[Avida-SVN] r2152 - in branches/collect: Avida.xcodeproj source/actions source/cpu source/main tests/energy_deme_level_res
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Tue Oct 23 20:34:18 PDT 2007
Author: blwalker
Date: 2007-10-23 23:34:18 -0400 (Tue, 23 Oct 2007)
New Revision: 2152
Added:
branches/collect/source/main/cDemeCellEvent.cc
branches/collect/source/main/cDemeCellEvent.h
Removed:
branches/collect/tests/energy_deme_level_res/expected/
Modified:
branches/collect/Avida.xcodeproj/project.pbxproj
branches/collect/source/actions/EnvironmentActions.cc
branches/collect/source/actions/PopulationActions.cc
branches/collect/source/actions/PrintActions.cc
branches/collect/source/cpu/cHardwareBase.cc
branches/collect/source/cpu/cHardwareCPU.cc
branches/collect/source/cpu/cHardwareCPU.h
branches/collect/source/main/cAvidaConfig.h
branches/collect/source/main/cDeme.cc
branches/collect/source/main/cDeme.h
branches/collect/source/main/cOrganism.cc
branches/collect/source/main/cPhenotype.cc
branches/collect/source/main/cPhenotype.h
branches/collect/source/main/cPopulation.cc
branches/collect/source/main/cPopulationCell.cc
branches/collect/source/main/cPopulationCell.h
Log:
Porting development 2053:2070 to the collect branch.
Note: This will not build properly, as r2070 contains a problem with CMakeLists.txt (subsequently fixed in r2073).
Modified: branches/collect/Avida.xcodeproj/project.pbxproj
===================================================================
--- branches/collect/Avida.xcodeproj/project.pbxproj 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/Avida.xcodeproj/project.pbxproj 2007-10-24 03:34:18 UTC (rev 2152)
@@ -195,6 +195,7 @@
70F9FC100C469DD70083B788 /* cASTDumpVisitor.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70F9FC0F0C469DC10083B788 /* cASTDumpVisitor.cc */; };
B4FA258A0C5EB65E0086D4B5 /* cPlasticPhenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = B4FA25810C5EB6510086D4B5 /* cPlasticPhenotype.cc */; };
B4FA25A90C5EB7880086D4B5 /* cPhenPlastGenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = B4FA259E0C5EB7600086D4B5 /* cPhenPlastGenotype.cc */; };
+ B516AF840C91E2D400023D53 /* cDemeCellEvent.cc in Sources */ = {isa = PBXBuildFile; fileRef = B516AF790C91E24600023D53 /* cDemeCellEvent.cc */; };
DCD8AC1F0C8A7C30004CBE6F /* cAnalyzeGenotypeTreeStats.cc in Sources */ = {isa = PBXBuildFile; fileRef = DCA4BEC10C8A758800D81B58 /* cAnalyzeGenotypeTreeStats.cc */; };
/* End PBXBuildFile section */
@@ -211,6 +212,23 @@
};
/* End PBXBuildRule section */
+/* Begin PBXBuildStyle section */
+ B516AF180C91DC7700023D53 /* Development */ = {
+ isa = PBXBuildStyle;
+ buildSettings = {
+ COPY_PHASE_STRIP = NO;
+ };
+ name = Development;
+ };
+ B516AF190C91DC7700023D53 /* Deployment */ = {
+ isa = PBXBuildStyle;
+ buildSettings = {
+ COPY_PHASE_STRIP = YES;
+ };
+ name = Deployment;
+ };
+/* End PBXBuildStyle section */
+
/* Begin PBXContainerItemProxy section */
56F555DA0C3B36FC00E2E929 /* PBXContainerItemProxy */ = {
isa = PBXContainerItemProxy;
@@ -818,6 +836,8 @@
B4FA25810C5EB6510086D4B5 /* cPlasticPhenotype.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cPlasticPhenotype.cc; sourceTree = "<group>"; };
B4FA25820C5EB6510086D4B5 /* cPlasticPhenotype.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cPlasticPhenotype.h; sourceTree = "<group>"; };
B4FA259E0C5EB7600086D4B5 /* cPhenPlastGenotype.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cPhenPlastGenotype.cc; sourceTree = "<group>"; };
+ B516AF790C91E24600023D53 /* cDemeCellEvent.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; name = cDemeCellEvent.cc; path = source/main/cDemeCellEvent.cc; sourceTree = SOURCE_ROOT; };
+ B516AF7A0C91E24600023D53 /* cDemeCellEvent.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = cDemeCellEvent.h; path = source/main/cDemeCellEvent.h; sourceTree = SOURCE_ROOT; };
DCA4BEC10C8A758800D81B58 /* cAnalyzeGenotypeTreeStats.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cAnalyzeGenotypeTreeStats.cc; sourceTree = "<group>"; };
DCA4BEC20C8A758800D81B58 /* cAnalyzeGenotypeTreeStats.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cAnalyzeGenotypeTreeStats.h; sourceTree = "<group>"; };
DCC30FCF0762539D008F7A48 /* Doxyfile */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = Doxyfile; sourceTree = "<group>"; };
@@ -1336,6 +1356,8 @@
70C1EFA308C39F2100F50912 /* cHardwareBase.cc */,
70C1EF9E08C39F0E00F50912 /* cHardwareBase.h */,
70C1EFA508C39F2100F50912 /* cHardwareCPU.cc */,
+ B516AF790C91E24600023D53 /* cDemeCellEvent.cc */,
+ B516AF7A0C91E24600023D53 /* cDemeCellEvent.h */,
70C1EFA008C39F0E00F50912 /* cHardwareCPU.h */,
423335880BC067E3000DF681 /* cHardwareGX.cc */,
423335890BC067E3000DF681 /* cHardwareGX.h */,
@@ -1774,6 +1796,12 @@
DCC30C4D0762532C008F7A48 /* Project object */ = {
isa = PBXProject;
buildConfigurationList = 702442D70859E0B00059BD9B /* Build configuration list for PBXProject "Avida" */;
