clear();
+ flowRateTuples[i].attemptsToKillEvents.Clear();
+ flowRateTuples[i].AvgEnergyUsageRatio.Clear();
+ flowRateTuples[i].totalBirths.Clear();
+ flowRateTuples[i].currentSleeping.Clear();
+ }
+}
+
+bool cDeme::KillCellEvent(const int eventID) {
+ eventKillAttemptsThisSlot++;
+
+ if(eventID <= 0)
+ return false;
+ for(int i = 0; i < cell_events.Size(); i++) {
+ cDemeCellEvent& event = cell_events[i];
+ if(event.IsActive() && event.GetEventID() == eventID) {
+ // remove event ID from all cells
+ int eventCell = event.GetNextEventCellID();
+ while(eventCell != -1) {
+ if(event.GetEventID() == m_world->GetPopulation().GetCell(GetCellID(eventCell)).GetCellData()) { // eventID == CellData
+ //set cell data to 0
+ m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(0);
+
+ // TODO // remove energy outflow from these cells
+
+ }
+ eventCell = event.GetNextEventCellID();
+ }
+ event.DeactivateEvent(); //event over
+ eventsKilled++;
+ eventsKilledThisSlot++;
+ eventKillAttempts++;
+ return true;
+ }
+ }
+ return false;
+}
+
double cDeme::CalculateTotalEnergy() {
assert(m_world->GetConfig().ENERGY_ENABLED.Get());
@@ -405,6 +559,9 @@
cOrganism* organism = cell.GetOrganism();
cPhenotype& phenotype = organism->GetPhenotype();
energy_sum += phenotype.GetStoredEnergy();
+ } else {
+ double energy_in_cell = cell.UptakeCellEnergy(1.0);
+ energy_sum += energy_in_cell * m_world->GetConfig().FRAC_ENERGY_TRANSFER.Get();
}
}
return energy_sum;
@@ -579,7 +736,7 @@
assert(cell_ids[0] <= absolute_cell_id);
assert(absolute_cell_id <= cell_ids[cell_ids.GetSize()-1]);
- cPopulation& pop = m_world->GetPopulation();
+// cPopulation& pop = m_world->GetPopulation();
int relative_cell_id = GetRelativeCellID(absolute_cell_id);
tArray<double> cell_resources = deme_resource_count.GetCellResources(relative_cell_id);
@@ -606,3 +763,14 @@
} //End AddPheromone()
+int cDeme::GetSlotFlowRate() const {
+ vector<pair<int, int> >::const_iterator iter = event_slot_end_points.begin();
+ while(iter != event_slot_end_points.end()) {
+ if(GetAge() <= (*iter).first) {
+ return (*iter).second;
+ }
+ iter++;
+ }
+// assert(false); // slots must be of equal size and fit perfectally in deme lifetime
+ return 0;
+}
Modified: development/source/main/cDeme.h
===================================================================
--- development/source/main/cDeme.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cDeme.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -24,6 +24,8 @@
#ifndef cDeme_h
#define cDeme_h
+#include <vector>
+
#include "cDemeCellEvent.h"
#include "cGermline.h"
#include "cPhenotype.h"
@@ -32,6 +34,7 @@
#include "tVector.h"
#include "cResourceCount.h"
#include "cStringList.h"
+#include "cDoubleSum.h"
class cResource;
class cWorld;
@@ -59,7 +62,7 @@
int cur_org_count; //!< Number of organisms are currently in this deme.
int last_org_count;
int injected_count; //<! Number of organisms that have been injected into this deme
-
+ int birth_count_perslot;
int _age; //!< Age of this deme, in updates.
int generation; //!< Generation of this deme
double total_org_energy; //! total amount of energy in organisms in this deme
@@ -67,6 +70,14 @@
int gestation_time; // Time used during last generation
double cur_normalized_time_used; // normalized by merit and number of orgs
double last_normalized_time_used;
+ double total_energy_testament; //! total amount of energy from suicide organisms for offspring deme
+ unsigned int eventsKilled;
+ unsigned int eventsKilledThisSlot;
+ unsigned int eventKillAttempts;
+ unsigned int eventKillAttemptsThisSlot;
+ unsigned int consecutiveSuccessfulEventPeriods;
+ int sleeping_count; //!< Number of organisms currently sleeping
+ cDoubleSum energyUsage;
tArray<int> cur_task_exe_count;
tArray<int> cur_reaction_count;
@@ -93,6 +104,7 @@
tArray<int> energy_res_ids; //!< IDs of energy resources
tVector<cDemeCellEvent> cell_events;
+ std::vector<std::pair<int, int> > event_slot_end_points; // (slot end point, slot flow rate)
int m_germline_genotype_id; // Genotype id of germline (if in use)
tArray<int> m_founder_genotype_ids; // List of genotype ids used to found deme.
@@ -106,9 +118,11 @@
tVector<cOrgMovementPredicate*> movement_pred_list; // Movement Predicates
public:
- cDeme() : _id(0), width(0), cur_birth_count(0), last_birth_count(0), cur_org_count(0), last_org_count(0),
- injected_count(0), _age(0), generation(0), total_org_energy(0.0),
- time_used(0), gestation_time(0), cur_normalized_time_used(0.0), last_normalized_time_used(0.0),
+ cDeme() : _id(0), width(0), cur_birth_count(0), last_birth_count(0), cur_org_count(0), last_org_count(0), injected_count(0), birth_count_perslot(0),
+ _age(0), generation(0), total_org_energy(0.0),
+ time_used(0), gestation_time(0), cur_normalized_time_used(0.0), last_normalized_time_used(0.0), total_energy_testament(0.0),
+ eventsKilled(0), eventsKilledThisSlot(0), eventKillAttempts(0), eventKillAttemptsThisSlot(0),
+ consecutiveSuccessfulEventPeriods(0), sleeping_count(0),
avg_founder_generation(0.0), generations_per_lifetime(0.0),
deme_resource_count(0), m_germline_genotype_id(0) { ; }
~cDeme() { ; }
@@ -132,17 +146,22 @@
//! Kills all organisms currently in this deme.
void KillAll();
+
void UpdateStats();
int GetBirthCount() const { return cur_birth_count; }
int GetLastBirthCount() const { return last_birth_count; }
- void IncBirthCount() { cur_birth_count++; }
+ void IncBirthCount() { cur_birth_count++; birth_count_perslot++;}
int GetOrgCount() const { return cur_org_count; }
int GetLastOrgCount() const { return last_org_count; }
void IncOrgCount() { cur_org_count++; }
void DecOrgCount() { cur_org_count--; }
+
+ int GetSleepingCount() const { return sleeping_count; }
+ void IncSleepingCount() { sleeping_count++; }
+ void DecSleepingCount() { sleeping_count--; }
int GetGeneration() const { return generation; }
@@ -151,6 +170,13 @@
bool IsEmpty() const { return cur_org_count == 0; }
bool IsFull() const { return cur_org_count == cell_ids.GetSize(); }
+
+ int GetSlotFlowRate() const;
+ int GetEventsKilled() const { return eventsKilled; }
+ int GetEventsKilledThisSlot() const { return eventsKilledThisSlot;}
+ int GetEventKillAttempts() const { return eventKillAttempts; }
+ int GetEventKillAttemptsThisSlot() const { return eventKillAttemptsThisSlot; }
+ int GetConsecutiveSuccessfulEventPeriods() const { return consecutiveSuccessfulEventPeriods;}
// -= Germline =-
//! Returns this deme's germline.
@@ -205,11 +231,19 @@
void Update(double time_step) { deme_resource_count.Update(time_step); }
int GetRelativeCellID(int absolute_cell_id) { return absolute_cell_id % GetSize(); } //!< assumes all demes are the same size
- void SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live, int ID = -1);
void SetCellEventGradient(int x1, int y1, int x2, int y2, int delay, int duration, bool static_pos, int time_to_live);
int GetNumEvents();
+ void SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, bool static_position, int total_events);
+ void SetCellEventSlots(int x1, int y1, int x2, int y2, int delay, int duration,
+ bool static_position, int m_total_slots, int m_total_events_per_slot_max,
+ int m_total_events_per_slot_min, int m_tolal_event_flow_levels);
+
+ bool KillCellEvent(const int eventID);
+ cDemeCellEvent* GetCellEvent(const int i) { return &cell_events[i]; };
double CalculateTotalEnergy();
+ double GetTotalEnergyTestament() { return total_energy_testament; }
+ void IncreaseTotalEnergyTestament(double increment) { total_energy_testament += increment; }
void IncTimeUsed(double merit)
{ time_used++; cur_normalized_time_used += 1.0/merit/(double)cur_org_count; }
@@ -248,8 +282,6 @@
// --- Pheromones --- //
void AddPheromone(int absolute_cell_id, double value);
-
-
};
#endif
Modified: development/source/main/cDemeCellEvent.cc
===================================================================
--- development/source/main/cDemeCellEvent.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cDemeCellEvent.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -2,28 +2,32 @@
#include "cDeme.h"
#include "cWorld.h"
-cDemeCellEvent::cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int deme_width, int deme_height, bool static_pos, int time_to_live, cDeme* deme) :
-m_delay(delay)
-, m_duration(duration)
-, m_iter(0)
-, m_deme_width(deme_width)
-, m_deme_height(deme_height)
-, m_time_to_live(time_to_live)
-, m_use_gradient(false)
-, m_active(false)
-, m_static_pos(static_pos)
-, m_dead (false)
-, m_id_set(false)
-, m_deme(deme)
+cDemeCellEvent::cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int deme_width, int deme_height, bool static_pos, cDeme* deme, cWorld* world) :
+ m_delay(delay)
+ , m_duration(duration)
+ , m_iter(0)
+ , m_deme_width(deme_width)
+ , m_deme_height(deme_height)
+ , m_event_width(x2-x1)
+ , m_event_height(y2-y1)
+ , m_active(false)
+ , m_static_pos(static_pos)
+ , m_deme(deme)
+ , m_world(world)
{
assert(x1 <= x2);
assert(y1 <= y2);
assert(y1 < deme_width && y2 < deme_width);
- assert(delay >= 0);
+ assert(x1 < deme_height && x2 < deme_height);
+ assert(delay >= -1);
assert(duration >= 0);
m_event_cells.ResizeClear((x2-x1+1) * (y2-y1+1));
int i = 0;
+ if(m_delay == -1) {
+ m_delay = m_world->GetRandom().GetInt(m_world->GetConfig().DEMES_MAX_AGE.Get() - m_duration);
+ }
+
if(m_static_pos) {
for(int j = y1; j <= y2; j++) {
for(int k = x1; k <= x2; k++) {
@@ -49,7 +53,7 @@
return -1;
}
-void cDemeCellEvent::ActivateEvent(cWorld* m_world) {
+void cDemeCellEvent::ActivateEvent() {
if(m_dead) {
return;
@@ -72,6 +76,19 @@
pair<int, int> centerTopRight = make_pair((int)ceil((m_event_width/2.0)), (int)ceil((m_event_height/2.0)));
center = make_pair(centerBottomleft, centerTopRight);
}
+
+ if(!m_static_pos) {
+ //non-static event position
+ int rand_x1 = m_world->GetRandom().GetInt(m_deme_width-m_event_width);
+ int rand_y1 = m_world->GetRandom().GetInt(m_deme_height-m_event_height);
+ int i = 0;
+ for(int j = rand_y1; j <= rand_y1+m_event_height; j++) {
+ for(int k = rand_x1; k <= rand_x1+m_event_width; k++) {
+ m_event_cells[i] = j*m_deme_width+k;
+ i++;
+ }
+ }
+ }
m_active = true;
}
@@ -157,3 +174,11 @@
}
return rp;
}
+
+// should be called before organisms in deme are running
+void cDemeCellEvent::ConfineToTimeSlot(int min_delay, int max_delay) {
+ assert(!m_active);
+ assert(max_delay > min_delay);
+
+ m_delay = (m_delay % (max_delay - min_delay)) + min_delay;
+}
Modified: development/source/main/cDemeCellEvent.h
===================================================================
--- development/source/main/cDemeCellEvent.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cDemeCellEvent.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -15,13 +15,14 @@
int m_event_width, m_event_height, m_time_to_live;
bool m_use_gradient, m_active, m_static_pos, m_dead, m_id_set;
std::pair<std::pair<int, int>, std::pair<int, int> > center;
- cDeme* m_deme;
+ cDeme* m_deme;
+ cWorld* m_world;
std::pair<double, double> GetCenter() const;
public:
- cDemeCellEvent() { cDemeCellEvent(-1, -1, -1, -1, 0, 0, 0, 0, true, 0, NULL); m_id_set = false;}
- cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int deme_width, int deme_height, bool static_pos, int time_to_live, cDeme* deme);
+ cDemeCellEvent() { cDemeCellEvent(-1, -1, -1, -1, 0, 0, 0, 0, true, NULL, NULL); }
+ cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int deme_width, int deme_height, bool static_pos, cDeme* deme, cWorld* world);
int GetNextEventCellID();
int GetDelay();
cDeme* GetDeme() const { return m_deme; }
@@ -38,11 +39,13 @@
void SetEventID(int ID) { m_eventID = ID; m_id_set = true;}
void DecayEventIDFromCenter() { m_use_gradient = true; }
- void ActivateEvent(cWorld* m_world);
+ void ActivateEvent();
void DeactivateEvent();
void Terminate() { m_dead = true; }
// gradient generators
double linmap(const double dp, const double ds, const double de, const double rs, const double re) const;
+
+ void ConfineToTimeSlot(int min_delay, int max_delay);
};
#endif
Modified: development/source/main/cOrgInterface.h
===================================================================
--- development/source/main/cOrgInterface.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cOrgInterface.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -59,6 +59,9 @@
virtual cDeme* GetDeme() = 0;
virtual void SetCellID(int in_id) = 0;
virtual void SetDemeID(int in_id) = 0;
+
+ virtual int GetCellData() = 0;
+ virtual void SetCellData(const int newData) = 0;
virtual int GetPrevSeenCellID() = 0;
virtual int GetPrevTaskCellID() = 0;
@@ -69,8 +72,10 @@
virtual bool Divide(cAvidaContext& ctx, cOrganism* parent, cGenome& child_genome) = 0;
virtual cOrganism* GetNeighbor() = 0;
+ virtual bool IsNeighborCellOccupied() = 0;
virtual int GetNumNeighbors() = 0;
virtual int GetFacing() = 0; //!< Returns the facing of this organism.
+ virtual int GetNeighborCellContents() = 0;
virtual void Rotate(int direction = 1) = 0;
virtual void Breakpoint() = 0;
virtual int GetInputAt(int& input_pointer) = 0;
@@ -93,6 +98,9 @@
virtual bool UpdateMerit(double new_merit) = 0;
virtual bool TestOnDivide() = 0;
virtual bool SendMessage(cOrgMessage& msg) = 0;
+
+ virtual bool BcastAlarm(int jump_jabel, int bcast_range) = 0;
+ virtual void DivideOrgTestamentAmongDeme(double value) = 0;
};
Modified: development/source/main/cOrgMovementPredicate.h
===================================================================
--- development/source/main/cOrgMovementPredicate.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cOrgMovementPredicate.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -149,8 +149,8 @@
, m_event_received(false)
, m_stats_updated(false)
, m_events(events)
- , m_total_orgs(1) // TODO: eventually, want to make this a parameter. problem is cPopulation::AddDemePred takes only 1 arg
- , m_total_times(times) {
+ , m_total_times(times)
+ , m_total_orgs(1) { // TODO: eventually, want to make this a parameter. problem is cPopulation::AddDemePred takes only 1 arg
m_event_success.clear();
for(int i = 0; i < m_events.Size(); i++) {
Modified: development/source/main/cOrganism.cc
===================================================================
--- development/source/main/cOrganism.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cOrganism.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -66,13 +66,14 @@
, m_sent_value(0)
, m_sent_active(false)
, m_test_receive_pos(0)
+ , m_pher_drop(false)
, m_max_executed(-1)
, m_is_running(false)
, m_is_sleeping(false)
, m_is_dead(false)
+ , killed_event(false)
, m_net(NULL)
, m_msg(0)
- , m_pher_drop(false)
{
// Initialization of structures...
m_hardware = m_world->GetHardwareManager().Create(this);
@@ -673,3 +674,19 @@
DoOutput(ctx);
} //End cOrganism::Move()
+bool cOrganism::BcastAlarmMSG(cAvidaContext& ctx, int jump_label, int bcast_range) {
+ assert(m_interface);
+
+ // If we're able to succesfully send an alarm...
+ if(m_interface->BcastAlarm(jump_label, bcast_range)) {
+ // check to see if we've performed any tasks...
+ DoOutput(ctx);
+ return true;
+ }
+ return false;
+}
+
+void cOrganism::moveIPtoAlarmLabel(int jump_label) {
+ // move IP to alarm_label
+ m_hardware->Jump_To_Alarm_Label(jump_label);
+}
Modified: development/source/main/cOrganism.h
===================================================================
--- development/source/main/cOrganism.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cOrganism.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -27,6 +27,7 @@
#define cOrganism_h
#include <iostream>
+#include <string>
#include <vector>
#ifndef cCPUMemory_h
@@ -126,6 +127,8 @@
bool m_is_sleeping; // Is this organisms sleeping?
bool m_is_dead; // Is this organism dead?
+ bool killed_event;
+
class cNetSupport
{
public:
@@ -195,8 +198,10 @@
// -------- cOrgInterface Methods --------
cHardwareBase& GetHardware() { return *m_hardware; }
cOrganism* GetNeighbor() { return m_interface->GetNeighbor(); }
+ bool IsNeighborCellOccupied() { return m_interface->IsNeighborCellOccupied(); }
int GetNeighborhoodSize() { return m_interface->GetNumNeighbors(); }
int GetFacing() { assert(m_interface); return m_interface->GetFacing(); } // Returns the facing of this organism.