+ buildSettings = {
+ };
+ buildStyles = (
+ B516AF180C91DC7700023D53 /* Development */,
+ B516AF190C91DC7700023D53 /* Deployment */,
+ );
hasScannedForEncodings = 0;
mainGroup = DCC30C490762532C008F7A48;
productRefGroup = DCC3164E07626CF3008F7A48 /* Products */;
@@ -1957,6 +1985,7 @@
70436B6C0C36C98900A05ABA /* PlatformExpert.cc in Sources */,
B4FA258A0C5EB65E0086D4B5 /* cPlasticPhenotype.cc in Sources */,
B4FA25A90C5EB7880086D4B5 /* cPhenPlastGenotype.cc in Sources */,
+ B516AF840C91E2D400023D53 /* cDemeCellEvent.cc in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
Modified: branches/collect/source/actions/EnvironmentActions.cc
===================================================================
--- branches/collect/source/actions/EnvironmentActions.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/actions/EnvironmentActions.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -455,8 +455,40 @@
}
};
+class cActionDelayedDemeEvent : 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
+
+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)
+ {
+ 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();
+ }
+
+ static const cString GetDescription() { return "Arguments: <int x1> <int y1> <int x2> <int y2> <int delay> <int duraion>"; }
+
+ 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);
+ }
+ }
+};
+
void RegisterEnvironmentActions(cActionLibrary* action_lib)
{
+ action_lib->Register<cActionDelayedDemeEvent>("DelayedDemeEvent");
action_lib->Register<cActionInjectResource>("InjectResource");
action_lib->Register<cActionInjectScaledResource>("InjectScaledResource");
action_lib->Register<cActionOutflowScaledResource>("OutflowScaledResource");
Modified: branches/collect/source/actions/PopulationActions.cc
===================================================================
--- branches/collect/source/actions/PopulationActions.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/actions/PopulationActions.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -988,6 +988,7 @@
'all' - ...all non-empty demes in the population.
'full_deme' - ...demes that have been filled up.
'corners' - ...demes with upper left and lower right corners filled.
+ 'deme-age' - ...demes that are a certain age
*/
class cActionReplicateDemes : public cAction
Modified: branches/collect/source/actions/PrintActions.cc
===================================================================
--- branches/collect/source/actions/PrintActions.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/actions/PrintActions.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -2126,7 +2126,96 @@
}
};
+class cActionDumpEnergyGrid : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionDumpEnergyGrid(cWorld* world, const cString& args) : cAction(world, args), m_filename("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ }
+ static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ void Process(cAvidaContext& ctx)
+ {
+ cString filename(m_filename);
+ if (filename == "") filename.Set("grid_energy.%d.dat", m_world->GetStats().GetUpdate());
+ ofstream& fp = m_world->GetDataFileOFStream(filename);
+
+ for (int i = 0; i < m_world->GetPopulation().GetWorldY(); i++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldX(); j++) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(i * m_world->GetPopulation().GetWorldX() + j);
+ double cell_energy = (cell.IsOccupied()) ? cell.GetOrganism()->GetPhenotype().GetStoredEnergy() : 0.0;
+ fp << cell_energy << " ";
+ }
+ fp << endl;
+ }
+ m_world->GetDataFileManager().Remove(filename);
+ }
+};
+class cActionDumpExecutionRatioGrid : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionDumpExecutionRatioGrid(cWorld* world, const cString& args) : cAction(world, args), m_filename("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ }
+ static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ void Process(cAvidaContext& ctx)
+ {
+ cString filename(m_filename);
+ if (filename == "") filename.Set("grid_exe_ratio.%d.dat", m_world->GetStats().GetUpdate());
+ ofstream& fp = m_world->GetDataFileOFStream(filename);
+
+ for (int i = 0; i < m_world->GetPopulation().GetWorldY(); i++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldX(); j++) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(i * m_world->GetPopulation().GetWorldX() + j);
+ double cell_executionRatio = (cell.IsOccupied()) ? cell.GetOrganism()->GetPhenotype().GetEnergyUsageRatio() : 1.0;
+ fp << cell_executionRatio << " ";
+ }
+ fp << endl;
+ }
+ m_world->GetDataFileManager().Remove(filename);
+ }
+};
+
+class cActionDumpCellDataGrid : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionDumpCellDataGrid(cWorld* world, const cString& args) : cAction(world, args), m_filename("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ }
+ static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ void Process(cAvidaContext& ctx)
+ {
+ cString filename(m_filename);
+ if (filename == "") filename.Set("grid_cell_data.%d.dat", m_world->GetStats().GetUpdate());
+ ofstream& fp = m_world->GetDataFileOFStream(filename);
+
+ for (int i = 0; i < m_world->GetPopulation().GetWorldY(); i++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldX(); j++) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(i * m_world->GetPopulation().GetWorldX() + j);
+ double cell_data = cell.GetCellData();
+ fp << cell_data << " ";
+ }
+ fp << endl;
+ }
+ m_world->GetDataFileManager().Remove(filename);
+ }
+};
+
class cActionDumpFitnessGrid : public cAction
{
private:
@@ -2250,6 +2339,35 @@
}
};
+class cActionDumpSleepGrid : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionDumpSleepGrid(cWorld* world, const cString& args) : cAction(world, args), m_filename("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ }
+ static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ void Process(cAvidaContext& ctx)
+ {
+ cString filename(m_filename);
+ if (filename == "") filename.Set("grid_sleep.%d.dat", m_world->GetStats().GetUpdate());
+ ofstream& fp = m_world->GetDataFileOFStream(filename);
+
+ for (int i = 0; i < m_world->GetPopulation().GetWorldY(); i++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldX(); j++) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(i * m_world->GetPopulation().GetWorldX() + j);
+ double cell_energy = (cell.IsOccupied()) ? cell.GetOrganism()->IsSleeping() : 0.0;
+ fp << cell_energy << " ";
+ }
+ fp << endl;
+ }
+ m_world->GetDataFileManager().Remove(filename);
+ }
+};
class cActionDumpTaskGrid : public cAction
{
@@ -2567,6 +2685,10 @@
action_lib->Register<cActionDumpTaskGrid>("DumpTaskGrid");
action_lib->Register<cActionDumpDonorGrid>("DumpDonorGrid");
action_lib->Register<cActionDumpReceiverGrid>("DumpReceiverGrid");
+ action_lib->Register<cActionDumpEnergyGrid>("DumpEnergyGrid");
+ action_lib->Register<cActionDumpExecutionRatioGrid>("DumpExecutionRatioGrid");
+ action_lib->Register<cActionDumpCellDataGrid>("DumpCellDataGrid");
+ action_lib->Register<cActionDumpSleepGrid>("DumpSleepGrid");
// Print Settings
action_lib->Register<cActionSetVerbose>("SetVerbose");
Modified: branches/collect/source/cpu/cHardwareBase.cc
===================================================================
--- branches/collect/source/cpu/cHardwareBase.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/cpu/cHardwareBase.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -817,8 +817,11 @@
}
bool cHardwareBase::Inst_DoubleEnergyUsage(cAvidaContext& ctx) {
- organism->GetPhenotype().DoubleEnergyUsage();
- return true;
+ 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);
}
bool cHardwareBase::Inst_HalfEnergyUsage(cAvidaContext& ctx) {
@@ -826,7 +829,6 @@
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.
@@ -840,6 +842,7 @@
double energy_req = inst_energy_cost[cur_inst.GetOp()] * (organism->GetPhenotype().GetMerit().GetDouble() / 100.0); //compensate by factor of 100
if (energy_req > 0.0) {
+ int cellID = organism->GetCellID();
if (organism->GetPhenotype().GetStoredEnergy() >= energy_req) {
inst_energy_cost[cur_inst.GetOp()] = 0;
// subtract energy used from current org energy.
@@ -847,7 +850,6 @@
// tracking sleeping organisms
cString instName = m_world->GetHardwareManager().GetInstSet().GetName(cur_inst);
- int cellID = organism->GetCellID();
if( instName == cString("sleep") || instName == cString("sleep1") || instName == cString("sleep2") ||
instName == cString("sleep3") || instName == cString("sleep4")) {
cPopulation& pop = m_world->GetPopulation();
@@ -857,7 +859,8 @@
pop.GetCell(cellID).GetOrganism()->SetSleeping(true);
m_world->GetStats().incNumAsleep(pop.GetCell(cellID).GetDemeID());
}
- } else { // not enough energy
+ } else {
+ organism->GetPhenotype().SetToDie();
return false;
}
}
Modified: branches/collect/source/cpu/cHardwareCPU.cc
===================================================================
--- branches/collect/source/cpu/cHardwareCPU.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/cpu/cHardwareCPU.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -50,6 +50,7 @@
#include <climits>
#include <fstream>
+#include <cmath>
using namespace std;
@@ -203,7 +204,9 @@
tInstLibEntry<tMethod>("sense", &cHardwareCPU::Inst_SenseLog2), // If you add more sense instructions
tInstLibEntry<tMethod>("sense-unit", &cHardwareCPU::Inst_SenseUnit), // and want to keep stats, also add
tInstLibEntry<tMethod>("sense-m100", &cHardwareCPU::Inst_SenseMult100), // the names to cStats::cStats() @JEB
-
+ // Data collection
+ tInstLibEntry<tMethod>("collect-cell-data", &cHardwareCPU::Inst_CollectCellData),
+
tInstLibEntry<tMethod>("collect", &cHardwareCPU::Inst_Collect),
tInstLibEntry<tMethod>("donate-rnd", &cHardwareCPU::Inst_DonateRandom),
@@ -223,11 +226,12 @@
tInstLibEntry<tMethod>("rotate-r", &cHardwareCPU::Inst_RotateR),
tInstLibEntry<tMethod>("rotate-left-one", &cHardwareCPU::Inst_RotateLeftOne),