+ int GetNeighborCellContents() const { return m_interface->GetNeighborCellContents(); }
void Rotate(int direction) { m_interface->Rotate(direction); }
void DoBreakpoint() { m_interface->Breakpoint(); }
int GetNextInput() { return m_interface->GetInputAt(m_input_pointer); }
@@ -223,10 +228,12 @@
int GetPrevTaskCellID() const { return m_interface->GetPrevTaskCellID(); }
void SetPrevSeenCellID(int id) const { m_interface->SetPrevSeenCellID(id); }
void SetPrevTaskCellID(int id) const { m_interface->SetPrevTaskCellID(id); }
- int GetNumTaskCellsReached() const { m_interface->GetNumTaskCellsReached(); }
+ int GetNumTaskCellsReached() const { return m_interface->GetNumTaskCellsReached(); }
void AddReachedTaskCell() { m_interface->AddReachedTaskCell(); }
-
+ int GetCellData() { return m_interface->GetCellData(); }
+ void SetCellData(const int data) { m_interface->SetCellData(data); }
+
// -------- Input and Output Methods --------
void DoInput(const int value);
void DoInput(tBuffer<int>& input_buffer, tBuffer<int>& output_buffer, const int value);
@@ -374,9 +381,17 @@
}
// -------- BDC Movement ---------
-public:
void Move(cAvidaContext& ctx);
+
+ /***** context switch********/
+ bool BcastAlarmMSG(cAvidaContext& ctx, int jump_label, int bcast_range);
+ void moveIPtoAlarmLabel(int jump_label);
+
+ void DivideOrgTestamentAmongDeme(double value) { m_interface->DivideOrgTestamentAmongDeme(value); }
+
+ void SetEventKilled() { killed_event = true; }
+ bool GetEventKilled() { return killed_event; }
};
Modified: development/source/main/cPhenotype.cc
===================================================================
--- development/source/main/cPhenotype.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cPhenotype.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -87,9 +87,10 @@
// 1. These are values calculated at the last divide (of self or offspring)
merit = in_phen.merit;
- executionRatio = in_phen.executionRatio;
+ executionRatio = in_phen.executionRatio;
energy_store = in_phen.energy_store;
energy_tobe_applied = in_phen.energy_tobe_applied;
+ energy_testament = in_phen.energy_testament;
genome_length = in_phen.genome_length;
bonus_instruction_count = in_phen.bonus_instruction_count;
copied_size = in_phen.copied_size;
@@ -261,9 +262,14 @@
{
// Copy divide values from parent, which should already be setup.
merit = parent_phenotype.merit;
- executionRatio = 1.0;
+ if(m_world->GetConfig().INHERIT_EXE_RATE.Get() == 0)
+ executionRatio = 1.0;
+ else
+ executionRatio = parent_phenotype.executionRatio;
+
energy_store = min(energy_store, (double) m_world->GetConfig().ENERGY_CAP.Get());
energy_tobe_applied = 0.0;
+ energy_testament = 0.0;
genome_length = _genome.GetSize();
copied_size = parent_phenotype.child_copied_size;
executed_size = parent_phenotype.executed_size;
@@ -413,6 +419,7 @@
executed_size = genome_length;
energy_store = min(m_world->GetConfig().ENERGY_GIVEN_ON_INJECT.Get(), m_world->GetConfig().ENERGY_CAP.Get());
energy_tobe_applied = 0.0;
+ energy_testament = 0.0;
executionRatio = 1.0;
gestation_time = 0;
gestation_start = 0;
@@ -551,8 +558,10 @@
}
merit = cur_merit_base * cur_bonus;
- //BB:TODO update energy store
SetEnergy(energy_store + cur_energy_bonus);
+ m_world->GetStats().SumEnergyTestamentAcceptedByOrganisms().Add(energy_testament);
+ energy_testament = 0.0;
+
genome_length = _genome.GetSize();
(void) copied_size; // Unchanged
@@ -662,7 +671,7 @@
// A few final changes if the parent was supposed to be be considered
// a second child on the divide.
- if (m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) {
+ if(m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) {
gestation_start = 0;
cpu_cycles_used = 0;
time_used = 0;
@@ -826,9 +835,13 @@
energy_store = clone_phenotype.energy_store;
energy_tobe_applied = 0.0;
- executionRatio = 1.0;
-
- executionRatio = clone_phenotype.executionRatio;
+ energy_testament = 0.0;
+
+ if(m_world->GetConfig().INHERIT_EXE_RATE.Get() == 0)
+ executionRatio = 1.0;
+ else
+ executionRatio = clone_phenotype.executionRatio;
+
genome_length = clone_phenotype.genome_length;
copied_size = clone_phenotype.copied_size;
// copied_size = clone_phenotype.child_copied_size;
@@ -1399,19 +1412,19 @@
energy_store = max(0.0, min(value, (double) m_world->GetConfig().ENERGY_CAP.Get()));
}
-bool cPhenotype::DoubleEnergyUsage(double energy_req) {
- if(GetStoredEnergy() < energy_req) {
- return false;
- }
+void cPhenotype::DoubleEnergyUsage() {
executionRatio *= 2.0;
- return true;
}
void cPhenotype::HalfEnergyUsage() {
executionRatio *= 0.5;
}
+void cPhenotype::DefaultEnergyUsage() {
+ executionRatio = 1.0;
+}
+
/**
Credit organism with energy reward, but only update energy store if APPLY_ENERGY_METHOD = "on task completion" (1)
*/
@@ -1422,6 +1435,8 @@
energy_tobe_applied += cur_energy_bonus;
} else if(m_world->GetConfig().APPLY_ENERGY_METHOD.Get() == 1) {
SetEnergy(energy_store + cur_energy_bonus);
+ m_world->GetStats().SumEnergyTestamentAcceptedByOrganisms().Add(energy_testament);
+ energy_testament = 0.0;
} else {
cerr<< "Unknown APPLY_ENERGY_METHOD value " << m_world->GetConfig().APPLY_ENERGY_METHOD.Get();
exit(-1);
@@ -1432,9 +1447,18 @@
void cPhenotype::ApplyToEnergyStore() {
SetEnergy(energy_store + energy_tobe_applied);
+ m_world->GetStats().SumEnergyTestamentAcceptedByOrganisms().Add(energy_testament);
+ energy_testament = 0.0;
energy_tobe_applied = 0.0;
+ energy_testament = 0.0;
}
+void cPhenotype::EnergyTestament(const double value) {
+ assert(value > 0.0);
+ energy_tobe_applied += value;
+ energy_testament += value;
+} //! external energy given to organism
+
double cPhenotype::ExtractParentEnergy() {
assert(m_world->GetConfig().ENERGY_ENABLED.Get() > 0);
// energy model config variables
@@ -1619,8 +1643,9 @@
}
merit = cur_merit_base * cur_bonus;
- //BB:TODO update energy store
SetEnergy(energy_store + cur_energy_bonus);
+ m_world->GetStats().SumEnergyTestamentAcceptedByOrganisms().Add(energy_testament);
+ energy_testament = 0.0;
genome_length = _genome.GetSize();
gestation_start = time_used;
Modified: development/source/main/cPhenotype.h
===================================================================
--- development/source/main/cPhenotype.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cPhenotype.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -94,7 +94,6 @@
cMerit merit; // Relative speed of CPU
double executionRatio; // ratio of current execution merit over base execution merit
double energy_store; // Amount of energy. Determines relative speed of CPU when turned on.
- double energy_tobe_applied; //Energy that has not yet been added to energy store.
int genome_length; // Number of instructions in genome.
int bonus_instruction_count; // Number of times MERIT_BONUS_INT is in genome.
int copied_size; // Instructions copied into genome.
@@ -108,6 +107,8 @@
// 2. These are "in progress" variables, updated as the organism operates
double cur_bonus; // Current Bonus
double cur_energy_bonus; // Current energy bonus
+ double energy_tobe_applied; // Energy that has not yet been added to energy store.
+ double energy_testament;
int cur_num_errors; // Total instructions executed illeagally.
int cur_num_donates; // Number of donations so far
tArray<int> cur_task_count; // Total times each task was performed
@@ -458,10 +459,13 @@
bool& ChildFertile() { assert(initialized == true); return child_fertile; }
bool& IsMultiThread() { assert(initialized == true); return is_multi_thread; }
- bool DoubleEnergyUsage(double inst_energy_cost);
+ void DoubleEnergyUsage();
void HalfEnergyUsage();
+ void DefaultEnergyUsage();
+
void RefreshEnergy();
void ApplyToEnergyStore();
+ void EnergyTestament(const double value); //! external energy given to organism
double ExtractParentEnergy();
bool operator<(const cPhenotype& rhs) const;
Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cPopulation.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -100,13 +100,13 @@
if (world->GetVerbosity() > VERBOSE_NORMAL) {
cout << "Building world " << world_x << "x" << world_y << " = " << num_cells << " organisms." << endl;
switch(geometry) {
- case nGeometry::GRID: { cout << "Geometry: Bounded grid" << endl; break; }
- case nGeometry::TORUS: { cout << "Geometry: Torus" << endl; break; }
- case nGeometry::CLIQUE: { cout << "Geometry: Clique" << endl; break; }
- case nGeometry::HEX: { cout << "Geometry: Hex" << endl; break; }
- default:
- cout << "Unknown geometry!" << endl;
- assert(false);
+ case nGeometry::GRID: { cout << "Geometry: Bounded grid" << endl; break; }
+ case nGeometry::TORUS: { cout << "Geometry: Torus" << endl; break; }
+ case nGeometry::CLIQUE: { cout << "Geometry: Clique" << endl; break; }
+ case nGeometry::HEX: { cout << "Geometry: Hex" << endl; break; }
+ default:
+ cout << "Unknown geometry!" << endl;
+ assert(false);
}
}
@@ -114,7 +114,7 @@
if (num_demes <= 0) {
num_demes = 1; // One population == one deme.
}
-
+
// The following combination of options creates an infinite rotate-loop:
assert(!((m_world->GetConfig().DEMES_ORGANISM_PLACEMENT.Get()==0)
&& (m_world->GetConfig().DEMES_ORGANISM_FACING.Get()==1)
@@ -130,7 +130,7 @@
#ifdef DEBUG
const int birth_method = m_world->GetConfig().BIRTH_METHOD.Get();
-
+
if(num_demes > 1) {
assert(birth_method != POSITION_CHILD_FULL_SOUP_ELDEST);
}
@@ -178,23 +178,23 @@
// We're cheating here; we're using the random access nature of an iterator
// to index beyond the end of the cell_array.
switch(geometry) {
- case nGeometry::GRID:
- build_grid(&cell_array.begin()[i], &cell_array.begin()[i+deme_size], deme_size_x, deme_size_y);
- break;
- case nGeometry::TORUS:
- build_torus(&cell_array.begin()[i], &cell_array.begin()[i+deme_size], deme_size_x, deme_size_y);
- break;
- case nGeometry::CLIQUE:
- build_clique(&cell_array.begin()[i], &cell_array.begin()[i+deme_size], deme_size_x, deme_size_y);
- break;
- case nGeometry::HEX:
- build_hex(&cell_array.begin()[i], &cell_array.begin()[i+deme_size], deme_size_x, deme_size_y);
- break;
- default:
- assert(false);
+ case nGeometry::GRID:
+ build_grid(&cell_array.begin()[i], &cell_array.begin()[i+deme_size], deme_size_x, deme_size_y);
+ break;
+ case nGeometry::TORUS:
+ build_torus(&cell_array.begin()[i], &cell_array.begin()[i+deme_size], deme_size_x, deme_size_y);
+ break;
+ case nGeometry::CLIQUE:
+ build_clique(&cell_array.begin()[i], &cell_array.begin()[i+deme_size], deme_size_x, deme_size_y);
+ break;
+ case nGeometry::HEX:
+ build_hex(&cell_array.begin()[i], &cell_array.begin()[i+deme_size], deme_size_x, deme_size_y);
+ break;
+ default:
+ assert(false);
}
}
-
+
BuildTimeSlicer(0);
// Setup the resources...
@@ -202,7 +202,7 @@
int global_res_index = -1;
int deme_res_index = -1;
int num_deme_res = 0;
-
+
//setting size of global and deme-level resources
for(int i = 0; i < resource_lib.GetSize(); i++) {
cResource * res = resource_lib.GetResource(i);
@@ -219,7 +219,7 @@
GetDeme(i).SetDemeResourceCount(tmp_deme_res_count);
GetDeme(i).ResizeSpatialGrids(deme_size_x, deme_size_y);
}
-
+
for (int i = 0; i < resource_lib.GetSize(); i++) {
cResource * res = resource_lib.GetResource(i);
if (!res->GetDemeResource()) {
@@ -247,16 +247,16 @@
exit(1);
}
}
-
+
}
void cPopulation::InitiatePop() {
-
+
// Load a clone if one is provided, otherwise setup start organism.
if (m_world->GetConfig().CLONE_FILE.Get() == "-" || m_world->GetConfig().CLONE_FILE.Get() == "") {
cGenome start_org(0);
const cString& filename = m_world->GetConfig().START_CREATURE.Get();
-
+
if (filename != "-" && filename != "") {
if (!cGenomeUtil::LoadGenome(filename, m_world->GetHardwareManager().GetInstSet(), start_org)) {
cerr << "Error: Unable to load start creature" << endl;
@@ -299,7 +299,7 @@
{
if (m_world->GetConfig().FASTFORWARD_NUM_ORGS.Get() > 0 && GetNumOrganisms() >= m_world->GetConfig().FASTFORWARD_NUM_ORGS.Get())
{
- return true;
+ return true;
}
assert(&parent_organism != NULL);
@@ -361,7 +361,7 @@
// Reset inputs and re-calculate merit if required
if (m_world->GetConfig().RESET_INPUTS_ON_DIVIDE.Get() > 0){
environment.SetupInputs(ctx, parent_cell.m_inputs);
-
+
int pc_phenotype = m_world->GetConfig().PRECALC_PHENOTYPE.Get();
if (pc_phenotype){
cCPUTestInfo test_info;
@@ -404,7 +404,7 @@
//@JEB - we may want to pass along some state information from parent to child
if ( (m_world->GetConfig().EPIGENETIC_METHOD.Get() == EPIGENETIC_METHOD_OFFSPRING)
- || (m_world->GetConfig().EPIGENETIC_METHOD.Get() == EPIGENETIC_METHOD_BOTH) ) {
+ || (m_world->GetConfig().EPIGENETIC_METHOD.Get() == EPIGENETIC_METHOD_BOTH) ) {
child_array[i]->GetHardware().InheritState(parent_organism.GetHardware());
}
@@ -463,7 +463,7 @@
{
assert(in_organism != NULL);
assert(in_organism->GetGenome().GetSize() >= 1);
-
+
in_organism->SetOrgInterface(new cPopulationInterface(m_world));
// If the organism does not have a genotype, give it one! No parent
@@ -491,7 +491,7 @@
// Setup the inputs in the target cell.
environment.SetupInputs(ctx, target_cell.m_inputs);
-
+
// Precalculate the phenotype if requested
int pc_phenotype = m_world->GetConfig().PRECALC_PHENOTYPE.Get();
if (pc_phenotype){
@@ -508,7 +508,7 @@
delete test_cpu;
}
// Update the archive...
-
+
in_genotype->AddOrganism();
if (old_genotype != NULL) {
@@ -527,7 +527,7 @@
// Keep track of statistics for organism counts...
num_organisms++;
-
+
if (deme_array.GetSize() > 0) {
deme_array[target_cell.GetDemeID()].IncOrgCount();
}
@@ -568,7 +568,7 @@
#ifdef DEBBUG
int sID, dID, xx1, yy1, xx2, yy2;
#endif
-
+
// Swap inputs between cells to fix bus error when Avidian moves into an unoccupied cell
environment.SwapInputs(ctx, src_cell.m_inputs, dest_cell.m_inputs);
@@ -583,13 +583,13 @@
actualNeighborhoodSize = 8;
}
}
-
+
// Swap cell facings between cells, so that if movement is directed, it continues to be associated with
// the same organism
// Determine absolute facing for each cell
fromFacing = src_cell.GetFacing();
destFacing = dest_cell.GetFacing();
-
+
// Set facing in source cell
success = 0;
newFacing = destFacing;
@@ -603,7 +603,7 @@
break;
}
}
-// @DMB this doesn't compile properly -- #ifdef DEBUG
+ // @DMB this doesn't compile properly -- #ifdef DEBUG
#if 0
if (!success) {
sID = src_cell.GetID();
@@ -622,32 +622,32 @@
}
#endif
- // Set facing in destinatiion cell
- success = 0;
- newFacing = fromFacing;
- for(int i = 0; i < actualNeighborhoodSize; i++) {
- if (dest_cell.GetFacing() != newFacing) {
- dest_cell.ConnectionList().CircNext();
- // cout << "MO: dest_cell facing not yet at " << newFacing << endl;
- } else {
- // cout << "MO: dest_cell facing successfully set to " << newFacing << endl;
- success = 1;
- break;
- }
+// Set facing in destinatiion cell
+success = 0;
+newFacing = fromFacing;
+for(int i = 0; i < actualNeighborhoodSize; i++) {
+ if (dest_cell.GetFacing() != newFacing) {
+ dest_cell.ConnectionList().CircNext();
+ // cout << "MO: dest_cell facing not yet at " << newFacing << endl;
+ } else {
+ // cout << "MO: dest_cell facing successfully set to " << newFacing << endl;
+ success = 1;
+ break;
}
+}
// @DMB this doesn't compile properly -- #ifdef DEBUG
#if 0
- if (!success) {
- sID = src_cell.GetID();
- dID = dest_cell.GetID();
- src_cell.GetPosition(xx1,yy1);
- dest_cell.GetPosition(xx2,yy2);
- if (1 == abs(xx2-xx1)+abs(yy2-yy1)) {
- cout << "MO: src: " << sID << "@ (" << xx1 << "," << yy1 << ") dest: " << dID << "@ (" << xx2 << "," << yy2 << "), FAILED to set dest_cell facing to " << newFacing << endl;
- }
+if (!success) {
+ sID = src_cell.GetID();
+ dID = dest_cell.GetID();
+ src_cell.GetPosition(xx1,yy1);
+ dest_cell.GetPosition(xx2,yy2);
+ if (1 == abs(xx2-xx1)+abs(yy2-yy1)) {
+ cout << "MO: src: " << sID << "@ (" << xx1 << "," << yy1 << ") dest: " << dID << "@ (" << xx2 << "," << yy2 << "), FAILED to set dest_cell facing to " << newFacing << endl;
}
+}
#endif
-
+
}
void cPopulation::KillOrganism(cPopulationCell& in_cell)
@@ -661,10 +661,10 @@
m_world->GetStats().RecordDeath();
int cellID = in_cell.GetID();
-
- if(GetCell(cellID).GetOrganism()->IsSleeping()) {
- GetCell(cellID).GetOrganism()->SetSleeping(false);
- m_world->GetStats().decNumAsleep(GetCell(cellID).GetDemeID());
+
+ if(organism->IsSleeping()) {
+ organism->SetSleeping(false);
+ organism->GetOrgInterface().GetDeme()->DecSleepingCount();
}
if(m_world->GetConfig().LOG_SLEEP_TIMES.Get() == 1) {
if(sleep_log[cellID].Size() > 0) {
@@ -675,19 +675,18 @@
}
}
-
tList<tListNode<cSaleItem> >* sold_items = organism->GetSoldItems();
if (sold_items)
{
- tListIterator<tListNode<cSaleItem> > sold_it(*sold_items);
- tListNode<cSaleItem> * test_node;
+ tListIterator<tListNode<cSaleItem> > sold_it(*sold_items);
+ tListNode<cSaleItem> * test_node;
- while ( (test_node = sold_it.Next()) != NULL)
- {
+ while ( (test_node = sold_it.Next()) != NULL)
+ {
tListIterator<cSaleItem> market_it(market[test_node->data->GetLabel()]);
market_it.Set(test_node);
delete market_it.Remove();
- }
+ }
}
// Do the lineage handling
if (m_world->GetConfig().LOG_LINEAGES.Get()) { m_world->GetClassificationManager().RemoveLineageOrganism(organism); }
@@ -761,78 +760,78 @@
void cPopulation::AddSellValue(const int data, const int label, const int sell_price, const int org_id, const int cell_id)
{
- // find list under appropriate label, labels more than 8 nops long are simply the same
- // as a smaller label modded by the market size
- //int pos = label % market.GetSize();
+ // find list under appropriate label, labels more than 8 nops long are simply the same
+ // as a smaller label modded by the market size
+ //int pos = label % market.GetSize();
- //// id of genotype currently residing in cell that seller live(d) in compared to
- //// id of genotype of actual seller, if different than seller is dead, remove item from list
- //while ( market[pos].GetSize() > 0 &&
- // (!GetCell(market[pos].GetFirst()->GetCellID()).IsOccupied() ||
- // GetCell(market[pos].GetFirst()->GetCellID()).GetOrganism()->GetID()
- // != market[pos].GetFirst()->GetOrgID()) )
- //{
- // market[pos].Pop();
- //}
+ //// id of genotype currently residing in cell that seller live(d) in compared to
+ //// id of genotype of actual seller, if different than seller is dead, remove item from list
+ //while ( market[pos].GetSize() > 0 &&
+ // (!GetCell(market[pos].GetFirst()->GetCellID()).IsOccupied() ||
+ // GetCell(market[pos].GetFirst()->GetCellID()).GetOrganism()->GetID()
+ // != market[pos].GetFirst()->GetOrgID()) )
+ //{
+ // market[pos].Pop();
+ //}
- // create sale item
- cSaleItem *new_item = new cSaleItem(data, label, sell_price, org_id, cell_id);
+ // create sale item
+ cSaleItem *new_item = new cSaleItem(data, label, sell_price, org_id, cell_id);
- // place into array by label, array is big enough for labels up to 8 nops long
- tListNode<cSaleItem>* sell_node = market[label].PushRear(new_item);
- tListNode<tListNode<cSaleItem> >* org_node = GetCell(cell_id).GetOrganism()->AddSoldItem(sell_node);
- sell_node->data->SetNodePtr(org_node);
+ // place into array by label, array is big enough for labels up to 8 nops long
+ tListNode<cSaleItem>* sell_node = market[label].PushRear(new_item);
+ tListNode<tListNode<cSaleItem> >* org_node = GetCell(cell_id).GetOrganism()->AddSoldItem(sell_node);
+ sell_node->data->SetNodePtr(org_node);
- //:7 for Kolby
+ //:7 for Kolby
}
int cPopulation::BuyValue(const int label, const int buy_price, const int cell_id)
{
- // find list under appropriate label, labels more than 8 nops long are simply the same
- // as a smaller label modded by the market size
- //int pos = label % market.GetSize();
+ // find list under appropriate label, labels more than 8 nops long are simply the same
+ // as a smaller label modded by the market size
+ //int pos = label % market.GetSize();
- //// id of genotype currently residing in cell that seller live(d) in compared to
- //// id of genotype of actual seller, if different than seller is dead, remove item from list
- //while ( market[pos].GetSize() > 0 &&
- // (!GetCell(market[pos].GetFirst()->GetCellID()).IsOccupied() ||
- // GetCell(market[pos].GetFirst()->GetCellID()).GetOrganism()->GetID()
- // != market[pos].GetFirst()->GetOrgID()) )
- //{
- // market[pos].Pop();
- //}
+ //// id of genotype currently residing in cell that seller live(d) in compared to
+ //// id of genotype of actual seller, if different than seller is dead, remove item from list
+ //while ( market[pos].GetSize() > 0 &&
+ // (!GetCell(market[pos].GetFirst()->GetCellID()).IsOccupied() ||
+ // GetCell(market[pos].GetFirst()->GetCellID()).GetOrganism()->GetID()
+ // != market[pos].GetFirst()->GetOrgID()) )
+ //{
+ // market[pos].Pop();
+ //}
- // if there's nothing in the list don't bother with rest
- if (market[label].GetSize() <= 0)
- return 0;
+ // if there's nothing in the list don't bother with rest
+ if (market[label].GetSize() <= 0)
+ return 0;
- // if the sell price is higher than we're willing to pay no purchase made
- if (market[label].GetFirst()->GetPrice() > buy_price)
- return 0;
+ // if the sell price is higher than we're willing to pay no purchase made
+ if (market[label].GetFirst()->GetPrice() > buy_price)
+ return 0;
- // if the buy price is higher than buying org's current merit no purchase made
- if (GetCell(cell_id).GetOrganism()->GetPhenotype().GetMerit().GetDouble() < buy_price)
- return 0;
+ // if the buy price is higher than buying org's current merit no purchase made
+ if (GetCell(cell_id).GetOrganism()->GetPhenotype().GetMerit().GetDouble() < buy_price)
+ return 0;
- // otherwise transaction should be completed!
- cSaleItem* chosen = market[label].Pop();
- tListIterator<tListNode<cSaleItem> > sold_it(*GetCell(chosen->GetCellID()).GetOrganism()->GetSoldItems());
- sold_it.Set(chosen->GetNodePtr());
- sold_it.Remove();
+ // otherwise transaction should be completed!
+ cSaleItem* chosen = market[label].Pop();
+ tListIterator<tListNode<cSaleItem> > sold_it(*GetCell(chosen->GetCellID()).GetOrganism()->GetSoldItems());
+ sold_it.Set(chosen->GetNodePtr());
+ sold_it.Remove();
- // first update sellers merit
- double cur_merit = GetCell(chosen->GetCellID()).GetOrganism()->GetPhenotype().GetMerit().GetDouble();
- cur_merit += buy_price;
-
- GetCell(chosen->GetCellID()).GetOrganism()->UpdateMerit(cur_merit);
-
- // next remove sold item from list in market
- //market[pos].Remove(chosen);
+ // first update sellers merit
+ double cur_merit = GetCell(chosen->GetCellID()).GetOrganism()->GetPhenotype().GetMerit().GetDouble();
+ cur_merit += buy_price;
+ GetCell(chosen->GetCellID()).GetOrganism()->UpdateMerit(cur_merit);
- // finally return recieve value, buyer merit will be updated if return a valid value here
- int receive_value = chosen->GetData();
- return receive_value;
+ // next remove sold item from list in market
+ //market[pos].Remove(chosen);
+
+
+ // finally return recieve value, buyer merit will be updated if return a valid value here
+ int receive_value = chosen->GetData();
+ return receive_value;
}
void cPopulation::SwapCells(cPopulationCell & cell1, cPopulationCell & cell2)
@@ -938,7 +937,7 @@
}
break;
case 4: // deme fitness = 2^(-deme fitness rank)
- // first find all the deme fitness values ...
+ // first find all the deme fitness values ...
{
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cDoubleSum single_deme_fitness;
@@ -1067,6 +1066,11 @@
cDeme & from_deme = deme_array[from_deme_id];
cDeme & to_deme = deme_array[to_deme_id];
+
+ /// ReplaceDeme(cDeme& source_deme, cDeme& target_deme)
+
+
+
// Do the actual copy!
for (int i = 0; i < from_deme.GetSize(); i++) {
int from_cell_id = from_deme.GetCellID(i);
@@ -1098,19 +1102,19 @@
/*! Compete all demes with each other based on the given vector of fitness values.
-
- This form of compete demes uses fitness-proportional selection on a vector of deme
- fitnesses for group selection. It integrates with the various deme replication options
- used in ReplicateDemes.
-
- Note: New deme competition fitness functions are added in PopulationActions.cc by subclassing
- cActionAbstractCompeteDemes and overriding cActionAbstractCompeteDemes::Fitness(cDeme&). (Don't forget
- to register the action and add it to the events file).
-
- Another note: To mimic the behavior of the other version of CompeteDemes (which is kept around
- for backwards compatibility), change the config option DEMES_REPLICATE_SIZE to be the size of
- each deme.
- */
+
+This form of compete demes uses fitness-proportional selection on a vector of deme
+fitnesses for group selection. It integrates with the various deme replication options
+used in ReplicateDemes.
+
+Note: New deme competition fitness functions are added in PopulationActions.cc by subclassing
+cActionAbstractCompeteDemes and overriding cActionAbstractCompeteDemes::Fitness(cDeme&). (Don't forget
+ to register the action and add it to the events file).
+
+Another note: To mimic the behavior of the other version of CompeteDemes (which is kept around
+ for backwards compatibility), change the config option DEMES_REPLICATE_SIZE to be the size of
+each deme.
+*/
void cPopulation::CompeteDemes(const std::vector<double>& fitness) {
// Each deme must have a fitness:
assert((int)fitness.size() == deme_array.GetSize());
@@ -1181,6 +1185,7 @@
3: 'deme-age' - ...demes who have reached their maximum age
4: 'birth-count' ...demes that have had a certain number of births.
5: 'sat-mov-pred'...demes whose movement predicate was previously satisfied
+6: 'events-killed' ...demes that have killed a certian number of events
*/
@@ -1229,6 +1234,22 @@
if(!(source_deme.MovPredSatisfiedPreviously())) continue;
break;
}
+ case 6: {
+ int currentSlotSuccessful = 0;
+ double kill_ratio = 0.0;
+
+ if(source_deme.GetSlotFlowRate() == 0)
+ kill_ratio = 1.0;
+ else
+ kill_ratio = static_cast<double>(source_deme.GetEventsKilledThisSlot()) / static_cast<double>(source_deme.GetSlotFlowRate());
+
+ if(kill_ratio >= m_world->GetConfig().DEMES_MIM_EVENTS_KILLED_RATIO.Get())
+ currentSlotSuccessful = 1;
+
+ // Replicate demes that have killed a certain number of event.
+ if(source_deme.GetConsecutiveSuccessfulEventPeriods()+currentSlotSuccessful < m_world->GetConfig().DEMES_MIM_SUCCESSFUL_EVENT_PERIODS.Get()) continue;
+ break;
+ }
default: {
cerr << "ERROR: Invalid replication trigger " << rep_trigger
<< " in cPopulation::ReplicateDemes()" << endl;
@@ -1244,70 +1265,72 @@
*/
void cPopulation::ReplicateDeme(cDeme & source_deme)
{
- // Doesn't make sense to try and replicate a deme that *has no organisms*.
- if(source_deme.IsEmpty()) return;
+ // Doesn't make sense to try and replicate a deme that *has no organisms*.
+ if(source_deme.IsEmpty()) return;
+
+ // Prevent sterile demes from replicating.
+ if(m_world->GetConfig().DEMES_PREVENT_STERILE.Get() && (source_deme.GetBirthCount() == 0)) {
+ // assumes that all group level tasks cannot be solved by a single organism
+ source_deme.KillAll();
+ return;
+ }
+
+ //Option to bridge between kin and group selection.
+ if (m_world->GetConfig().DEMES_REPLICATION_ONLY_RESETS.Get())
+ {
+ //Reset deme (resources and births, among other things)
+ bool source_deme_resource_reset = m_world->GetConfig().DEMES_RESET_RESOURCES.Get() == 0;
+ source_deme.DivideReset(source_deme, source_deme_resource_reset);
- // Prevent sterile demes from replicating.
- if(m_world->GetConfig().DEMES_PREVENT_STERILE.Get() && (source_deme.GetBirthCount() == 0)) {
- return;
- }
-
- //Option to bridge between kin and group selection.
- if (m_world->GetConfig().DEMES_REPLICATION_ONLY_RESETS.Get())
- {
- //Reset deme (resources and births, among other things)
- bool source_deme_resource_reset = m_world->GetConfig().DEMES_RESET_RESOURCES.Get() == 0;
- source_deme.DivideReset(source_deme, source_deme_resource_reset);
-
- //Reset all organisms in deme, by re-injecting them?
- if (m_world->GetConfig().DEMES_REPLICATION_ONLY_RESETS.Get() == 2) {
- for (int i=0; i<source_deme.GetSize(); i++) {
- int cellid = source_deme.GetCellID(i);
- if (GetCell(cellid).IsOccupied()) {
- int lineage = GetCell(cellid).GetOrganism()->GetLineageLabel();
- cGenome genome = GetCell(cellid).GetOrganism()->GetGenome();
- InjectGenome(cellid, genome, lineage);
- }
+ //Reset all organisms in deme, by re-injecting them?
+ if (m_world->GetConfig().DEMES_REPLICATION_ONLY_RESETS.Get() == 2) {
+ for (int i=0; i<source_deme.GetSize(); i++) {
+ int cellid = source_deme.GetCellID(i);
+ if (GetCell(cellid).IsOccupied()) {
+ int lineage = GetCell(cellid).GetOrganism()->GetLineageLabel();
+ cGenome genome = GetCell(cellid).GetOrganism()->GetGenome();
+ InjectGenome(cellid, genome, lineage);
}
}
- return;
}
+ return;
+ }
+
+ // Pick a target deme to replicate to, making sure that
+ // we don't try to replicate over ourself, i.e. DEMES_REPLACE_PARENT 0
+
+ int target_id = -1;
+ if (m_world->GetConfig().DEMES_PREFER_EMPTY.Get()) {
- // Pick a target deme to replicate to, making sure that
- // we don't try to replicate over ourself, i.e. DEMES_REPLACE_PARENT 0
-
- int target_id = -1;
- if (m_world->GetConfig().DEMES_PREFER_EMPTY.Get()) {
-
- //@JEB -- use empty_cell_id_array to hold empty demes
- //so we don't have to allocate a list
- int num_empty = 0;
- for (int i=0; i<GetNumDemes(); i++) {
- if (GetDeme(i).IsEmpty()) {
- empty_cell_id_array[num_empty] = i;
- num_empty++;
- }
- }
- if (num_empty > 0) {
- target_id = empty_cell_id_array[m_world->GetRandom().GetUInt(num_empty)];
+ //@JEB -- use empty_cell_id_array to hold empty demes
+ //so we don't have to allocate a list
+ int num_empty = 0;
+ for (int i=0; i<GetNumDemes(); i++) {
+ if (GetDeme(i).IsEmpty()) {
+ empty_cell_id_array[num_empty] = i;
+ num_empty++;
}
+ }
+ if (num_empty > 0) {
+ target_id = empty_cell_id_array[m_world->GetRandom().GetUInt(num_empty)];
}
-
- // if we haven't found one yet, choose a random one
- if (target_id == -1) {
- target_id = source_deme.GetID();
- const int num_demes = GetNumDemes();
- while(target_id == source_deme.GetID()) {
- target_id = m_world->GetRandom().GetUInt(num_demes);
- }
+ }
+
+ // if we haven't found one yet, choose a random one
+ if (target_id == -1) {
+ target_id = source_deme.GetID();
+ const int num_demes = GetNumDemes();
+ while(target_id == source_deme.GetID()) {
+ target_id = m_world->GetRandom().GetUInt(num_demes);
}
- ReplaceDeme(source_deme, deme_array[target_id]);
+ }
+ ReplaceDeme(source_deme, deme_array[target_id]);
}
/*! ReplaceDeme is a helper method that handles all the different configuration
options related to the replacement of a target deme by a source. It works with
both CompeteDemes and ReplicateDemes (and can be called directly via an event if
-so desired).
+ so desired).
@refactor Replace manual mutation with strategy pattern.
*/
@@ -1319,7 +1342,8 @@
// used to pass energy to offspring demes (set to zero if energy model is not enabled)
double source_deme_energy(0.0), deme_energy_decay(0.0), parent_deme_energy(0.0), offspring_deme_energy(0.0);
if(m_world->GetConfig().ENERGY_ENABLED.Get()) {
- source_deme_energy = source_deme.CalculateTotalEnergy();
+ source_deme_energy = source_deme.CalculateTotalEnergy() + source_deme.GetTotalEnergyTestament();
+ m_world->GetStats().SumEnergyTestamentAcceptedByDeme().Add(source_deme.GetTotalEnergyTestament());
deme_energy_decay = 1.0 - m_world->GetConfig().FRAC_ENERGY_DECAY_AT_DEME_BIRTH.Get();
parent_deme_energy = source_deme_energy * deme_energy_decay * (1.0 - m_world->GetConfig().FRAC_PARENT_ENERGY_GIVEN_TO_DEME_AT_BIRTH.Get());
offspring_deme_energy = source_deme_energy * deme_energy_decay * m_world->GetConfig().FRAC_PARENT_ENERGY_GIVEN_TO_DEME_AT_BIRTH.Get();
@@ -1359,7 +1383,7 @@
// mutated germ to ONLY the target's germline. The source remains unchanged.
target_deme.ReplaceGermline(source_deme.GetGermline());
target_deme.GetGermline().Add(next_germ);
-
+
// Germline stats tracking.
m_world->GetStats().GermlineReplication(source_deme.GetGermline(), target_deme.GetGermline());
@@ -1406,12 +1430,12 @@
target_deme.ReplaceGermline(*new_germline_genotype);
SeedDeme(source_deme, *new_germline_genotype);
SeedDeme(target_deme, *new_germline_genotype);
-
+
} else {
// Not using germlines; things are much simpler. Seed the target from the source.
target_successfully_seeded = SeedDeme(source_deme, target_deme);
}
-
+
// The source's merit must be transferred to the target, and then the source has
// to rotate its heritable merit to its current merit.
if (target_successfully_seeded) target_deme.UpdateDemeMerit(source_deme);
@@ -1448,8 +1472,8 @@
if (target_successfully_seeded) target_deme.DivideReset(source_deme, target_deme_resource_reset);
source_deme.DivideReset(source_deme, source_deme_resource_reset);
}
-
+
// do our post-replication stats tracking.
m_world->GetStats().DemePostReplication(source_deme, target_deme);
}
@@ -1495,13 +1519,13 @@
*/
bool cPopulation::SeedDeme(cDeme& source_deme, cDeme& target_deme) {
cRandom& random = m_world->GetRandom();
-
+
bool successfully_seeded = true;
-
+
// Check to see if we're doing probabilistic organism replication from source
// to target deme.
if(m_world->GetConfig().DEMES_PROB_ORG_TRANSFER.Get() == 0.0) {
-
+
//@JEB -- old method is default for consistency!
if (m_world->GetConfig().DEMES_SEED_METHOD.Get() == 0) {
// Here's the idea: store up a list of the genotypes from the source that we
@@ -1518,10 +1542,10 @@
// because the cGenotype* from cOrganism::GetGenotype may not live after
// a call to cDeme::KillAll.
std::vector<std::pair<cGenome,int> > xfer; // List of genomes we're going to transfer.