tInstLibEntry<tMethod>("rotate-right-one", &cHardwareCPU::Inst_RotateRightOne),
-
tInstLibEntry<tMethod>("rotate-label", &cHardwareCPU::Inst_RotateLabel),
tInstLibEntry<tMethod>("set-cmut", &cHardwareCPU::Inst_SetCopyMut),
tInstLibEntry<tMethod>("mod-cmut", &cHardwareCPU::Inst_ModCopyMut),
+ tInstLibEntry<tMethod>("get-cell-xy", &cHardwareCPU::Inst_GetCellPosition),
+ tInstLibEntry<tMethod>("dist-from-diag", &cHardwareCPU::Inst_GetDistanceFromDiagonal),
// @WRE additions for movement
tInstLibEntry<tMethod>("tumble", &cHardwareCPU::Inst_Tumble),
tInstLibEntry<tMethod>("move", &cHardwareCPU::Inst_Move),
@@ -358,6 +362,8 @@
// Promoter Model
tInstLibEntry<tMethod>("promoter", &cHardwareCPU::Inst_Promoter),
tInstLibEntry<tMethod>("terminate", &cHardwareCPU::Inst_Terminate),
+ tInstLibEntry<tMethod>("promoter", &cHardwareCPU::Inst_Promoter),
+ tInstLibEntry<tMethod>("terminate", &cHardwareCPU::Inst_Terminate),
tInstLibEntry<tMethod>("regulate", &cHardwareCPU::Inst_Regulate),
tInstLibEntry<tMethod>("numberate", &cHardwareCPU::Inst_Numberate),
@@ -368,7 +374,7 @@
// Messaging
tInstLibEntry<tMethod>("send-msg", &cHardwareCPU::Inst_SendMessage),
tInstLibEntry<tMethod>("retrieve-msg", &cHardwareCPU::Inst_RetrieveMessage),
-
+
// Placebo instructions
tInstLibEntry<tMethod>("skip", &cHardwareCPU::Inst_Skip),
@@ -3217,6 +3223,13 @@
return true;
}
+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();
+ return true;
+}
+
void cHardwareCPU::DoDonate(cOrganism* to_org)
{
assert(to_org != NULL);
@@ -3248,12 +3261,12 @@
//update energy store and merit of donor
organism->GetPhenotype().ReduceEnergy(energy_given);
- double senderMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy(), m_world) * organism->GetPhenotype().GetExecutionRatio();
+ double senderMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio(), m_world);
organism->UpdateMerit(senderMerit);
// update energy store and merit of donee
to_org->GetPhenotype().ReduceEnergy(-1.0*energy_given);
- double receiverMerit = cMerit::EnergyToMerit(to_org->GetPhenotype().GetStoredEnergy(), m_world) * to_org->GetPhenotype().GetExecutionRatio();
+ double receiverMerit = cMerit::EnergyToMerit(to_org->GetPhenotype().GetStoredEnergy() * to_org->GetPhenotype().GetEnergyUsageRatio(), m_world);
to_org->UpdateMerit(receiverMerit);
}
@@ -4353,17 +4366,17 @@
bool cHardwareCPU::Inst_Sleep(cAvidaContext& ctx) {
cPopulation& pop = m_world->GetPopulation();
+ int cellID = organism->GetCellID();
if(m_world->GetConfig().LOG_SLEEP_TIMES.Get() == 1) {
- pop.AddEndSleep(organism->GetCellID(), m_world->GetStats().GetUpdate());
+ pop.AddEndSleep(cellID, m_world->GetStats().GetUpdate());
}
- int cellID = organism->GetCellID();
organism->SetSleeping(false); //this instruction get executed at the end of a sleep cycle
m_world->GetStats().decNumAsleep(pop.GetCell(cellID).GetDemeID());
if(m_world->GetConfig().APPLY_ENERGY_METHOD.Get() == 2) {
organism->GetPhenotype().RefreshEnergy();
organism->GetPhenotype().ApplyToEnergyStore();
- double newMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy(), m_world) * organism->GetPhenotype().GetExecutionRatio();
- pop.UpdateMerit(organism->GetCellID(), newMerit);
+ double newMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio(), m_world);
+ pop.UpdateMerit(cellID, newMerit);
}
return true;
}
@@ -4374,13 +4387,40 @@
return true;
}
+bool cHardwareCPU::Inst_GetCellPosition(cAvidaContext& ctx) {
+ int absolute_cell_ID = organism->GetCellID();
+ int deme_id = organism->GetOrgInterface().GetDemeID();
+ std::pair<int, int> pos = m_world->GetPopulation().GetDeme(deme_id).GetCellPosition(absolute_cell_ID);
+ const int xreg = FindModifiedRegister(REG_BX);
+ const int yreg = FindNextRegister(xreg);
+ GetRegister(xreg) = pos.first;
+ GetRegister(yreg) = pos.second;
+ return true;
+}
+bool cHardwareCPU::Inst_GetDistanceFromDiagonal(cAvidaContext& ctx) {
+ int absolute_cell_ID = organism->GetOrgInterface().GetCellID();
+ int deme_id = organism->GetOrgInterface().GetDemeID();
+ std::pair<int, int> pos = m_world->GetPopulation().GetDeme(deme_id).GetCellPosition(absolute_cell_ID);
+ const int reg = FindModifiedRegister(REG_BX);
+
+ if(pos.first > pos.second) {
+ GetRegister(reg) = (int)ceil((pos.first - pos.second)/2.0);
+ } else {
+ GetRegister(reg) = (int)floor((pos.first - pos.second)/2.0);
+ }
+// std::cerr<<"x = "<<pos.first<<" y = "<<pos.second<<" ans = "<<GetRegister(reg)<<std::endl;
+ return true;
+}
+
//// Promoter Model ////
bool cHardwareCPU::Inst_Promoter(cAvidaContext& ctx)
{
// Promoters don't do anything themselves
return true;
+// std::cerr<<"x = "<<pos.first<<" y = "<<pos.second<<" ans = "<<GetRegister(reg)<<std::endl;
+ return true;
}
// Move the instruction ptr to the next active promoter
@@ -4564,7 +4604,6 @@
return code;
}
-
/*! Send a message to the organism that is currently faced by this cell,
where the label field of sent message is from register ?BX?, and the data field
is from register ~?BX?.