-
+
switch(m_world->GetConfig().DEMES_ORGANISM_SELECTION.Get()) {
case 0: { // Random w/ replacement (meaning, we don't prevent the same genotype from
- // being selected more than once).
+ // being selected more than once).
while((int)xfer.size() < m_world->GetConfig().DEMES_REPLICATE_SIZE.Get()) {
int cellid = source_deme.GetCellID(random.GetUInt(source_deme.GetSize()));
if(cell_array[cellid].IsOccupied()) {
@@ -1543,7 +1567,7 @@
}
default: {
cout << "Undefined value (" << m_world->GetConfig().DEMES_ORGANISM_SELECTION.Get()
- << ") for DEMES_ORGANISM_SELECTION." << endl;
+ << ") for DEMES_ORGANISM_SELECTION." << endl;
exit(1);
}
}
@@ -1553,23 +1577,24 @@
// Clear the demes.
source_deme.UpdateStats();
source_deme.KillAll();
-
+
target_deme.UpdateStats();
target_deme.KillAll();
-
+
// And now populate the source and target.
int j=0;
for(std::vector<std::pair<cGenome,int> >::iterator i=xfer.begin(); i!=xfer.end(); ++i, ++j) {
int cellid = DemeSelectInjectionCell(source_deme, j);
InjectGenome(cellid, i->first, i->second);
DemePostInjection(source_deme, cell_array[cellid]);
-
+
cellid = DemeSelectInjectionCell(target_deme, j);
InjectGenome(cellid, i->first, i->second);
DemePostInjection(target_deme, cell_array[cellid]);
+
}
} else /* if (m_world->GetConfig().DEMES_SEED_METHOD.Get() != 0) */{
-
+
// @JEB
// Updated seed deme method that maintains genotype inheritance.
@@ -1577,57 +1602,57 @@
tArray<cOrganism*> source_founders; // List of organisms we're going to transfer.
tArray<cOrganism*> target_founders; // List of organisms we're going to transfer.
- /*
- // Debug Code
- cGenotype * original_source_founder_genotype = NULL;
- if (1) {
- tArray<int>& source_founders = source_deme.GetFounderGenotypeIDs();
- if (source_founders.GetSize() > 0) {
- original_source_founder_genotype = m_world->GetClassificationManager().FindGenotype(source_founders[0]);
- cout << "Source:" << endl << original_source_founder_genotype->GetGenome().AsString() << endl;
- }
- tArray<int>& target_founders = target_deme.GetFounderGenotypeIDs();
- if (target_founders.GetSize() > 0) {
- cGenotype * target_founder_genotype = m_world->GetClassificationManager().FindGenotype(target_founders[0]);
- cout << "Target:" << endl << target_founder_genotype->GetGenome().AsString() << endl;
- }
- }
-
- tArray<int>& source_founders = source_deme.GetFounders();
- cerr << "Original source genotype ids:" << endl;
- for(int i=0; i<source_founders.GetSize(); i++) {
- cerr << source_founders[i] << " ";
- }
- cerr << endl;
-
- tArray<int>& target_founders = target_deme.GetFounders();
- cerr << "Original target genotype ids:" << endl;
- for(int i=0; i<target_founders.GetSize(); i++) {
- cerr << target_founders[i] << " ";
- }
- cerr << endl;
+ /*
+ // Debug Code
+ cGenotype * original_source_founder_genotype = NULL;
+ if (1) {
+ tArray<int>& source_founders = source_deme.GetFounderGenotypeIDs();
+ if (source_founders.GetSize() > 0) {
+ original_source_founder_genotype = m_world->GetClassificationManager().FindGenotype(source_founders[0]);
+ cout << "Source:" << endl << original_source_founder_genotype->GetGenome().AsString() << endl;
+ }
+ tArray<int>& target_founders = target_deme.GetFounderGenotypeIDs();
+ if (target_founders.GetSize() > 0) {
+ cGenotype * target_founder_genotype = m_world->GetClassificationManager().FindGenotype(target_founders[0]);
+ cout << "Target:" << endl << target_founder_genotype->GetGenome().AsString() << endl;
+ }
+ }
+
+ tArray<int>& source_founders = source_deme.GetFounders();
+ cerr << "Original source genotype ids:" << endl;
+ for(int i=0; i<source_founders.GetSize(); i++) {
+ cerr << source_founders[i] << " ";
+ }
+ cerr << endl;
+
+ tArray<int>& target_founders = target_deme.GetFounders();
+ cerr << "Original target genotype ids:" << endl;
+ for(int i=0; i<target_founders.GetSize(); i++) {
+ cerr << target_founders[i] << " ";
+ }
+ cerr << endl;
+
+ // Debug Code
+ //// Count the number of orgs in each deme.
+ int count = 0;
+ for(int i=0; i<target_deme.GetSize(); ++i) {
+ int cell_id = target_deme.GetCellID(i);
+ if(cell_array[cell_id].IsOccupied()) count++;
+ }
+ cout << "Initial orgs in target deme: " << count << endl;
+
+ count = 0;
+ for(int i=0; i<source_deme.GetSize(); ++i) {
+ int cell_id = source_deme.GetCellID(i);
+ if(cell_array[cell_id].IsOccupied()) count++;
+ }
+ cout << "Initial orgs in source deme: " << count << endl;
+ */
- // Debug Code
- //// Count the number of orgs in each deme.
- int count = 0;
- for(int i=0; i<target_deme.GetSize(); ++i) {
- int cell_id = target_deme.GetCellID(i);
- if(cell_array[cell_id].IsOccupied()) count++;
- }
- cout << "Initial orgs in target deme: " << count << endl;
-
- count = 0;
- for(int i=0; i<source_deme.GetSize(); ++i) {
- int cell_id = source_deme.GetCellID(i);
- if(cell_array[cell_id].IsOccupied()) count++;
- }
- cout << "Initial orgs in source deme: " << count << endl;
- */
-
switch(m_world->GetConfig().DEMES_ORGANISM_SELECTION.Get()) {
case 0: { // Random w/ replacement (meaning, we don't prevent the same genotype from
- // being selected more than once).
+ // being selected more than once).
tArray<cOrganism*> founders; // List of organisms we're going to transfer.
while(founders.GetSize() < m_world->GetConfig().DEMES_REPLICATE_SIZE.Get()) {
int cellid = source_deme.GetCellID(random.GetUInt(source_deme.GetSize()));
@@ -1656,34 +1681,34 @@
//Die if not >= two organisms.
if (source_deme.GetOrgCount() >= 2) {
-
+
//Collect prospective founder organisms into a list
for (int i=0; i < source_deme.GetSize(); i++) {
if ( GetCell(source_deme.GetCellID(i)).IsOccupied() ) {
- prospective_founders.Push( GetCell(source_deme.GetCellID(i)).GetOrganism() );
+ prospective_founders.Push( GetCell(source_deme.GetCellID(i)).GetOrganism() );
}
}
-
+
//add orgs alternately to source and target founders until
//we run out or each reaches DEMES_REPLICATE_SIZE.
int num_chosen_orgs = 0;
while( ((target_founders.GetSize() < m_world->GetConfig().DEMES_REPLICATE_SIZE.Get())
- || (source_founders.GetSize() < m_world->GetConfig().DEMES_REPLICATE_SIZE.Get()))
- && (prospective_founders.GetSize() > 0) ) {
-
+ || (source_founders.GetSize() < m_world->GetConfig().DEMES_REPLICATE_SIZE.Get()))
+ && (prospective_founders.GetSize() > 0) ) {
+
int chosen_org = random.GetUInt(prospective_founders.GetSize());
if (num_chosen_orgs % 2 == 0) {
source_founders.Push(prospective_founders.PopPos(chosen_org));
} else {
target_founders.Push(prospective_founders.PopPos(chosen_org));
}
-
+
num_chosen_orgs++;
}
}
break;
}
-
+
case 2:
case 3:
case 4:
@@ -1696,9 +1721,9 @@
// 4: same as 3: but replication to target fails if only one germ.
// 5: same as 3: but replication fails and source dies if fewer than two germs.
tArray<cOrganism*> founders; // List of organisms we're going to transfer.
-
+
if (source_deme.GetOrgCount() >= 2) {
-
+
if (m_world->GetConfig().DEMES_DIVIDE_METHOD.Get() != 0) {
m_world->GetDriver().RaiseFatalException(1, "Germline DEMES_ORGANISM_SELECTION methods 2 and 3 can only be used with DEMES_DIVIDE_METHOD 0.");
}
@@ -1723,19 +1748,19 @@
if (m_world->GetVerbosity() >= VERBOSE_ON) cout << "Num prospective founders: " << prospective_founders.GetSize() << endl;
if (prospective_founders.GetSize() < 2) {
-
+
// there were not enough orgs with nonzero germlines
// pick additional orgs at random without replacement,
// unless our method forbids this
-
+
// leave the founder list empty for method 5
if (m_world->GetConfig().DEMES_ORGANISM_SELECTION.Get() != 5) {
-
+
founders = prospective_founders;
//do not add additional founders randomly for method 4
if (m_world->GetConfig().DEMES_ORGANISM_SELECTION.Get() != 4) {
-
+
while(founders.GetSize() < 2) {
int cellid = source_deme.GetCellID(random.GetUInt(source_deme.GetSize()));
if( cell_array[cellid].IsOccupied() ) {
@@ -1750,15 +1775,15 @@
}
}
} else {
-
- // pick two orgs based on germline propensities from prospective founders
-
+
+ // pick two orgs based on germline propensities from prospective founders
+
while(founders.GetSize() < 2) {
-
+
double choice = (m_world->GetConfig().DEMES_ORGANISM_SELECTION.Get() == 2)
- ? random.GetDouble( gp_sum.Sum() ) : random.GetDouble( gp_sum.Count() );
-
-
+ ? random.GetDouble( gp_sum.Sum() ) : random.GetDouble( gp_sum.Count() );
+
+
//cout << "Count: " << gp_sum.Count() << endl;
// find the next organism to choose
@@ -1776,8 +1801,8 @@
// if it wasn't already chosen, then we count down...
if (!found) {
choice -= (m_world->GetConfig().DEMES_ORGANISM_SELECTION.Get() == 2)
- ? org->GetPhenotype().GetPermanentGermlinePropensity()
- : (org->GetPhenotype().GetPermanentGermlinePropensity() > 0);
+ ? org->GetPhenotype().GetPermanentGermlinePropensity()
+ : (org->GetPhenotype().GetPermanentGermlinePropensity() > 0);
}
on++;
}
@@ -1792,34 +1817,34 @@
if (founders.GetSize() > 1) target_founders.Push(founders[1]);
/*
- // Debug Code
- cout << endl;
- cout << "sum " << gp_sum.Sum() << endl;
- cout << "min " << min << endl;
- cout << "choice " << choice << endl;
- */
-
+ // Debug Code
+ cout << endl;
+ cout << "sum " << gp_sum.Sum() << endl;
+ cout << "min " << min << endl;
+ cout << "choice " << choice << endl;
+ */
+
//cout << "Chose germline propensity " << chosen_org->GetPhenotype().GetLastGermlinePropensity() << endl;
} else {
//Failure because we didn't have at least two organisms...
//m_world->GetDriver().RaiseFatalException(1, "Germline DEMES_ORGANISM_SELECTION method didn't find at least two organisms in deme.");
}
-
- break;
+
+ break;
}
default: {
cout << "Undefined value (" << m_world->GetConfig().DEMES_ORGANISM_SELECTION.Get()
- << ") for DEMES_ORGANISM_SELECTION." << endl;
+ << ") for DEMES_ORGANISM_SELECTION." << endl;
exit(1);
}
}
-
+
// We'd better have at *least* one genome.
// Methods that require a germline can sometimes come up short...
//assert(source_founders.GetSize()>0);
//assert(target_founders.GetSize()>0);
-
+
// We clear the deme, but trick cPopulation::KillOrganism
// to NOT delete the organisms, by pretending
// the orgs are running. This way we can still create
@@ -1827,29 +1852,29 @@
// We also need to defer adjusting the genotype
// or it will be prematurely deleted before we are done!
- // cDoubleSum gen;
+ // cDoubleSum gen;
tArray<cOrganism*> old_source_organisms;
for(int i=0; i<source_deme.GetSize(); ++i) {
int cell_id = source_deme.GetCellID(i);
-
+
if(cell_array[cell_id].IsOccupied()) {
cOrganism * org = cell_array[cell_id].GetOrganism();
old_source_organisms.Push(org);
org->SetRunning(true);
org->GetGenotype()->IncDeferAdjust();
- // cout << org->GetPhenotype().GetGeneration()-source_deme.GetAvgFounderGeneration() << " ";
- // gen.Add(org->GetPhenotype().GetGeneration()-source_deme.GetAvgFounderGeneration());
+ // cout << org->GetPhenotype().GetGeneration()-source_deme.GetAvgFounderGeneration() << " ";
+ // gen.Add(org->GetPhenotype().GetGeneration()-source_deme.GetAvgFounderGeneration());
}
}
//cout << endl;
//cout << "Average: " << gen.Average() << endl;
-
+
tArray<cOrganism*> old_target_organisms;
for(int i=0; i<target_deme.GetSize(); ++i) {
int cell_id = target_deme.GetCellID(i);
-
+
if(cell_array[cell_id].IsOccupied()) {
cOrganism * org = cell_array[cell_id].GetOrganism();
old_target_organisms.Push(org);
@@ -1868,16 +1893,16 @@
}
//cout << founders.GetSize() << " founders." << endl;
-
+
// Now populate the target (and optionally the source) using InjectGenotype.
// In the future InjectClone could be used, but this would require the
// deme keeping complete copies of the founder organisms when
// we wanted to re-seed from the original founders.
for(int i=0; i<target_founders.GetSize(); i++) {
- int cellid = DemeSelectInjectionCell(target_deme, i);
- InjectDemeFounder(cellid, *target_founders[i]->GetGenotype(), &target_founders[i]->GetPhenotype());
- target_deme.AddFounder(*target_founders[i]->GetGenotype(), &target_founders[i]->GetPhenotype());
- DemePostInjection(target_deme, cell_array[cellid]);
+ int cellid = DemeSelectInjectionCell(target_deme, i);
+ InjectDemeFounder(cellid, *target_founders[i]->GetGenotype(), &target_founders[i]->GetPhenotype());
+ target_deme.AddFounder(*target_founders[i]->GetGenotype(), &target_founders[i]->GetPhenotype());
+ DemePostInjection(target_deme, cell_array[cellid]);
}
// We either repeat this procedure in the source deme,
@@ -1886,7 +1911,7 @@
// source deme is replaced in the same way as the target
if (m_world->GetConfig().DEMES_DIVIDE_METHOD.Get() == 0) {
-
+
source_deme.ClearFounders();
source_deme.UpdateStats();
source_deme.KillAll();
@@ -1910,7 +1935,7 @@
tArray<int>& source_founders = source_deme.GetFounderGenotypeIDs();
tArray<cPhenotype>& source_founder_phenotypes = source_deme.GetFounderPhenotypes();
for(int i=0; i<source_founders.GetSize(); i++) {
-
+
int cellid = DemeSelectInjectionCell(source_deme, i);
//cout << "founder: " << source_founders[i] << endl;
cGenotype * genotype = m_world->GetClassificationManager().FindGenotype(source_founders[i]);
@@ -1927,66 +1952,66 @@
else {
m_world->GetDriver().RaiseFatalException(1, "Unknown DEMES_DIVIDE_METHOD");
}
+
+ /*
+ // Debug Code
+ //// Count the number of orgs in each deme.
+ count = 0;
+ for(int i=0; i<target_deme.GetSize(); ++i) {
+ int cell_id = target_deme.GetCellID(i);
+ if(cell_array[cell_id].IsOccupied()) count++;
+ }
+ cout << "Final orgs in target deme: " << count << endl;
- /*
- // Debug Code
- //// Count the number of orgs in each deme.