Modified: branches/collect/source/cpu/cHardwareCPU.h
===================================================================
--- branches/collect/source/cpu/cHardwareCPU.h 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/cpu/cHardwareCPU.h 2007-10-24 03:34:18 UTC (rev 2152)
@@ -441,9 +441,9 @@
bool Inst_SenseUnit(cAvidaContext& ctx);
bool Inst_SenseMult100(cAvidaContext& ctx);
bool DoSense(cAvidaContext& ctx, int conversion_method, double base);
-
bool FindModifiedResource(int& start_index, int& end_index);
bool Inst_Collect(cAvidaContext& ctx);
+ bool Inst_CollectCellData(cAvidaContext& ctx);
void DoDonate(cOrganism * to_org);
void DoEnergyDonate(cOrganism* to_org);
@@ -473,6 +473,8 @@
bool Inst_RotateLabel(cAvidaContext& ctx);
bool Inst_SetCopyMut(cAvidaContext& ctx);
bool Inst_ModCopyMut(cAvidaContext& ctx);
+ bool Inst_GetCellPosition(cAvidaContext& ctx);
+ bool Inst_GetDistanceFromDiagonal(cAvidaContext& ctx);
// @WRE additions for movement
bool Inst_Tumble(cAvidaContext& ctx);
bool Inst_Move(cAvidaContext& ctx);
Modified: branches/collect/source/main/cAvidaConfig.h
===================================================================
--- branches/collect/source/main/cAvidaConfig.h 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cAvidaConfig.h 2007-10-24 03:34:18 UTC (rev 2152)
@@ -299,7 +299,7 @@
CONFIG_ADD_VAR(DEMES_HAVE_MERIT, int, 0, "Whether demes have merit; 0=no");
CONFIG_ADD_VAR(GERMLINE_COPY_MUT, double, 0.0075, "Prob. of copy mutations occuring during\ngermline replication.");
CONFIG_ADD_VAR(GERMLINE_REPLACES_SOURCE, int, 0, "Whether the source germline is updated\non replication; 0=no.");
- CONFIG_ADD_VAR(GERMLINE_RANDOM_PLACEMENT, int, 0, "Whether the seed for a germline is placed\n randomly within the deme; 0=no.");
+ CONFIG_ADD_VAR(GERMLINE_RANDOM_PLACEMENT, int, 0, "Defines how the seed for a germline is placed\n within the deme;\n0 = organisms is placed in center of deme, no orientation\n1 = organisms is placed in center of deme and oriented\n2 = organism is randomly placed in deme, no orientation");
CONFIG_ADD_VAR(MAX_DEME_AGE, int, 500, "The maximum age of a deme (in updates) to be\nused for age-based replication (default=500).");
CONFIG_ADD_GROUP(REPRODUCTION_GROUP, "Birth and Death");
Modified: branches/collect/source/main/cDeme.cc
===================================================================
--- branches/collect/source/main/cDeme.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cDeme.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -22,15 +22,17 @@
*/
#include "cDeme.h"
+#include "cPopulation.h"
#include "cPopulationCell.h"
#include "cResource.h"
+#include "cWorld.h"
-
-void cDeme::Setup(const tArray<int> & in_cells, int in_width)
+void cDeme::Setup(const tArray<int> & in_cells, int in_width, cWorld* world)
{
cell_ids = in_cells;
birth_count = 0;
org_count = 0;
+ m_world = world;
// If width is negative, set it to the full number of cells.
width = in_width;
@@ -60,11 +62,36 @@
return std::make_pair(cellid % GetWidth(), cellid / GetWidth());
}
+void cDeme::ProcessUpdate() {
+ for(int i = 0; i < cell_events.GetSize(); i++) {
+ cDemeCellEvent& event = cell_events[i];
+ if(event.GetDelay() == _age) {
+ event.ActivateEvent(m_world); //start event
+ int eventCell = event.GetNextEventCellID();
+ while(eventCell != -1) {
+ // place event ID in cells' data
+ m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(event.GetEventID());
+ eventCell = event.GetNextEventCellID();
+ }
+ } else if(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();
+ }
+ }
+ event.DeactivateEvent(); //event over
+ }
+ }
+ ++_age;
+}
void cDeme::Reset()
{
birth_count = 0;
- _age = 0;
+ _age = 0;
//clear cell energy
deme_resource_count.ReinitializeResources();
@@ -141,3 +168,8 @@
}
deme_resource_count.ModifyCell(cell_resources, relative_cell_id);
}
+
+void cDeme::SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration) {
+ cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width);
+ cell_events.Push(demeEvent);
+}
Modified: branches/collect/source/main/cDeme.h
===================================================================
--- branches/collect/source/main/cDeme.h 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cDeme.h 2007-10-24 03:34:18 UTC (rev 2152)
@@ -24,12 +24,14 @@
#ifndef cDeme_h
#define cDeme_h
+#include "cDemeCellEvent.h"
#include "cGermline.h"
#include "tArray.h"
#include "cResourceCount.h"
#include "cStringList.h"
class cResource;
+class cWorld;
/*! Demes are groups of cells in the population that are somehow bound together
as a unit. The deme object is used from within cPopulation to manage these
@@ -38,6 +40,7 @@
class cDeme
{
private:
+ cWorld* m_world;
tArray<int> cell_ids;
int width; //!< Width of this deme.
int birth_count; //!< Number of organisms that have been born into this deme since reset.
@@ -51,11 +54,13 @@
cResourceCount deme_resource_count; //!< Resources available to the deme
tArray<int> energy_res_ids; //!< IDs of energy resources
+ tArray<cDemeCellEvent> cell_events;
+
public:
cDeme() : width(0), birth_count(0), org_count(0), _age(0), deme_resource_count(0) { ; }
~cDeme() { ; }
- void Setup(const tArray<int>& in_cells, int in_width = -1);
+ void Setup(const tArray<int>& in_cells, int in_width = -1, cWorld* world = NULL);
int GetSize() const { return cell_ids.GetSize(); }
int GetCellID(int pos) const { return cell_ids[pos]; }
@@ -85,7 +90,7 @@
// -= Update support =-
//! Called once, at the end of every update.
- void ProcessUpdate() { ++_age; }
+ void ProcessUpdate();
/*! Returns the age of this deme, updates. Age is defined as the number of
updates since the last time Reset() was called. */
int GetAge() const { return _age; }
@@ -100,6 +105,8 @@
void UpdateDemeRes() { deme_resource_count.GetResources(); }
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);
};
#endif
Copied: branches/collect/source/main/cDemeCellEvent.cc (from rev 2070, development/source/main/cDemeCellEvent.cc)
===================================================================
--- branches/collect/source/main/cDemeCellEvent.cc (rev 0)
+++ branches/collect/source/main/cDemeCellEvent.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -0,0 +1,41 @@
+#include "cDemeCellEvent.h"
+#include "cWorld.h"
+
+cDemeCellEvent::cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int width) :
+ m_delay(delay)
+ , m_duration(duration)
+ , m_iter(0)
+ , m_active(false)
+{
+ assert(x1 <= x2);
+ assert(y1 <= y2);
+ assert(y1 < width && y2 < width);
+ assert(delay >= 0);
+ assert(duration >= 0);
+ m_event_cells.ResizeClear((x2-x1+1) * (y2-y1+1));
+
+ int i = 0;
+ for(int j = y1; j <= y2; j++) {
+ for(int k = x1; k <= x2; k++) {
+ m_event_cells[i] = j*width+k;
+ i++;
+ }
+ }
+}
+
+int cDemeCellEvent::GetNextEventCellID() {
+ if(m_active && m_iter < m_event_cells.GetSize()) {
+ return m_event_cells[m_iter++];
+ }
+ m_iter = 0;
+ return -1;
+}
+
+void cDemeCellEvent::ActivateEvent(cWorld* m_world) {
+ m_eventID = m_world->GetRandom().GetInt(0x7FFFFFFF);
+ m_active = true;
+}
+
+void cDemeCellEvent::DeactivateEvent() {
+ m_active = false;
+}
Copied: branches/collect/source/main/cDemeCellEvent.h (from rev 2070, development/source/main/cDemeCellEvent.h)
===================================================================
--- branches/collect/source/main/cDemeCellEvent.h (rev 0)
+++ branches/collect/source/main/cDemeCellEvent.h 2007-10-24 03:34:18 UTC (rev 2152)
@@ -0,0 +1,24 @@
+#ifndef cDemeCellEvent_h
+#define cDemeCellEvent_h
+
+#include "tArray.h"
+class cWorld;
+
+class cDemeCellEvent {
+private:
+ tArray<int> m_event_cells;
+ int m_delay, m_duration, m_eventID, m_iter;
+ bool m_active;
+
+public:
+ cDemeCellEvent() { cDemeCellEvent(-1, -1, -1, -1, 0, 0, 0); }
+ cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int width);
+ int GetNextEventCellID();
+ int GetDelay() { return m_delay; }
+ int GetDuration() { return m_duration; }
+ int GetEventID() { return m_eventID; }
+
+ void ActivateEvent(cWorld* m_world);
+ void DeactivateEvent();
+};
+#endif
Modified: branches/collect/source/main/cOrganism.cc
===================================================================
--- branches/collect/source/main/cOrganism.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cOrganism.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -288,7 +288,7 @@
if(m_world->GetConfig().ENERGY_ENABLED.Get() && m_world->GetConfig().APPLY_ENERGY_METHOD.Get() == 1 && task_completed) {
m_phenotype.RefreshEnergy();
m_phenotype.ApplyToEnergyStore();
- double newMerit = cMerit::EnergyToMerit(GetPhenotype().GetStoredEnergy(), m_world) * GetPhenotype().GetExecutionRatio();
+ double newMerit = cMerit::EnergyToMerit(GetPhenotype().GetStoredEnergy() * GetPhenotype().GetEnergyUsageRatio(), m_world);
if(newMerit != -1) {
m_interface->UpdateMerit(newMerit);
}
Modified: branches/collect/source/main/cPhenotype.cc
===================================================================
--- branches/collect/source/main/cPhenotype.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cPhenotype.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -1458,6 +1458,19 @@
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;
+ }
+ executionRatio *= 2.0;
+ return true;
+}
+
+void cPhenotype::HalfEnergyUsage() {
+ executionRatio *= 0.5;
+}
+
+
/**
Credit organism with energy reward, but only update energy store if APPLY_ENERGY_METHOD = "on task completion" (1)
*/
@@ -1505,13 +1518,9 @@
ReduceEnergy(child_energy - 2*energy_given_at_birth); // 2*energy_given_at_birth: 1 in child_energy & 1 for parent
//TODO: add energy_given_at_birth to Stored_energy
- cMerit parentMerit = cMerit(cMerit::EnergyToMerit(GetStoredEnergy(), m_world) * GetExecutionRatio());