- count = 0;
- for(int i=0; i<target_deme.GetSize(); ++i) {
- int cell_id = target_deme.GetCellID(i);
- if(cell_array[cell_id].IsOccupied()) count++;
- }
- cout << "Final orgs in target deme: " << count << endl;
-
- count = 0;
- for(int i=0; i<source_deme.GetSize(); ++i) {
- int cell_id = source_deme.GetCellID(i);
- if(cell_array[cell_id].IsOccupied()) count++;
- }
- cout << "Final orgs in source deme: " << count << endl;
-
- if (1) {
- tArray<int>& source_founders = source_deme.GetFounderGenotypeIDs();
- cGenotype * source_founder_genotype = m_world->GetClassificationManager().FindGenotype(source_founders[0]);
- tArray<int>& target_founders = target_deme.GetFounderGenotypeIDs();
- cGenotype * target_founder_genotype = m_world->GetClassificationManager().FindGenotype(target_founders[0]);
- if (original_source_founder_genotype->GetGenome().AsString() != source_founder_genotype->GetGenome().AsString())
- {
- cout << "Original source founder does not equal final source founder!!!!" << endl;
- }
+ count = 0;
+ for(int i=0; i<source_deme.GetSize(); ++i) {
+ int cell_id = source_deme.GetCellID(i);
+ if(cell_array[cell_id].IsOccupied()) count++;
+ }
+ cout << "Final orgs in source deme: " << count << endl;
+
+ if (1) {
+ tArray<int>& source_founders = source_deme.GetFounderGenotypeIDs();
+ cGenotype * source_founder_genotype = m_world->GetClassificationManager().FindGenotype(source_founders[0]);
+ tArray<int>& target_founders = target_deme.GetFounderGenotypeIDs();
+ cGenotype * target_founder_genotype = m_world->GetClassificationManager().FindGenotype(target_founders[0]);
+ if (original_source_founder_genotype->GetGenome().AsString() != source_founder_genotype->GetGenome().AsString())
+ {
+ cout << "Original source founder does not equal final source founder!!!!" << endl;
+ }
+
+ cout << "Source:" << endl << source_founder_genotype->GetGenome().AsString() << endl;
+ cout << "Target:" << endl << target_founder_genotype->GetGenome().AsString() << endl;
+ }
+
+ // Debug
+ tArray<int>& new_source_founders = source_deme.GetFounders();
+ cerr << "New source genotype ids:" << endl;
+ for(int i=0; i<new_source_founders.GetSize(); i++) {
+ cerr << new_source_founders[i] << " ";
+ }
+ cerr << endl;
+
+ tArray<int>& new_target_founders = target_deme.GetFounders();
+ cerr << "New target genotype ids:" << endl;
+ for(int i=0; i<new_target_founders.GetSize(); i++) {
+ cerr << new_target_founders[i] << " ";
+ }
+ cerr << endl;
+ */
+
+ // remember to delete the old target organisms and adjust their genotypes
+ for(int i=0; i<old_target_organisms.GetSize(); ++i) {
+ old_target_organisms[i]->SetRunning(false);
+ cGenotype * genotype = old_target_organisms[i]->GetGenotype();
+ genotype->DecDeferAdjust();
+ m_world->GetClassificationManager().AdjustGenotype(*genotype);
- cout << "Source:" << endl << source_founder_genotype->GetGenome().AsString() << endl;
- cout << "Target:" << endl << target_founder_genotype->GetGenome().AsString() << endl;
+ // ONLY delete target orgs if seeding was successful
+ // otherwise they still exist in the population!!!
+ if (successfully_seeded) delete old_target_organisms[i];
}
- // Debug
- tArray<int>& new_source_founders = source_deme.GetFounders();
- cerr << "New source genotype ids:" << endl;
- for(int i=0; i<new_source_founders.GetSize(); i++) {
- cerr << new_source_founders[i] << " ";
- }
- cerr << endl;
-
- tArray<int>& new_target_founders = target_deme.GetFounders();
- cerr << "New target genotype ids:" << endl;
- for(int i=0; i<new_target_founders.GetSize(); i++) {
- cerr << new_target_founders[i] << " ";
- }
- cerr << endl;
- */
-
- // remember to delete the old target organisms and adjust their genotypes
- for(int i=0; i<old_target_organisms.GetSize(); ++i) {
- old_target_organisms[i]->SetRunning(false);
- cGenotype * genotype = old_target_organisms[i]->GetGenotype();
- genotype->DecDeferAdjust();
- m_world->GetClassificationManager().AdjustGenotype(*genotype);
-
- // ONLY delete target orgs if seeding was successful
- // otherwise they still exist in the population!!!
- if (successfully_seeded) delete old_target_organisms[i];
- }
-
for(int i=0; i<old_source_organisms.GetSize(); ++i) {
old_source_organisms[i]->SetRunning(false);
cGenotype * genotype = old_source_organisms[i]->GetGenotype();
@@ -1995,8 +2020,8 @@
// delete old source organisms ONLY if source was replaced
if ( (m_world->GetConfig().DEMES_DIVIDE_METHOD.Get() == 0)
- || (m_world->GetConfig().DEMES_DIVIDE_METHOD.Get() == 1) ) {
- delete old_source_organisms[i];
+ || (m_world->GetConfig().DEMES_DIVIDE_METHOD.Get() == 1) ) {
+ delete old_source_organisms[i];
}
}
@@ -2011,7 +2036,7 @@
// Kill all the organisms in the target deme.
target_deme.KillAll();
-
+
// Check all the organisms in the source deme to see if they get transferred
// to the target.
for(int i=0,j=0; i<source_deme.GetSize(); ++i) {
@@ -2038,8 +2063,8 @@
//}
}
}
-
- return successfully_seeded;
+
+return successfully_seeded;
}
void cPopulation::InjectDemeFounder(int _cell_id, cGenotype& _genotype, cPhenotype* _phenotype)
@@ -2051,8 +2076,8 @@
// At this point, the cell had better be occupied...
assert(GetCell(_cell_id).IsOccupied());
cOrganism * organism = GetCell(_cell_id).GetOrganism();
-
-
+
+
//Now we need to set up the phenotype of this organism...
if (_phenotype) {
//If we want founders to have their proper phenotypes
@@ -2060,7 +2085,7 @@
//organism->SetPhenotype(*_phenotype);
// Re-initialize the time-slice for this new organism.
//AdjustSchedule(_cell_id, organism->GetPhenotype().GetMerit());
-
+
// For now, just copy the generation...
organism->GetPhenotype().SetGeneration( _phenotype->GetGeneration() );
@@ -2073,12 +2098,12 @@
}
/* It requires much more than this to correctly implement, do later if needed @JEB
- //Optionally, set the first organism's merit to a constant value
- //actually, we need to add so the first organism is seeded this way too...
- if (m_world->GetConfig().DEMES_DEFAULT_MERIT.Get()) {
- organism->GetPhenotype().SetMerit( cMerit(m_world->GetConfig().DEMES_DEFAULT_MERIT.Get()) );
- AdjustSchedule(GetCell(_cell_id), organism->GetPhenotype().GetMerit());
- }
+ //Optionally, set the first organism's merit to a constant value
+ //actually, we need to add so the first organism is seeded this way too...
+ if (m_world->GetConfig().DEMES_DEFAULT_MERIT.Get()) {
+ organism->GetPhenotype().SetMerit( cMerit(m_world->GetConfig().DEMES_DEFAULT_MERIT.Get()) );
+ AdjustSchedule(GetCell(_cell_id), organism->GetPhenotype().GetMerit());
+ }
*/
}
@@ -2087,8 +2112,8 @@
Respects all of the different placement options that are relevant for deme replication.
@param sequence The number of times DemeSelectInjectionCell has been called on this deme
- already. Used for replicating multiple organisms from the source to the
- target deme in a sensible fashion.
+already. Used for replicating multiple organisms from the source to the
+target deme in a sensible fashion.
*/
int cPopulation::DemeSelectInjectionCell(cDeme& deme, int sequence) {
int cellid = -1;
@@ -2262,90 +2287,90 @@
// Print out statistics about donations
-
+
void cPopulation::PrintDonationStats()
{
cDoubleSum donation_makers;
cDoubleSum donation_receivers;
cDoubleSum donation_cheaters;
-
+
cDoubleSum edit_donation_makers;
cDoubleSum edit_donation_receivers;
cDoubleSum edit_donation_cheaters;
-
+
cDoubleSum kin_donation_makers;
cDoubleSum kin_donation_receivers;
cDoubleSum kin_donation_cheaters;
-
+
cDoubleSum threshgb_donation_makers;
cDoubleSum threshgb_donation_receivers;
cDoubleSum threshgb_donation_cheaters;
-
+
cDoubleSum quanta_threshgb_donation_makers;
cDoubleSum quanta_threshgb_donation_receivers;
cDoubleSum quanta_threshgb_donation_cheaters;
-
+
cStats& stats = m_world->GetStats();
-
+
cDataFile & dn_donors = m_world->GetDataFile("donations.dat");
dn_donors.WriteComment("Info about organisms giving donations in the population");
dn_donors.WriteTimeStamp();
dn_donors.Write(stats.GetUpdate(), "update");
-
-
+
+
for (int i = 0; i < cell_array.GetSize(); i++)
- {
- // Only look at cells with organisms in them.
- if (cell_array[i].IsOccupied() == false) continue;
- cOrganism * organism = cell_array[i].GetOrganism();
- const cPhenotype & phenotype = organism->GetPhenotype();
-
- // donors & receivers in general
- if (phenotype.IsDonorLast()) donation_makers.Add(1); //found a donor
- if (phenotype.IsReceiverLast()){
- donation_receivers.Add(1); //found a receiver
- if (phenotype.IsDonorLast()==0){
- donation_cheaters.Add(1); //found a receiver whose parent did not give
- }
+ {
+ // Only look at cells with organisms in them.
+ if (cell_array[i].IsOccupied() == false) continue;
+ cOrganism * organism = cell_array[i].GetOrganism();
+ const cPhenotype & phenotype = organism->GetPhenotype();
+
+ // donors & receivers in general
+ if (phenotype.IsDonorLast()) donation_makers.Add(1); //found a donor
+ if (phenotype.IsReceiverLast()){
+ donation_receivers.Add(1); //found a receiver
+ if (phenotype.IsDonorLast()==0){
+ donation_cheaters.Add(1); //found a receiver whose parent did not give
}
- // edit donors & receivers
- if (phenotype.IsDonorEditLast()) edit_donation_makers.Add(1); //found a edit donor
- if (phenotype.IsReceiverEditLast()){
- edit_donation_receivers.Add(1); //found a edit receiver
- if (phenotype.IsDonorEditLast()==0){
- edit_donation_cheaters.Add(1); //found a edit receiver whose parent did...
- } //...not make a edit donation
- }
-
- // kin donors & receivers
- if (phenotype.IsDonorKinLast()) kin_donation_makers.Add(1); //found a kin donor
- if (phenotype.IsReceiverKinLast()){
- kin_donation_receivers.Add(1); //found a kin receiver
- if (phenotype.IsDonorKinLast()==0){
- kin_donation_cheaters.Add(1); //found a kin receiver whose parent did...
- } //...not make a kin donation
- }
-
- // threshgb donors & receivers
- if (phenotype.IsDonorThreshGbLast()) threshgb_donation_makers.Add(1); //found a threshgb donor
- if (phenotype.IsReceiverThreshGbLast()){
- threshgb_donation_receivers.Add(1); //found a threshgb receiver
- if (phenotype.IsDonorThreshGbLast()==0){
- threshgb_donation_cheaters.Add(1); //found a threshgb receiver whose parent did...
- } //...not make a threshgb donation
- }
-
- // quanta_threshgb donors & receivers
- if (phenotype.IsDonorQuantaThreshGbLast()) quanta_threshgb_donation_makers.Add(1); //found a quanta threshgb donor
- if (phenotype.IsReceiverQuantaThreshGbLast()){
- quanta_threshgb_donation_receivers.Add(1); //found a quanta threshgb receiver
- if (phenotype.IsDonorQuantaThreshGbLast()==0){
- quanta_threshgb_donation_cheaters.Add(1); //found a quanta threshgb receiver whose parent did...
- } //...not make a quanta threshgb donation
- }
-
}
-
+ // edit donors & receivers
+ if (phenotype.IsDonorEditLast()) edit_donation_makers.Add(1); //found a edit donor
+ if (phenotype.IsReceiverEditLast()){
+ edit_donation_receivers.Add(1); //found a edit receiver
+ if (phenotype.IsDonorEditLast()==0){
+ edit_donation_cheaters.Add(1); //found a edit receiver whose parent did...
+ } //...not make a edit donation
+ }
+
+ // kin donors & receivers
+ if (phenotype.IsDonorKinLast()) kin_donation_makers.Add(1); //found a kin donor
+ if (phenotype.IsReceiverKinLast()){
+ kin_donation_receivers.Add(1); //found a kin receiver
+ if (phenotype.IsDonorKinLast()==0){
+ kin_donation_cheaters.Add(1); //found a kin receiver whose parent did...
+ } //...not make a kin donation
+ }
+
+ // threshgb donors & receivers
+ if (phenotype.IsDonorThreshGbLast()) threshgb_donation_makers.Add(1); //found a threshgb donor
+ if (phenotype.IsReceiverThreshGbLast()){
+ threshgb_donation_receivers.Add(1); //found a threshgb receiver
+ if (phenotype.IsDonorThreshGbLast()==0){
+ threshgb_donation_cheaters.Add(1); //found a threshgb receiver whose parent did...
+ } //...not make a threshgb donation
+ }
+
+ // quanta_threshgb donors & receivers
+ if (phenotype.IsDonorQuantaThreshGbLast()) quanta_threshgb_donation_makers.Add(1); //found a quanta threshgb donor
+ if (phenotype.IsReceiverQuantaThreshGbLast()){
+ quanta_threshgb_donation_receivers.Add(1); //found a quanta threshgb receiver
+ if (phenotype.IsDonorQuantaThreshGbLast()==0){
+ quanta_threshgb_donation_cheaters.Add(1); //found a quanta threshgb receiver whose parent did...
+ } //...not make a quanta threshgb donation
+ }
+
+ }
+
dn_donors.Write(donation_makers.Sum(), "parent made at least one donation");
dn_donors.Write(donation_receivers.Sum(), "parent received at least one donation");
dn_donors.Write(donation_cheaters.Sum(), "parent received at least one donation but did not make one");
@@ -2361,7 +2386,7 @@
dn_donors.Write(quanta_threshgb_donation_makers.Sum(), "parent made at least one quanta_threshgb_donation");
dn_donors.Write(quanta_threshgb_donation_receivers.Sum(), "parent received at least one quanta_threshgb_donation");
dn_donors.Write(quanta_threshgb_donation_cheaters.Sum(), "parent received at least one quanta_threshgb_donation but did not make one");
-
+
dn_donors.Endl();
}
// Copy a single indvidual out of a deme into a new one (which is first purged
@@ -2435,17 +2460,17 @@
}
void cPopulation::CheckImplicitDemeRepro(cDeme& deme) {
-
+
if (GetNumDemes() <= 1) return;
if (m_world->GetConfig().DEMES_REPLICATE_CPU_CYCLES.Get()
- && (deme.GetTimeUsed() >= m_world->GetConfig().DEMES_REPLICATE_CPU_CYCLES.Get())) ReplicateDeme(deme);
+ && (deme.GetTimeUsed() >= m_world->GetConfig().DEMES_REPLICATE_CPU_CYCLES.Get())) ReplicateDeme(deme);
else if (m_world->GetConfig().DEMES_REPLICATE_TIME.Get()
- && (deme.GetNormalizedTimeUsed() >= m_world->GetConfig().DEMES_REPLICATE_TIME.Get())) ReplicateDeme(deme);
+ && (deme.GetNormalizedTimeUsed() >= m_world->GetConfig().DEMES_REPLICATE_TIME.Get())) ReplicateDeme(deme);
else if (m_world->GetConfig().DEMES_REPLICATE_BIRTHS.Get()
- && (deme.GetBirthCount() >= m_world->GetConfig().DEMES_REPLICATE_BIRTHS.Get())) ReplicateDeme(deme);
+ && (deme.GetBirthCount() >= m_world->GetConfig().DEMES_REPLICATE_BIRTHS.Get())) ReplicateDeme(deme);
else if (m_world->GetConfig().DEMES_REPLICATE_ORGS.Get()
- && (deme.GetOrgCount() >= m_world->GetConfig().DEMES_REPLICATE_ORGS.Get())) ReplicateDeme(deme);
+ && (deme.GetOrgCount() >= m_world->GetConfig().DEMES_REPLICATE_ORGS.Get())) ReplicateDeme(deme);
}
// Print out all statistics about individual demes
@@ -2460,13 +2485,32 @@
PrintDemeMutationRate();
PrintDemeResource();
PrintDemeInstructions();
-
+
if(m_world->GetConfig().ENERGY_ENABLED.Get() == 1) {
PrintDemeSpatialEnergyData();
PrintDemeSpatialSleepData();
}
}
+void cPopulation::PrintDemeTestamentStats(const cString& filename) {
+ cStats& stats = m_world->GetStats();
+
+ cDataFile& df = m_world->GetDataFile(filename);
+ df.WriteTimeStamp();
+ df.Write(m_world->GetStats().GetUpdate(), "Update");
+ df.Write(stats.SumEnergyTestamentToDemeOrganisms().Average(), "Energy Testament to Deme Organisms");
+ df.Write(stats.SumEnergyTestamentToFutureDeme().Average(), "Energy Testament to Future Deme");
+ df.Write(stats.SumEnergyTestamentToNeighborOrganisms().Average(), "Energy Testament to Neighbor Organisms");