+ cMerit parentMerit = cMerit(cMerit::EnergyToMerit(GetStoredEnergy() * GetEnergyUsageRatio(), m_world));
SetMerit(parentMerit);
-/* if(m_world->GetConfig().ENERGY_VERBOSE.Get()) {
- cerr<<"child merit: "<<merit_array[0]<<endl<<"child energy: "<< child_energy <<endl
- <<"parent merit: "<<GetMerit()<<endl<<"parent energy: "<< GetStoredEnergy() <<endl;
- }*/
return child_energy;
}
Modified: branches/collect/source/main/cPhenotype.h
===================================================================
--- branches/collect/source/main/cPhenotype.h 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cPhenotype.h 2007-10-24 03:34:18 UTC (rev 2152)
@@ -280,7 +280,7 @@
///////////////////// Accessors -- Retrieving ////////////////////
const cMerit & GetMerit() const { assert(initialized == true); return merit; }
- double GetExecutionRatio() const { assert(initialized == true); return executionRatio; }
+ double GetEnergyUsageRatio() const { assert(initialized == true); return executionRatio; }
int GetGenomeLength() const { assert(initialized == true); return genome_length; }
int GetCopiedSize() const { assert(initialized == true); return copied_size; }
int GetExecutedSize() const { assert(initialized == true); return executed_size; }
@@ -474,8 +474,8 @@
bool& ChildFertile() { assert(initialized == true); return child_fertile; }
bool& IsMultiThread() { assert(initialized == true); return is_multi_thread; }
- void DoubleEnergyUsage() { executionRatio *= 2.0; }
- void HalfEnergyUsage() { executionRatio *= 0.5; }
+ bool DoubleEnergyUsage(double inst_energy_cost);
+ void HalfEnergyUsage();
void RefreshEnergy();
void ApplyToEnergyStore();
double ExtractParentEnergy();
Modified: branches/collect/source/main/cPopulation.cc
===================================================================
--- branches/collect/source/main/cPopulation.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cPopulation.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -119,7 +119,6 @@
// Allocate the cells, resources, and market.
cell_array.ResizeClear(num_cells);
-// resource_count.ResizeSpatialGrids(world_x, world_y);
market.Resize(MARKET_SIZE);
// Setup the cells. Do things that are not dependent upon topology here.
@@ -145,7 +144,7 @@
deme_cells[offset] = cell_id;
cell_array[cell_id].SetDemeID(deme_id);
}
- deme_array[deme_id].Setup(deme_cells, deme_size_x);
+ deme_array[deme_id].Setup(deme_cells, deme_size_x, m_world);
}
// Setup the topology.
@@ -195,11 +194,7 @@
for(int i = 0; i < GetNumDemes(); i++) {
cResourceCount tmp_deme_res_count(num_deme_res);
GetDeme(i).SetDemeResourceCount(tmp_deme_res_count);
- //TODO: make sure grid is the right grid/size
- //GetDeme(i).GetDemeResourceCount().ResizeSpatialGrids(world_x, world_y);
-
GetDeme(i).ResizeSpatialGrids(deme_size_x, deme_size_y);
-// GetDeme(i).GetDemeResourceCount().
}
for (int i = 0; i < resource_lib.GetSize(); i++) {
@@ -1065,6 +1060,7 @@
0: 'all' - ...all non-empty demes in the population.
1: 'full_deme' - ...demes that have been filled up.
2: 'corners' - ...demes with upper left and lower right corners filled.
+3: 'deme-age' - ...demes who have reached their maximum age
*/
void cPopulation::ReplicateDemes(int rep_trigger)
@@ -1170,18 +1166,33 @@
source_deme.Reset();
target_deme.Reset();
- // Lineage label is wrong here; fix.
- if(m_world->GetConfig().GERMLINE_RANDOM_PLACEMENT.Get()) {
- InjectGenome(source_deme.GetCellID(m_world->GetRandom().GetInt(0, source_deme.GetSize()-1)),
- source_germline.GetLatest(), 0);
- InjectGenome(target_deme.GetCellID(m_world->GetRandom().GetInt(0, target_deme.GetSize()-1)),
- target_germline.GetLatest(), 0);
+ int source_deme_inject_cell;
+ int target_deme_inject_cell;
+
+ if(m_world->GetConfig().GERMLINE_RANDOM_PLACEMENT.Get() == 2) {
+ // organism is randomly placed in deme
+ source_deme_inject_cell = source_deme.GetCellID(m_world->GetRandom().GetInt(0, source_deme.GetSize()-1));
+ target_deme_inject_cell = target_deme.GetCellID(m_world->GetRandom().GetInt(0, target_deme.GetSize()-1));
} else {
- InjectGenome(source_deme.GetCellID(source_deme.GetSize()/2), source_germline.GetLatest(), 0);
- InjectGenome(target_deme.GetCellID(target_deme.GetSize()/2), target_germline.GetLatest(), 0);
+ // organisms is placed in center of deme
+ source_deme_inject_cell = source_deme.GetCellID(source_deme.GetSize()/2);
+ target_deme_inject_cell = target_deme.GetCellID(target_deme.GetSize()/2);
}
+ // Lineage label is wrong here; fix.
+ InjectGenome(source_deme_inject_cell, source_germline.GetLatest(), 0); // source deme
+ InjectGenome(target_deme_inject_cell, target_germline.GetLatest(), 0); // target deme
- // Note: not rotating the clones.
+ if(m_world->GetConfig().GERMLINE_RANDOM_PLACEMENT.Get() == 1) {
+ // Rotate both injected cells to face northwest.
+ int offset = source_deme.GetCellID(0);
+ cell_array[source_deme_inject_cell].Rotate(cell_array[GridNeighbor(source_deme_inject_cell-offset,
+ source_deme.GetWidth(),
+ source_deme.GetHeight(), -1, -1)+offset]);
+ offset = target_deme.GetCellID(0);
+ cell_array[target_deme_inject_cell].Rotate(cell_array[GridNeighbor(target_deme_inject_cell-offset,
+ target_deme.GetWidth(),
+ target_deme.GetHeight(), -1, -1)+offset]);
+ }
} else {
// Not using germline; choose a random organism from this deme.
int cell1_id = -1;
@@ -1194,7 +1205,7 @@
cGenome seed_genome = seed_org->GetGenome();
int seed_lineage = seed_org->GetLineageLabel();
- // Kill all the organisms in the source deme. Orgs. in dest. deme are already killed
+ // Kill all the organisms in the source deme. Orgs. in target deme have already been killed
for (int i=0; i<source_deme.GetSize(); i++) {
KillOrganism(cell_array[source_deme.GetCellID(i)]);
}
@@ -1202,9 +1213,23 @@
source_deme.Reset();
target_deme.Reset();
- InjectGenome(source_deme.GetCellID(source_deme.GetSize()/2), seed_genome, seed_lineage); // source deme
- InjectGenome(target_deme.GetCellID(target_deme.GetSize()/2), seed_genome, seed_lineage); // destination deme
+ int source_deme_inject_cell = source_deme.GetCellID(source_deme.GetSize()/2);
+ int target_deme_inject_cell = target_deme.GetCellID(target_deme.GetSize()/2);
+ InjectGenome(source_deme_inject_cell, seed_genome, seed_lineage); // source deme
+ InjectGenome(target_deme_inject_cell, seed_genome, seed_lineage); // target deme
+
+ // Rotate both injected cells to face northwest.
+ int offset = source_deme.GetCellID(0);
+ cell_array[source_deme_inject_cell].Rotate(cell_array[GridNeighbor(source_deme_inject_cell-offset,
+ source_deme.GetWidth(),
+ source_deme.GetHeight(), -1, -1)+offset]);
+ offset = target_deme.GetCellID(0);
+ cell_array[target_deme_inject_cell].Rotate(cell_array[GridNeighbor(target_deme_inject_cell-offset,
+ target_deme.GetWidth(),
+ target_deme.GetHeight(), -1, -1)+offset]);
+
+
} else {
cOrganism* seed = cell_array[cell1_id].GetOrganism();
@@ -1231,8 +1256,7 @@
cell_array[cell3_id].Rotate(cell_array[GridNeighbor(cell3_id-offset,
source_deme.GetWidth(),
source_deme.GetHeight(), -1, -1)+offset]);
-
-
+
// This is in the wrong place. Reset should be done after the demes are cleared and before the org. is injected.
source_deme.Reset();
target_deme.Reset();
Modified: branches/collect/source/main/cPopulationCell.cc
===================================================================
--- branches/collect/source/main/cPopulationCell.cc 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cPopulationCell.cc 2007-10-24 03:34:18 UTC (rev 2152)
@@ -45,6 +45,7 @@
, m_cell_id(in_cell.m_cell_id)
, m_deme_id(in_cell.m_deme_id)
, m_organism_count(in_cell.m_organism_count)
+ , m_cell_data(in_cell.m_cell_data)
{
// Copy the mutation rates into a new structure
m_mut_rates = new cMutationRates(*in_cell.m_mut_rates);
@@ -64,6 +65,7 @@
m_cell_id = in_cell.m_cell_id;
m_deme_id = in_cell.m_deme_id;
m_organism_count = in_cell.m_organism_count;
+ m_cell_data = in_cell.m_cell_data;
// Copy the mutation rates, constructing the structure as necessary
if (m_mut_rates == NULL)
@@ -84,6 +86,7 @@
m_x = x;
m_y = y;
m_deme_id = -1;
+ m_cell_data = 0;
if (m_mut_rates == NULL)
m_mut_rates = new cMutationRates(in_rates);
@@ -179,7 +182,7 @@
if(uptake_energy != 0.0) {
// update energy and merit
m_organism->GetPhenotype().ReduceEnergy(-1.0 * uptake_energy);
- m_organism->GetPhenotype().SetMerit(cMerit(cMerit::EnergyToMerit(m_organism->GetPhenotype().GetStoredEnergy(), m_world) * m_organism->GetPhenotype().GetExecutionRatio()));
+ m_organism->GetPhenotype().SetMerit(cMerit(cMerit::EnergyToMerit(m_organism->GetPhenotype().GetStoredEnergy() * m_organism->GetPhenotype().GetEnergyUsageRatio(), m_world)));
}
}
}
Modified: branches/collect/source/main/cPopulationCell.h
===================================================================
--- branches/collect/source/main/cPopulationCell.h 2007-10-24 03:05:21 UTC (rev 2151)
+++ branches/collect/source/main/cPopulationCell.h 2007-10-24 03:34:18 UTC (rev 2152)
@@ -59,6 +59,7 @@
int m_cell_id; // Unique id for position of cell in population.
int m_deme_id; // ID of the deme that this cell is part of.
int m_organism_count; // Total number of orgs to ever inhabit this cell.
+ int m_cell_data; // "data" that is local to the cell and can be retrieaved by the org.
// location in population
int m_x; //!< The x-coordinate of the position of this cell in the environment.
@@ -98,6 +99,8 @@
inline int GetID() const { return m_cell_id; }
inline int GetDemeID() const { return m_deme_id; }
inline int GetOrganismCount() const { return m_organism_count; }
+ inline int GetCellData() const { return m_cell_data; }
+ void SetCellData(const int data) { m_cell_data = data; }
inline bool IsOccupied() const { return m_organism != NULL; }
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