+ df.Write(stats.SumEnergyTestamentAcceptedByDeme().Average(), "Energy Testament Accepted by Future Deme");
+ df.Write(stats.SumEnergyTestamentAcceptedByOrganisms().Average(), "Energy Testament Accepted by Organisms");
+ df.Endl();
+
+
+ stats.SumEnergyTestamentToDemeOrganisms().Clear();
+ stats.SumEnergyTestamentToFutureDeme().Clear();
+ stats.SumEnergyTestamentToNeighborOrganisms().Clear();
+}
+
void cPopulation::PrintDemeDonor() {
cStats& stats = m_world->GetStats();
const int num_demes = deme_array.GetSize();
@@ -2474,12 +2518,12 @@
df_donor.WriteComment("Num orgs doing doing a donate for each deme in population");
df_donor.WriteTimeStamp();
df_donor.Write(stats.GetUpdate(), "update");
-
+
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cString comment;
const cDeme & cur_deme = deme_array[deme_id];
cDoubleSum single_deme_donor;
-
+
for (int i = 0; i < cur_deme.GetSize(); i++) {
int cur_cell = cur_deme.GetCellID(i);
if (cell_array[cur_cell].IsOccupied() == false) continue;
@@ -2504,7 +2548,7 @@
cString comment;
const cDeme & cur_deme = deme_array[deme_id];
cDoubleSum single_deme_fitness;
-
+
for (int i = 0; i < cur_deme.GetSize(); i++) {
int cur_cell = cur_deme.GetCellID(i);
if (cell_array[cur_cell].IsOccupied() == false) continue;
@@ -2524,12 +2568,12 @@
df_gest.WriteComment("Average gestation time for each deme in population");
df_gest.WriteTimeStamp();
df_gest.Write(stats.GetUpdate(), "update");
-
+
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cString comment;
const cDeme & cur_deme = deme_array[deme_id];
cDoubleSum single_deme_gest_time;
-
+
for (int i = 0; i < cur_deme.GetSize(); i++) {
int cur_cell = cur_deme.GetCellID(i);
if (cell_array[cur_cell].IsOccupied() == false) continue;
@@ -2557,7 +2601,7 @@
df_inst.WriteComment(comment);
df_inst.WriteTimeStamp();
df_inst.Write(stats.GetUpdate(), "update");
-
+
tArray<cIntSum> single_deme_inst(num_inst);
const cDeme & cur_deme = deme_array[deme_id];
@@ -2586,12 +2630,12 @@
df_life_fit.WriteComment("Average life fitnesses for each deme in the population");
df_life_fit.WriteTimeStamp();
df_life_fit.Write(stats.GetUpdate(), "update");
-
+
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cString comment;
const cDeme & cur_deme = deme_array[deme_id];
cDoubleSum single_deme_life_fitness;
-
+
for (int i = 0; i < cur_deme.GetSize(); i++) {
int cur_cell = cur_deme.GetCellID(i);
if (cell_array[cur_cell].IsOccupied() == false) continue;
@@ -2611,12 +2655,12 @@
df_merit.WriteComment("Average merits for each deme in population");
df_merit.WriteTimeStamp();
df_merit.Write(stats.GetUpdate(), "update");
-
+
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cString comment;
const cDeme & cur_deme = deme_array[deme_id];
cDoubleSum single_deme_merit;
-
+
for (int i = 0; i < cur_deme.GetSize(); i++) {
int cur_cell = cur_deme.GetCellID(i);
if (cell_array[cur_cell].IsOccupied() == false) continue;
@@ -2637,12 +2681,12 @@
df_mut_rates.WriteTimeStamp();
df_mut_rates.Write(stats.GetUpdate(), "update");
cDoubleSum total_mut_rate;
-
+
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cString comment;
const cDeme & cur_deme = deme_array[deme_id];
cDoubleSum single_deme_mut_rate;
-
+
for (int i = 0; i < cur_deme.GetSize(); i++) {
int cur_cell = cur_deme.GetCellID(i);
if (cell_array[cur_cell].IsOccupied() == false) continue;
@@ -2663,12 +2707,12 @@
df_receiver.WriteComment("Num orgs doing receiving a donate for each deme in population");
df_receiver.WriteTimeStamp();
df_receiver.Write(stats.GetUpdate(), "update");
-
+
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cString comment;
const cDeme & cur_deme = deme_array[deme_id];
cDoubleSum single_deme_receiver;
-
+
for (int i = 0; i < cur_deme.GetSize(); i++) {
int cur_cell = cur_deme.GetCellID(i);
if (cell_array[cur_cell].IsOccupied() == false) continue;
@@ -2678,7 +2722,7 @@
comment.Set("Deme %d", deme_id);
df_receiver.Write(single_deme_receiver.Sum(), comment);
}
- df_receiver.Endl();
+ df_receiver.Endl();
}
void cPopulation::PrintDemeResource() {
@@ -2688,10 +2732,10 @@
df_resources.WriteComment("Avida deme resource data");
df_resources.WriteTimeStamp();
df_resources.Write(stats.GetUpdate(), "update");
-
+
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cDeme & cur_deme = deme_array[deme_id];
-
+
cur_deme.UpdateDemeRes();
cResourceCount res = GetDeme(deme_id).GetDemeResourceCount();
for(int j = 0; j < res.GetSize(); j++) {
@@ -2715,10 +2759,10 @@
cDataFile& df = m_world->GetDataFile(tmpfilename);
cString UpdateStr = cStringUtil::Stringf( "deme_%07i_energy_%07i = [ ...", i, update );
df.WriteRaw(UpdateStr);
-
+
int gridsize = m_world->GetPopulation().GetDeme(i).GetSize();
int xsize = m_world->GetConfig().WORLD_X.Get();
-
+
// write grid to file
for (int j = 0; j < gridsize; j++) {
cPopulationCell& cell = m_world->GetPopulation().GetCell(cellID);
@@ -2740,13 +2784,13 @@
cString tmpfilename = cStringUtil::Stringf( "deme_spacial_resource_%s.m", tmpResName );
cDataFile& df = m_world->GetDataFile(tmpfilename);
cString UpdateStr = cStringUtil::Stringf( "deme_%07i_%s_%07i = [ ...", deme_id, static_cast<const char*>(res.GetResName(i)), m_world->GetStats().GetUpdate() );
-
+
df.WriteRaw(UpdateStr);
-
+
cSpatialResCount sp_res = res.GetSpatialResource(i);
int gridsize = sp_res.GetSize();
int xsize = m_world->GetConfig().WORLD_X.Get();
-
+
for (int j = 0; j < gridsize; j++) {
df.WriteBlockElement(sp_res.GetAmount(j), j, xsize);
}
@@ -2764,10 +2808,10 @@
for(int i = 0; i < m_world->GetPopulation().GetNumDemes(); i++) {
cString UpdateStr = cStringUtil::Stringf( "deme_%07i_sleep_%07i = [ ...", i, update);
df.WriteRaw(UpdateStr);
-
+
int gridsize = m_world->GetPopulation().GetDeme(i).GetSize();
int xsize = m_world->GetConfig().WORLD_X.Get();
-
+
// write grid to file
for (int j = 0; j < gridsize; j++) {
cPopulationCell cell = m_world->GetPopulation().GetCell(cellID);
@@ -2791,12 +2835,12 @@
df_task.WriteComment("Num orgs doing each task for each deme in population");
df_task.WriteTimeStamp();
df_task.Write(stats.GetUpdate(), "update");
-
+
for (int deme_id = 0; deme_id < num_demes; deme_id++) {
cString comment;
const cDeme & cur_deme = deme_array[deme_id];
tArray<cIntSum> single_deme_task(num_task);
-
+
for (int i = 0; i < cur_deme.GetSize(); i++) {
int cur_cell = cur_deme.GetCellID(i);
if (cell_array[cur_cell].IsOccupied() == false) continue;
@@ -2825,16 +2869,16 @@
<< "# 3+: founder genotype ids" << endl << endl;
for(int i=0; i<deme_array.GetSize(); i++) {
-
+
if(deme_array[i].IsEmpty()) continue;
tArray<int>& deme_founders = deme_array[i].GetFounderGenotypeIDs();
-
+
fp << i << " " << deme_founders.GetSize();
for(int j=0; j<deme_founders.GetSize(); j++) {
fp << " " << deme_founders[j];
}
-
+
fp << endl;
}
}
@@ -2874,10 +2918,10 @@
int gen_id = organism->GetGenotype()->GetID();
if (m_world->GetConfig().TRACK_CCLADES.Get() > 0)
{
- if (m_world->GetClassificationManager().IsCCladeFounder(gen_id))
- {
- organism->SetCCladeLabel(gen_id);
- }
+ if (m_world->GetClassificationManager().IsCCladeFounder(gen_id))
+ {
+ organism->SetCCladeLabel(gen_id);
+ }
}
}
@@ -2895,11 +2939,11 @@
assert(parent_cell.IsOccupied());
const int birth_method = m_world->GetConfig().BIRTH_METHOD.Get();
-
+
// @WRE carrying capacity handling
/* Pick and kill an organism here if needed
- * and then enter choices for birth method handling.
- */
+ * and then enter choices for birth method handling.
+ */
if ((0 < m_world->GetConfig().BIOMIMETIC_K.Get()) &&
(num_organisms >= m_world->GetConfig().BIOMIMETIC_K.Get())) {
// Measure temporary variables
@@ -2924,14 +2968,14 @@
}
KillOrganism(cell_array[max_msrndx]);
}
-
+
//@AWC -- decide wether the child will migrate to another deme -- if migrating we ignore the birth method.
if ((m_world->GetConfig().MIGRATION_RATE.Get() > 0.0) //@AWC -- Pedantic test to maintain consistancy.
&& m_world->GetRandom().P(m_world->GetConfig().MIGRATION_RATE.Get())) {
-
+
//cerr << "Attempting to migrate with rate " << m_world->GetConfig().MIGRATION_RATE.Get() << "!" << endl;
int deme_id = parent_cell.GetDemeID();
-
+
//get another -unadjusted- deme id
int rnd_deme_id = m_world->GetRandom().GetInt(deme_array.GetSize()-1);
@@ -2974,7 +3018,7 @@
// the cases. For now, a bunch of if's that return if they handle.
if (birth_method == POSITION_CHILD_FULL_SOUP_RANDOM) {
-
+
// Look randomly within empty cells first, if requested
if (m_world->GetConfig().PREFER_EMPTY.Get()) {
int num_empty_cells = UpdateEmptyCellIDArray();
@@ -2983,7 +3027,7 @@
return GetCell(empty_cell_id_array[out_pos]);
}
}
-
+
int out_pos = m_world->GetRandom().GetUInt(cell_array.GetSize());
while (parent_ok == false && out_pos == parent_cell.GetID()) {
out_pos = m_world->GetRandom().GetUInt(cell_array.GetSize());
@@ -3005,6 +3049,8 @@
return PositionDemeRandom(parent_cell.GetDemeID(), parent_cell, parent_ok);
}
else if (birth_method == POSITION_CHILD_PARENT_FACING) {
+ const int deme_id = parent_cell.GetDemeID();
+ deme_array[deme_id].IncBirthCount();
return parent_cell.GetCellFaced();
}
else if (birth_method == POSITION_CHILD_NEXT_CELL) {
@@ -3141,8 +3187,8 @@
}
void cPopulation::PositionEnergyUsed(cPopulationCell & parent_cell,
- tList<cPopulationCell> & found_list,
- bool parent_ok)
+ tList<cPopulationCell> & found_list,
+ bool parent_ok)
{
// Start with the parent organism as the replacement, and see if we can find
// anything equivilent or better.
@@ -3171,78 +3217,78 @@
// This function handles PositionChild() when there is migration between demes
cPopulationCell& cPopulation::PositionDemeMigration(cPopulationCell& parent_cell, bool parent_ok)
{
- //cerr << "Attempting to migrate with rate " << m_world->GetConfig().MIGRATION_RATE.Get() << "!" << endl;
- int deme_id = parent_cell.GetDemeID();
+ //cerr << "Attempting to migrate with rate " << m_world->GetConfig().MIGRATION_RATE.Get() << "!" << endl;
+ int deme_id = parent_cell.GetDemeID();
+
+ // Position randomly in any other deme
+ if (m_world->GetConfig().DEMES_MIGRATION_METHOD.Get() == 0) {
- // Position randomly in any other deme
- if (m_world->GetConfig().DEMES_MIGRATION_METHOD.Get() == 0) {
-
- //get another -unadjusted- deme id
- int rnd_deme_id = m_world->GetRandom().GetInt(deme_array.GetSize()-1);
-
- //if the -unadjusted- id is above the excluded id, bump it up one
- //insures uniform prob of landing in any deme but the parent's
- if(rnd_deme_id >= deme_id) rnd_deme_id++;
-
- //set the new deme_id
- deme_id = rnd_deme_id;
- }
+ //get another -unadjusted- deme id
+ int rnd_deme_id = m_world->GetRandom().GetInt(deme_array.GetSize()-1);
- //Position randomly in an adjacent deme in neighborhood (assuming torus)
- //Extremely hacked DEMES_NUM_X config setting simulates grid
- else if (m_world->GetConfig().DEMES_MIGRATION_METHOD.Get() == 1) {
+ //if the -unadjusted- id is above the excluded id, bump it up one
+ //insures uniform prob of landing in any deme but the parent's
+ if(rnd_deme_id >= deme_id) rnd_deme_id++;
- //get a random eight-neighbor
- int dir = m_world->GetRandom().GetInt(8);
-
- // 0 = NW, 1=N, continuing clockwise....
+ //set the new deme_id
+ deme_id = rnd_deme_id;
+ }
+
+ //Position randomly in an adjacent deme in neighborhood (assuming torus)
+ //Extremely hacked DEMES_NUM_X config setting simulates grid
+ else if (m_world->GetConfig().DEMES_MIGRATION_METHOD.Get() == 1) {
- // Up one row
- if (m_world->GetConfig().DEMES_NUM_X.Get() == 0) {
- m_world->GetDriver().RaiseFatalException(1, "DEMES_NUM_X must be non-zero if DEMES_MIGRATION_METHOD 1 used.");
- }
- int x_size = m_world->GetConfig().DEMES_NUM_X.Get();
- int y_size = (int) (m_world->GetConfig().NUM_DEMES.Get() / x_size);
-
- assert(y_size * x_size == m_world->GetConfig().NUM_DEMES.Get());
-
- int x = deme_id % x_size;
- int y = (int) (deme_id / x_size);
-
- if ( (dir == 0) || (dir == 1) || (dir == 2) ) y--;
- if ( (dir == 5) || (dir == 6) || (dir == 7) ) y++;
- if ( (dir == 0) || (dir == 3) || (dir == 5) ) x--;
- if ( (dir == 2) || (dir == 4) || (dir == 7) ) x++;
-
- //handle boundary conditions...
-
- x = (x + x_size) % x_size;
- y = (y + y_size) % y_size;
-
- //set the new deme_id
- deme_id = x + x_size * y;
-
- assert(deme_id > 0);
- assert(deme_id > 0);
- }
+ //get a random eight-neighbor
+ int dir = m_world->GetRandom().GetInt(8);
- //Random deme adjacent in list
- else if (m_world->GetConfig().DEMES_MIGRATION_METHOD.Get() == 2) {
-
- //get a random direction to move in deme list
- int rnd_deme_id = m_world->GetRandom().GetInt(1);
- if (rnd_deme_id == 0) rnd_deme_id = -1;
-
- //set the new deme_id
- deme_id = (deme_id + rnd_deme_id + GetNumDemes()) % GetNumDemes();
+ // 0 = NW, 1=N, continuing clockwise....
+
+ // Up one row
+ if (m_world->GetConfig().DEMES_NUM_X.Get() == 0) {
+ m_world->GetDriver().RaiseFatalException(1, "DEMES_NUM_X must be non-zero if DEMES_MIGRATION_METHOD 1 used.");
}
+ int x_size = m_world->GetConfig().DEMES_NUM_X.Get();
+ int y_size = (int) (m_world->GetConfig().NUM_DEMES.Get() / x_size);
- // TODO the above choice of deme does not respect PREFER_EMPTY
- // i.e., it does not preferentially pick a deme with empty cells if they are
- // it might make sense for that to happen...
+ assert(y_size * x_size == m_world->GetConfig().NUM_DEMES.Get());
- // Now return an empty cell from the chosen deme
- return PositionDemeRandom(deme_id, parent_cell, parent_ok);
+ int x = deme_id % x_size;
+ int y = (int) (deme_id / x_size);
+
+ if ( (dir == 0) || (dir == 1) || (dir == 2) ) y--;
+ if ( (dir == 5) || (dir == 6) || (dir == 7) ) y++;
+ if ( (dir == 0) || (dir == 3) || (dir == 5) ) x--;
+ if ( (dir == 2) || (dir == 4) || (dir == 7) ) x++;
+
+ //handle boundary conditions...
+
+ x = (x + x_size) % x_size;
+ y = (y + y_size) % y_size;
+
+ //set the new deme_id
+ deme_id = x + x_size * y;
+
+ assert(deme_id > 0);
+ assert(deme_id > 0);
+ }
+
+ //Random deme adjacent in list
+ else if (m_world->GetConfig().DEMES_MIGRATION_METHOD.Get() == 2) {
+
+ //get a random direction to move in deme list
+ int rnd_deme_id = m_world->GetRandom().GetInt(1);
+ if (rnd_deme_id == 0) rnd_deme_id = -1;
+
+ //set the new deme_id
+ deme_id = (deme_id + rnd_deme_id + GetNumDemes()) % GetNumDemes();
+ }
+
+ // TODO the above choice of deme does not respect PREFER_EMPTY
+ // i.e., it does not preferentially pick a deme with empty cells if they are
+ // it might make sense for that to happen...
+
+ // Now return an empty cell from the chosen deme
+ return PositionDemeRandom(deme_id, parent_cell, parent_ok);
}
// This function handles PositionChild() by returning a random cell from the entire deme.
@@ -3252,7 +3298,7 @@
const int deme_size = deme_array[deme_id].GetSize();
cDeme& deme = deme_array[deme_id];
-
+
// Look randomly within empty cells first, if requested
if (m_world->GetConfig().PREFER_EMPTY.Get()) {
@@ -3262,7 +3308,7 @@
return GetCell(empty_cell_id_array[out_pos]);
}
}
-
+
int out_pos = m_world->GetRandom().GetUInt(deme_size);
int out_cell_id = deme.GetCellID(out_pos);
@@ -3286,7 +3332,7 @@
// all cells in the cPopulation when it was created. Using functions
// that resize it (like Push) will slow this code down considerably.
// Instead, we keep track of how much of this memory we are using.
-
+
// Look at all cells
if (deme_id == -1) {
for (int i=0; i<cell_array.GetSize(); i++) {
@@ -3295,7 +3341,7 @@
}
// Look at a specific deme
else {
- cDeme& deme = deme_array[deme_id];
+ cDeme& deme = deme_array[deme_id];
for (int i=0; i<deme.GetSize(); i++) {
if (GetCell(deme.GetCellID(i)).IsOccupied() == false) empty_cell_id_array[num_empty_cells++] = deme.GetCellID(i);
}
@@ -3320,11 +3366,11 @@
cPopulationCell& cell = GetCell(cell_id);
assert(cell.IsOccupied()); // Unoccupied cell getting processor time!
cOrganism* cur_org = cell.GetOrganism();
-
+
cell.GetHardware()->SingleProcess(ctx);
if (cur_org->GetPhenotype().GetToDelete() == true) delete cur_org;
-
+
m_world->GetStats().IncExecuted();
resource_count.Update(step_size);
@@ -3332,7 +3378,7 @@
if (GetNumDemes() > 1)
{
for(int i = 0; i < GetNumDemes(); i++) GetDeme(i).Update(step_size);
-
+
cDeme & deme = GetDeme(GetCell(cell_id).GetDemeID());
deme.IncTimeUsed(cur_org->GetPhenotype().GetMerit().GetDouble());
CheckImplicitDemeRepro(deme);
@@ -3345,7 +3391,7 @@
assert(step_size > 0.0);
assert(cell_id < cell_array.GetSize());
assert(m_world->GetHardwareManager().SupportsSpeculative());
-
+
// If cell_id is negative, no cell could be found -- stop here.
if (cell_id < 0) return;
@@ -3373,15 +3419,15 @@
}
if (cur_org->GetPhenotype().GetToDelete() == true) delete cur_org;
-
+
m_world->GetStats().IncExecuted();
resource_count.Update(step_size);
-
- // Deme specific
+
+ // Deme specific
if (GetNumDemes() > 1)
{
for(int i = 0; i < GetNumDemes(); i++) GetDeme(i).Update(step_size);
-
+
cDeme & deme = GetDeme(GetCell(cell_id).GetDemeID());
deme.IncTimeUsed(cur_org->GetPhenotype().GetMerit().GetDouble());
CheckImplicitDemeRepro(deme);
@@ -3392,12 +3438,12 @@
// Loop through all the demes getting stats and doing calculations
// which must be done on a deme by deme basis.
void cPopulation::UpdateDemeStats() {
-
+
// bail early to save time if there are no demes
if (GetNumDemes() == 1) return ;
-
+
cStats& stats = m_world->GetStats();
-
+
stats.SumDemeAge().Clear();
stats.SumDemeBirthCount().Clear();
stats.SumDemeOrgCount().Clear();
@@ -3406,11 +3452,14 @@
stats.SumDemeGestationTime().Clear();
stats.SumDemeNormalizedTimeUsed().Clear();
stats.SumDemeMerit().Clear();
-
+
stats.SumDemeGenerationsPerLifetime().Clear();
-
+
stats.ClearNumOccupiedDemes();
-
+
+ stats.SumDemeEventsKilled().Clear();
+ stats.SumDemeAttemptsToKillEvents() .Clear();
+
for(int i = 0; i < GetNumDemes(); i++) {
cDeme& deme = GetDeme(i);
if(deme.IsEmpty()) // ignore empty demes
@@ -3423,15 +3472,18 @@
stats.SumDemeBirthCount().Add(deme.GetBirthCount());
stats.SumDemeOrgCount().Add(deme.GetOrgCount());
stats.SumDemeGeneration().Add(deme.GetGeneration());
-
+
stats.SumDemeLastBirthCount().Add(deme.GetLastBirthCount());
stats.SumDemeLastOrgCount().Add(deme.GetLastOrgCount());
-
+
stats.SumDemeGestationTime().Add(deme.GetGestationTime());
stats.SumDemeNormalizedTimeUsed().Add(deme.GetLastNormalizedTimeUsed());
stats.SumDemeMerit().Add(deme.GetDemeMerit().GetDouble());
stats.SumDemeGenerationsPerLifetime().Add(deme.GetGenerationsPerLifetime());
+
+ stats.SumDemeEventsKilled().Add(deme.GetEventsKilled());
+ stats.SumDemeAttemptsToKillEvents().Add(deme.GetEventKillAttempts());
}
}
@@ -3983,11 +4035,11 @@
current_cell += 1;
}
}
-
-// @DMB - This seems to be debugging output...
-// cout << (*it).id_num << " " << (*it).parent_id << " " << (*it).genotype->GetParentID() << " "
-// << (*it).genotype->GetNumOffspringGenotypes() << " " << (*it).num_cpus << " " << (*it).genotype->GetNumOrganisms() << endl;
+ // @DMB - This seems to be debugging output...
+ // cout << (*it).id_num << " " << (*it).parent_id << " " << (*it).genotype->GetParentID() << " "
+ // << (*it).genotype->GetNumOffspringGenotypes() << " " << (*it).num_cpus << " " << (*it).genotype->GetNumOrganisms() << endl;
+
if (soup_full) {
cout << "Warning: Too many organisms in population file, remainder ignored" << endl;
break;
@@ -4062,7 +4114,7 @@
InjectGenome(cell_id, genome, lineage_label);
cPhenotype& phenotype = GetCell(cell_id).GetOrganism()->GetPhenotype();
phenotype.SetNeutralMetric(neutral);
-
+
if (merit > 0) phenotype.SetMerit(cMerit(merit));
AdjustSchedule(GetCell(cell_id), phenotype.GetMerit());
@@ -4070,7 +4122,7 @@
if (GetNumDemes() > 1) {
cDeme& deme = deme_array[GetCell(cell_id).GetDemeID()];
-
+
// If we're using germlines, then we have to be a little careful here.
// This should probably not be within Inject() since we mainly want it to
// apply to the START_CREATURE? -- @JEB
@@ -4096,16 +4148,22 @@
}
GetCell(cell_id).GetOrganism()->GetPhenotype().SetPermanentGermlinePropensity
- (m_world->GetConfig().DEMES_FOUNDER_GERMLINE_PROPENSITY.Get());
-
-
+ (m_world->GetConfig().DEMES_FOUNDER_GERMLINE_PROPENSITY.Get());
+
+
if (m_world->GetConfig().DEMES_FOUNDER_GERMLINE_PROPENSITY.Get() >= 0.0) {
- GetCell(cell_id).GetOrganism()->GetPhenotype().SetPermanentGermlinePropensity
- ( m_world->GetConfig().DEMES_FOUNDER_GERMLINE_PROPENSITY.Get() );
+ GetCell(cell_id).GetOrganism()->GetPhenotype().SetPermanentGermlinePropensity
+ ( m_world->GetConfig().DEMES_FOUNDER_GERMLINE_PROPENSITY.Get() );
}
-
+
}
}
+ else if(m_world->GetConfig().DEMES_USE_GERMLINE.Get() == 2) {
+ //find the genotype we just created from the genome, and save it
+ cDeme& deme = deme_array[GetCell(cell_id).GetDemeID()];
+ cGenotype * genotype = m_world->GetClassificationManager().FindGenotype(genome, lineage_label);
+ deme.ReplaceGermline(*genotype);
+ }
}
void cPopulation::InjectParasite(const cCodeLabel& label, const cGenome& injected_code, int cell_id)
@@ -4226,7 +4284,7 @@
cAvidaContext& ctx = m_world->GetDefaultContext();
cOrganism* new_organism = new cOrganism(m_world, ctx, new_genotype->GetGenome());
-
+
//Coalescense Clade Setup
new_organism->SetCCladeLabel(-1);
@@ -4262,25 +4320,25 @@
// Activate the organism in the population...
ActivateOrganism(ctx, new_organism, cell_array[cell_id]);
-
+
// Log the injection of this organism if LOG_INJECT is set to 1 and
// the current update number is >= INJECT_LOG_START
if ( (m_world->GetConfig().LOG_INJECT.Get() == 1) &&
(m_world->GetStats().GetUpdate() >= m_world->GetConfig().INJECT_LOG_START.Get()) ){
-
- cString tmpfilename = cStringUtil::Stringf("injectlog.dat");
- cDataFile& df = m_world->GetDataFile(tmpfilename);
-
- int update = m_world->GetStats().GetUpdate();
- int orgid = new_organism->GetID();
- int deme_id = m_world->GetPopulation().GetCell(cell_id).GetDemeID();
- int facing = new_organism->GetFacing();
- const char *orgname = (const char *)new_genotype->GetName();
-
- cString UpdateStr = cStringUtil::Stringf("%d %d %d %d %d %s", update, orgid, cell_id, deme_id, facing, orgname);
- df.WriteRaw(UpdateStr);
+
+ cString tmpfilename = cStringUtil::Stringf("injectlog.dat");
+ cDataFile& df = m_world->GetDataFile(tmpfilename);
+
+ int update = m_world->GetStats().GetUpdate();
+ int orgid = new_organism->GetID();
+ int deme_id = m_world->GetPopulation().GetCell(cell_id).GetDemeID();
+ int facing = new_organism->GetFacing();
+ const char *orgname = (const char *)new_genotype->GetName();
+
+ cString UpdateStr = cStringUtil::Stringf("%d %d %d %d %d %s", update, orgid, cell_id, deme_id, facing, orgname);
+ df.WriteRaw(UpdateStr);
}
-
+
}
@@ -4329,7 +4387,7 @@
assert(cell_id >= 0 && cell_id < cell_array.GetSize());
cAvidaContext& ctx = m_world->GetDefaultContext();
-
+
// Do mutations on the child genome, but restore it to its current state afterward.
cGenome save_child = parent.ChildGenome();
parent.GetHardware().Divide_DoMutations(ctx);
@@ -4337,12 +4395,12 @@
parent.GetHardware().Divide_TestFitnessMeasures(ctx);
parent.ChildGenome() = save_child;
cOrganism* new_organism = new cOrganism(m_world, ctx, child_genome);
-
+
// Set the genotype...
assert(parent.GetGenotype());
cGenotype* new_genotype = m_world->GetClassificationManager().GetGenotype(child_genome, parent.GetGenotype(), NULL);
new_organism->SetGenotype(new_genotype);
-
+
// Setup the phenotype...
new_organism->GetPhenotype().SetupOffspring(parent.GetPhenotype(),child_genome);
@@ -4365,7 +4423,7 @@
// Activate the organism in the population...
ActivateOrganism(ctx, new_organism, cell_array[cell_id]);
-
+
}
@@ -4425,7 +4483,7 @@
//implementing a very poor man's hash...
tArray<int> phenotypes;
tArray<int> phenotype_counts;
-
+
for (int i = 0; i < cell_array.GetSize(); i++) {
// Only look at cells with organisms in them.
if (cell_array[i].IsOccupied() == false) continue;
@@ -4444,7 +4502,7 @@
}
ids.insert(id);
complete.insert(key);
-
+
// add one to our count for this key
int k;
for(k=0; k<phenotypes.GetSize(); k++)
@@ -4459,7 +4517,7 @@
phenotypes.Push(id);
phenotype_counts.Push(1);
}
-
+
// go through again to calculate Shannon Diversity of task counts
// now that we know the total number of tasks done
double shannon_diversity = 0;
@@ -4550,7 +4608,7 @@
phenotype.SetMerit( cMerit(new_merit) );
phenotype.SetLifeFitness(new_merit/phenotype.GetGestationTime());
if (new_merit <= old_merit) {
- phenotype.SetIsDonorCur(); }
+ phenotype.SetIsDonorCur(); }
else { phenotype.SetIsReceiver(); }
AdjustSchedule(GetCell(cell_id), phenotype.GetMerit());
@@ -4567,7 +4625,7 @@
void cPopulation::AddBeginSleep(int cellID, int start_time) {
sleep_log[cellID].Add(make_pair(start_time,-1));
}
-
+
void cPopulation::AddEndSleep(int cellID, int end_time) {
pair<int,int> p = sleep_log[cellID][sleep_log[cellID].Size()-1];
sleep_log[cellID].RemoveAt(sleep_log[cellID].Size()-1);
@@ -4583,14 +4641,14 @@
if (cell.IsOccupied())
{
cPhenotype & p = cell.GetOrganism()->GetPhenotype();
-
+
// Don't continue if the time used was zero
if (p.GetTrialTimeUsed() != 0)
{
// Correct gestation time for speculative execution
p.SetTrialTimeUsed(p.GetTrialTimeUsed() - cell.GetSpeculativeState());
p.SetTimeUsed(p.GetTimeUsed() - cell.GetSpeculativeState());
-
+
cell.GetOrganism()->NewTrial();
cell.GetOrganism()->GetHardware().Reset();
@@ -4607,21 +4665,21 @@
}
/*
- CompeteOrganisms
-
- parents_survive => for any organism represented by >=1 child, the first created is the parent (has no mutations)
- dynamic_scaling => rescale the time interval such that the geometric mean of the highest fitness versus lower fitnesses
- equals a time of 1 unit
-*/
+ CompeteOrganisms
+
+ parents_survive => for any organism represented by >=1 child, the first created is the parent (has no mutations)
+ dynamic_scaling => rescale the time interval such that the geometric mean of the highest fitness versus lower fitnesses
+ equals a time of 1 unit
+ */
void cPopulation::CompeteOrganisms(int competition_type, int parents_survive)
{
NewTrial();
-
+
double total_fitness = 0;
int num_cells = GetSize();
tArray<double> org_fitness(num_cells);
-
+
double lowest_fitness = -1.0;
double average_fitness = 0;
double highest_fitness = -1.0;
@@ -4630,14 +4688,14 @@
double highest_fitness_copied = -1.0;
int different_orgs_copied = 0;
int num_competed_orgs = 0;
-
+
int num_trials = -1;
int dynamic_scaling = 0;
-
+
if (competition_type==3) dynamic_scaling = 1;
else if (competition_type==4) dynamic_scaling = 2;
-
+
// How many trials were there? -- same for every organism
// we just need to find one...
for (int i = 0; i < num_cells; i++)
@@ -4663,12 +4721,12 @@
if (num_trials == 0) return;
if (m_world->GetVerbosity() > VERBOSE_SILENT) cout << "==Compete Organisms==" << endl;
-
+
tArray<double> min_trial_fitnesses(num_trials);
tArray<double> max_trial_fitnesses(num_trials);
tArray<double> avg_trial_fitnesses(num_trials);
avg_trial_fitnesses.SetAll(0);
-
+
bool init = false;
// What is the min and max fitness in each trial
for (int i = 0; i < num_cells; i++)
@@ -4714,7 +4772,7 @@
cPhenotype& p = GetCell(i).GetOrganism()->GetPhenotype();
//Don't need to reset trial_fitnesses because we will call cPhenotype::OffspringReset on the entire pop
tArray<double> trial_fitnesses = p.GetTrialFitnesses();
-
+
//If there are no trial fitnesses...use the actual fitness.
if (trial_fitnesses.GetSize() == 0)
{
@@ -4733,11 +4791,11 @@
{
fitness += log(trial_fitnesses[t]);
}
- fitness /= (double)trial_fitnesses.GetSize();
+ fitness /= (double)trial_fitnesses.GetSize();
fitness = exp( fitness );
- break;
-
- //Product
+ break;
+
+ //Product
case 5:
//Treat as logs to avoid overflow when multiplying very large fitnesses
fitness = 0;
@@ -4745,29 +4803,29 @@
{
fitness += log(trial_fitnesses[t]);
}
- fitness = exp( fitness );
- break;
-
- //Geometric Mean of normalized values
+ fitness = exp( fitness );
+ break;
+
+ //Geometric Mean of normalized values
case 1:
fitness = 1.0;
for (int t=0; t < trial_fitnesses.GetSize(); t++)
{
- fitness*=trial_fitnesses[t] / max_trial_fitnesses[t];
+ fitness*=trial_fitnesses[t] / max_trial_fitnesses[t];
}
- fitness = exp( (1.0/((double)trial_fitnesses.GetSize())) * log(fitness) );
- break;
-
- //Arithmetic Mean
+ fitness = exp( (1.0/((double)trial_fitnesses.GetSize())) * log(fitness) );
+ break;
+
+ //Arithmetic Mean
case 2:
fitness = 0;
for (int t=0; t < trial_fitnesses.GetSize(); t++)
{
fitness+=trial_fitnesses[t];
}
- fitness /= (double)trial_fitnesses.GetSize();
- break;
-
+ fitness /= (double)trial_fitnesses.GetSize();
+ break;
+
default:
m_world->GetDriver().RaiseFatalException(1, "Unknown CompeteOrganisms method");
}
@@ -4780,7 +4838,7 @@
} // end if occupied
}
average_fitness = total_fitness / num_competed_orgs;
-
+
//Rescale by the geometric mean of the difference from the top score and the average
if ( dynamic_scaling == 1 ) {
double dynamic_factor = 1.0;
@@ -4807,13 +4865,13 @@
dynamic_factor += log(org_fitness[i]);
}
}
-
+
cout << "Scaling factor = " << dynamic_factor << endl;
if (num_org > 0) dynamic_factor = exp(dynamic_factor / (double)num_org);
cout << "Scaling factor = " << dynamic_factor << endl;
total_fitness = 0;
-
+
for (int i = 0; i < num_cells; i++) {
if ( GetCell(i).IsOccupied() ) {
org_fitness[i] /= dynamic_factor;
@@ -4854,7 +4912,7 @@
// calling that twice would erase this information before it could potentially be output between NewTrial and CompeteOrganisms events.
for (int i = 0; i < num_cells; i++) {
if (m_world->GetVerbosity() >= VERBOSE_DETAILS) cout << "Cell " << i << " has " << org_count[i] << " copies in the next generation" << endl;
-
+
if (org_count[i] > 0) {
different_orgs_copied++;
cPhenotype& p = GetCell(i).GetOrganism()->GetPhenotype();
@@ -4903,7 +4961,7 @@
is_init[to_cell_id] = true;
}
-
+
if (!parents_survive)
{
// Now create children from remaining cells into themselves
@@ -4936,15 +4994,15 @@
}
/* This routine is designed to change values in the resource count in the
- middle of a run. This is designed to work with cActionChangeEnvironment
- routine BDB 22-Feb-2008 */
+middle of a run. This is designed to work with cActionChangeEnvironment
+routine BDB 22-Feb-2008 */
void cPopulation::UpdateResourceCount(const int Verbosity) {
const cResourceLib & resource_lib = environment.GetResourceLib();
int global_res_index = -1;
int deme_res_index = -1;
int num_deme_res = 0;
-
+
//setting size of global and deme-level resources
for(int i = 0; i < resource_lib.GetSize(); i++) {
cResource * res = resource_lib.GetResource(i);
@@ -4956,7 +5014,7 @@
cResourceCount tmp_deme_res_count(num_deme_res);
GetDeme(i).SetDemeResourceCount(tmp_deme_res_count);
}
-
+
for (int i = 0; i < resource_lib.GetSize(); i++) {
cResource * res = resource_lib.GetResource(i);
if (!res->GetDemeResource()) {
@@ -4984,5 +5042,5 @@
exit(1);
}
}
-
+
}
Modified: development/source/main/cPopulation.h
===================================================================
--- development/source/main/cPopulation.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cPopulation.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -227,6 +227,7 @@
// Deme-related stats methods
void PrintDemeAllStats();
+ void PrintDemeTestamentStats(const cString& filename);
void PrintDemeDonor();
void PrintDemeFitness();
void PrintDemeGestationTime();
Modified: development/source/main/cPopulationInterface.cc
===================================================================
--- development/source/main/cPopulationInterface.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cPopulationInterface.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -46,7 +46,14 @@
return &m_world->GetPopulation().GetDeme(m_deme_id);
}
+int cPopulationInterface::GetCellData() {
+ return m_world->GetPopulation().GetCell(m_cell_id).GetCellData();
+}
+void cPopulationInterface::SetCellData(const int newData) {
+ m_world->GetPopulation().GetCell(m_cell_id).SetCellData(newData);
+}
+
bool cPopulationInterface::Divide(cAvidaContext& ctx, cOrganism* parent, cGenome& child_genome)
{
assert(parent != NULL);
@@ -62,6 +69,11 @@
return cell.ConnectionList().GetFirst()->GetOrganism();
}
+bool cPopulationInterface::IsNeighborCellOccupied() {
+ cPopulationCell & cell = m_world->GetPopulation().GetCell(m_cell_id);
+ return cell.ConnectionList().GetFirst()->IsOccupied();
+}
+
int cPopulationInterface::GetNumNeighbors()
{
cPopulationCell & cell = m_world->GetPopulation().GetCell(m_cell_id);
@@ -77,6 +89,11 @@
return cell.GetFacing();
}
+int cPopulationInterface::GetNeighborCellContents() {
+ cPopulationCell & cell = m_world->GetPopulation().GetCell(m_cell_id);
+ return cell.ConnectionList().GetFirst()->GetCellData();
+}
+
void cPopulationInterface::Rotate(int direction)
{
cPopulationCell & cell = m_world->GetPopulation().GetCell(m_cell_id);
@@ -258,3 +275,63 @@
return true;
}
+
+bool cPopulationInterface::BcastAlarm(int jump_label, int bcast_range) {
+ bool successfully_sent(false);
+ cPopulationCell& scell = m_world->GetPopulation().GetCell(m_cell_id);
+ assert(scell.IsOccupied()); // This organism; sanity.
+
+ const int ALARM_SELF = m_world->GetConfig().ALARM_SELF.Get(); // does an alarm affect the sender; 0=no non-0=yes
+
+ if(bcast_range > 1) { // multi-hop messaging
+ cDeme& deme = m_world->GetPopulation().GetDeme(GetDemeID());
+ for(int i = 0; i < deme.GetSize(); i++) {
+ int possible_receiver_id = deme.GetCellID(i);
+ cPopulationCell& rcell = m_world->GetPopulation().GetCell(possible_receiver_id);
+
+ if(rcell.IsOccupied() && possible_receiver_id != GetCellID()) {
+ //check distance
+ pair<int, int> sender_pos = deme.GetCellPosition(GetCellID());
+ pair<int, int> possible_receiver_pos = deme.GetCellPosition(possible_receiver_id);
+ int hop_distance = max( abs(sender_pos.first - possible_receiver_pos.first),
+ abs(sender_pos.second - possible_receiver_pos.second));
+ if(hop_distance <= bcast_range) {
+ // send alarm to organisms
+ cOrganism* recvr = rcell.GetOrganism();
+ assert(recvr != NULL);
+ recvr->moveIPtoAlarmLabel(jump_label);
+ successfully_sent = true;
+ }
+ }
+ }
+ } else { // single hop messaging
+ for(int i = 0; i < scell.ConnectionList().GetSize(); i++) {
+ cPopulationCell* rcell = scell.ConnectionList().GetPos(i);
+ assert(rcell != NULL); // Cells should never be null.
+
+ // Fail if the cell we're facing is not occupied.
+ if(!rcell->IsOccupied())
+ continue;
+ cOrganism* recvr = rcell->GetOrganism();
+ assert(recvr != NULL);
+ recvr->moveIPtoAlarmLabel(jump_label);
+ successfully_sent = true;
+ }
+ }
+
+ if(ALARM_SELF) {
+ scell.GetOrganism()->moveIPtoAlarmLabel(jump_label);
+ }
+ return successfully_sent;
+}
+
+void cPopulationInterface::DivideOrgTestamentAmongDeme(double value){
+ cDeme* deme = GetDeme();
+ for(int i = 0; i < deme->GetSize(); i++) {
+ cPopulationCell& cell = deme->GetCell(i);
+ if(cell.IsOccupied()) {
+ cOrganism* org = cell.GetOrganism();
+ org->GetPhenotype().EnergyTestament(value/deme->GetOrgCount());
+ }
+ }
+}
Modified: development/source/main/cPopulationInterface.h
===================================================================
--- development/source/main/cPopulationInterface.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cPopulationInterface.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -65,6 +65,9 @@
cDeme* GetDeme();
void SetCellID(int in_id) { m_cell_id = in_id; }
void SetDemeID(int in_id) { m_deme_id = in_id; }
+
+ int GetCellData();
+ void SetCellData(const int newData);
int GetPrevSeenCellID() { return m_prevseen_cell_id; }
int GetPrevTaskCellID() { return m_prev_task_cell; }
@@ -75,8 +78,10 @@
bool Divide(cAvidaContext& ctx, cOrganism* parent, cGenome& child_genome);
cOrganism* GetNeighbor();
+ bool IsNeighborCellOccupied();
int GetNumNeighbors();
int GetFacing(); // Returns the facing of this organism.
+ int GetNeighborCellContents();
void Rotate(int direction = 1);
void Breakpoint() { m_world->GetDriver().SignalBreakpoint(); }
int GetInputAt(int& input_pointer);
@@ -100,7 +105,9 @@
bool TestOnDivide();
//! Send a message to the faced organism.
bool SendMessage(cOrgMessage& msg);
+ bool BcastAlarm(int jump_label, int bcast_range);
+ void DivideOrgTestamentAmongDeme(double value);
};
Modified: development/source/main/cResourceCount.cc
===================================================================
--- development/source/main/cResourceCount.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cResourceCount.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -492,8 +492,8 @@
}
}
-void cResourceCount::ReinitializeResources(){
+void cResourceCount::ReinitializeResources(double additional_resource){
for(int i = 0; i < resource_name.GetSize(); i++) {
- Set(i, resource_initial[i]);
+ Set(i, resource_initial[i]+additional_resource);
}
}
Modified: development/source/main/cResourceCount.h
===================================================================
--- development/source/main/cResourceCount.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cResourceCount.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -105,7 +105,7 @@
double Get(int id) const;
void ResizeSpatialGrids(int in_x, int in_y);
cSpatialResCount GetSpatialResource(int id) { return spatial_resource_count[id]; }
- void ReinitializeResources();
+ void ReinitializeResources(double additional_resource);
cString GetResName(int id) { return resource_name[id]; }
};
Modified: development/source/main/cStats.cc
===================================================================
--- development/source/main/cStats.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cStats.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -46,6 +46,7 @@
#include <cfloat>
#include <numeric>
#include <cmath>
+#include <sstream>
cStats::cStats(cWorld* world)
@@ -227,9 +228,6 @@
genotype_map.Resize( m_world->GetConfig().WORLD_X.Get() * m_world->GetConfig().WORLD_Y.Get() );
- numAsleep.Resize(m_world->GetConfig().NUM_DEMES.Get());
- numAsleep.SetAll(0);
-
if(m_world->GetConfig().NUM_DEMES.Get() == 0) {
relative_pos_event_count.ResizeClear(m_world->GetConfig().WORLD_X.Get(), m_world->GetConfig().WORLD_Y.Get());
relative_pos_pred_sat.ResizeClear(m_world->GetConfig().WORLD_X.Get(), m_world->GetConfig().WORLD_Y.Get());
@@ -601,8 +599,51 @@
df.Write(sum_deme_gestation_time.Average(), "Gestation Time");
df.Write(sum_deme_normalized_time_used.Average(), "Time Used (normalized by org fitness)");
df.Write(sum_deme_generations_per_lifetime.Average(), "Generations between current and last founders");
+ df.Write(sum_deme_events_killed.Average(), "Events killed");
+ df.Write(sum_deme_events_kill_attempts.Average(), "Attempts to kill event");
+
+ df.Endl();
+}
+void cStats::PrintFlowRateTuples(const cString& filename) {
+ cDataFile& df = m_world->GetDataFile(filename);
+
+ df.WriteComment("Flow Rate Tuples");
+ df.WriteTimeStamp();
+
+ df.Write(m_update, "Update");
+ // write each tuple
+ for(map<int, flow_rate_tuple>::iterator iter = flow_rate_tuples.begin(); iter != flow_rate_tuples.end(); iter++) {
+ ostringstream oss;
+ oss << "flow rate " << (*iter).first;
+ string flow_rate_str(oss.str());
+ string flow_rate_pop_size_str(flow_rate_str+" deme pop size");
+ string flow_rate_events_killed_str(flow_rate_str+" events killed");
+ string flow_rate_events_attempted_to_kill_str(flow_rate_str+" events attempted to kill");
+ string flow_rate_exe_ratio_str(flow_rate_str+" exe ratio");
+ string flow_rate_total_births_str(flow_rate_str+" total births");
+ string flow_rate_total_sleeping_str(flow_rate_str+" total sleeping");
+
+ df.Write((*iter).first, flow_rate_str.c_str());
+ df.Write((*iter).second.orgCount.Average(), flow_rate_pop_size_str.c_str());
+ df.Write((*iter).second.eventsKilled.Average(), flow_rate_events_killed_str.c_str());
+ df.Write((*iter).second.attemptsToKillEvents.Average(), flow_rate_events_attempted_to_kill_str.c_str());
+ df.Write((*iter).second.AvgEnergyUsageRatio.Average(), flow_rate_exe_ratio_str.c_str());
+ df.Write((*iter).second.totalBirths.Average(), flow_rate_total_births_str.c_str());
+ df.Write((*iter).second.currentSleeping.Average(), flow_rate_total_sleeping_str.c_str());
+
+ }
df.Endl();
+
+ // reset all tuples
+ for(map<int, flow_rate_tuple >::iterator iter = flow_rate_tuples.begin(); iter != flow_rate_tuples.end(); iter++) {
+ (*iter).second.orgCount.Clear();
+ (*iter).second.eventsKilled.Clear();
+ (*iter).second.attemptsToKillEvents.Clear();
+ (*iter).second.AvgEnergyUsageRatio.Clear();
+ (*iter).second.totalBirths.Clear();
+ (*iter).second.currentSleeping.Clear();
+ }
}
void cStats::PrintErrorData(const cString& filename)
@@ -1152,9 +1193,12 @@
df.WriteComment("total number of organisms sleeping" );
df.Write( GetUpdate(), "update" );
-
- for( int i=0; i < numAsleep.GetSize(); i++ ){
- df.Write(numAsleep[i], cStringUtil::Stringf("DemeID %d", i));
+
+ cPopulation& pop = m_world->GetPopulation();
+ int numDemes = pop.GetNumDemes();
+
+ for( int i=0; i < numDemes; i++ ){
+ df.Write(pop.GetDeme(i).GetSleepingCount(), cStringUtil::Stringf("DemeID %d", i));
}
df.Endl();
}
@@ -1313,10 +1357,6 @@
m_deme_births.Add(source_deme.GetBirthCount());
m_deme_merit.Add(source_deme.GetHeritableDemeMerit().GetDouble());
m_deme_generation.Add(source_deme.GetGeneration());
-
- // reset #orgs. sleeping in demes
- numAsleep[source_deme.GetID()]=0;
- numAsleep[target_deme.GetID()]=0;
}
Modified: development/source/main/cStats.h
===================================================================
--- development/source/main/cStats.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cStats.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -77,6 +77,15 @@
class cDeme;
class cGermline;
+struct flow_rate_tuple {
+ cIntSum orgCount;
+ cIntSum eventsKilled;
+ cIntSum attemptsToKillEvents;
+ cDoubleSum AvgEnergyUsageRatio;
+ cIntSum totalBirths;
+ cIntSum currentSleeping;
+};
+
class cStats
{
#if USE_tMemTrack
@@ -269,7 +278,7 @@
double max_competition_copied_fitness;
int num_orgs_replicated;
- tArray<int> numAsleep;
+// tArray<int> numAsleep;
// simple deme stats
cIntSum sum_deme_age;
@@ -284,6 +293,18 @@
cDoubleSum sum_deme_generations_per_lifetime;
int m_num_occupied_demes;
+ cIntSum sum_deme_events_killed;
+ cIntSum sum_deme_events_kill_attempts;
+
+ cDoubleSum EnergyTestamentToFutureDeme;
+ cDoubleSum EnergyTestamentToNeighborOrganisms;
+ cDoubleSum EnergyTestamentToDemeOrganisms;
+ cDoubleSum EnergyTestamentAcceptedByOrganisms;
+ cDoubleSum EnergyTestamentAcceptedByDeme;
+
+ //(event flow rate, (deme pop size, events killed))
+ std::map<int, flow_rate_tuple > flow_rate_tuples;
+
// deme predicate stats
tMatrix<int> relative_pos_event_count;
tMatrix<int> relative_pos_pred_sat;
@@ -435,6 +456,17 @@
cDoubleSum& SumDemeMerit() { return sum_deme_merit; }
cDoubleSum& SumDemeGenerationsPerLifetime() { return sum_deme_generations_per_lifetime; }
+ cIntSum& SumDemeEventsKilled() { return sum_deme_events_killed; }
+ cIntSum& SumDemeAttemptsToKillEvents() { return sum_deme_events_kill_attempts; }
+
+ cDoubleSum& SumEnergyTestamentToFutureDeme() { return EnergyTestamentToFutureDeme;}
+ cDoubleSum& SumEnergyTestamentToNeighborOrganisms() { return EnergyTestamentToNeighborOrganisms; }
+ cDoubleSum& SumEnergyTestamentToDemeOrganisms() { return EnergyTestamentToDemeOrganisms; }
+ cDoubleSum& SumEnergyTestamentAcceptedByOrganisms() { return EnergyTestamentAcceptedByOrganisms; }
+ cDoubleSum& SumEnergyTestamentAcceptedByDeme() { return EnergyTestamentAcceptedByDeme; }
+
+ std::map<int, flow_rate_tuple >& FlowRateTuples() { return flow_rate_tuples; }
+
#if INSTRUCTION_COUNT
void ZeroInst();
#endif
@@ -478,6 +510,17 @@
const cDoubleSum& SumDemeMerit() const { return sum_deme_merit; }
const cDoubleSum& SumDemeGenerationsPerLifetime() const { return sum_deme_generations_per_lifetime; }
+ const cIntSum& SumDemeEventsKilled() const { return sum_deme_events_killed; }
+ const cIntSum& SumDemeAttemptsToKillEvents() const { return sum_deme_events_kill_attempts; }
+
+ const cDoubleSum& SumEnergyTestamentToFutureDeme() const { return EnergyTestamentToFutureDeme;}
+ const cDoubleSum& SumEnergyTestamentToNeighborOrganisms() const { return EnergyTestamentToNeighborOrganisms; }
+ const cDoubleSum& SumEnergyTestamentToDemeOrganisms() const { return EnergyTestamentToDemeOrganisms; }
+ const cDoubleSum& SumEnergyTestamentAcceptedByOrganisms() const { return EnergyTestamentAcceptedByOrganisms; }
+ const cDoubleSum& SumEnergyTestamentAcceptedByDeme() const { return EnergyTestamentAcceptedByDeme; }
+
+ const std::map<int, flow_rate_tuple >& FlowRateTuples() const { return flow_rate_tuples; }
+
void IncResamplings() { ++num_resamplings; } // @AWC 06/29/06
void IncFailedResamplings() { ++num_failedResamplings; } // @AWC 06/29/06
@@ -650,10 +693,10 @@
int GetNumSenseSlots();
- int getNumAsleep(int demeID) { return numAsleep[demeID]; }
+/* int getNumAsleep(int demeID) { return numAsleep[demeID]; }
void incNumAsleep(int demeID) { numAsleep[demeID]++; }
void decNumAsleep(int demeID) { numAsleep[demeID]--; }
-
+*/
double GetAveSpeculative() const { return (m_spec_num) ? ((double)m_spec_total / (double)m_spec_num) : 0.0; }
int GetSpeculativeWaste() const { return m_spec_waste; }
@@ -669,6 +712,7 @@
// Public calls to output data files (for events)
void PrintAverageData(const cString& filename);
void PrintDemeAverageData(const cString& filename);
+ void PrintFlowRateTuples(const cString& filename);
void PrintErrorData(const cString& filename);
void PrintVarianceData(const cString& filename);
void PrintDominantData(const cString& filename);
Modified: development/source/main/cTaskLib.cc
===================================================================
--- development/source/main/cTaskLib.cc 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cTaskLib.cc 2008-06-16 15:40:36 UTC (rev 2648)
@@ -27,6 +27,7 @@
#include "cTaskLib.h"
#include "cArgSchema.h"
+#include "cDeme.h"
#include "cEnvReqs.h"
#include "tHashTable.h"
#include "cTaskState.h"
@@ -411,6 +412,11 @@
else if (name == "movebetweenevent")
NewTask(name, "Move to a target area", &cTaskLib::Task_MoveBetweenMovementEvent);
+ // event tasks
+ if(name == "move_to_event")
+ NewTask(name, "Moved into cell containing event", &cTaskLib::Task_MoveToEvent);
+ else if(name == "event_killed")
+ NewTask(name, "Killed event", &cTaskLib::Task_EventKilled);
// Make sure we have actually found a task
if (task_array.GetSize() == start_size) {
@@ -2971,7 +2977,7 @@
cOrgInterface* iface = ctx.GetOrgInterface();
int prev_target = deme.GetRelativeCellID(iface->GetPrevTaskCellID());
- int cellid = ctx.GetOrgInterface()->GetCellID();
+// int cellid = ctx.GetOrgInterface()->GetCellID();
// NOTE: as of now, orgs aren't rewarded if they touch a target more than
// once in a row. Could be useful in the future to have fractional reward
@@ -3007,3 +3013,21 @@
return 0.0;
}
+double cTaskLib::Task_MoveToEvent(cTaskContext& ctx) const {
+ cDeme* deme = ctx.GetOrganism()->GetOrgInterface().GetDeme();
+ int cell_data = ctx.GetOrganism()->GetOrgInterface().GetCellData();
+ if(cell_data <= 0)
+ return 0.0;
+
+ for(int i = 0; i < deme->GetNumEvents(); i++) {
+ if(deme->GetCellEvent(i)->GetEventID() == cell_data)
+ return 1.0;
+ }
+ return 0.0;
+}
+
+double cTaskLib::Task_EventKilled(cTaskContext& ctx) const {
+ if(ctx.GetOrganism()->GetEventKilled())
+ return 1.0;
+ return 0.0;
+}
Modified: development/source/main/cTaskLib.h
===================================================================
--- development/source/main/cTaskLib.h 2008-06-15 23:58:31 UTC (rev 2647)
+++ development/source/main/cTaskLib.h 2008-06-16 15:40:36 UTC (rev 2648)
@@ -293,6 +293,9 @@
double Task_MoveToMovementEvent(cTaskContext& ctx) const;
double Task_MoveBetweenMovementEvent(cTaskContext& ctx) const;
+ // movement
+ double Task_MoveToEvent(cTaskContext& ctx) const;
+ double Task_EventKilled(cTaskContext& ctx) const;
};
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