[Avida-SVN] r3338 - in branches/interrupt: documentation source/actions source/analyze source/classification source/cpu source/drivers source/main source/targets/avida-viewer source/tools source/utils/hist_map source/utils/process_map tests tests/collect_specification_analyze tests/collect_specification_analyze/config tests/collect_specification_analyze/expected tests/collect_specification_analyze/expected/data tests/interruptModel_quorumSensing
beckma24 at myxo.css.msu.edu
beckma24 at myxo.css.msu.edu
Thu Jun 25 13:57:37 PDT 2009
Author: beckma24
Date: 2009-06-25 16:57:37 -0400 (Thu, 25 Jun 2009)
New Revision: 3338
Added:
branches/interrupt/tests/collect_specification_analyze/
branches/interrupt/tests/collect_specification_analyze/config/
branches/interrupt/tests/collect_specification_analyze/config/analyze-spec.cfg
branches/interrupt/tests/collect_specification_analyze/config/avida.cfg
branches/interrupt/tests/collect_specification_analyze/config/default-classic.org
branches/interrupt/tests/collect_specification_analyze/config/detail-200000.pop
branches/interrupt/tests/collect_specification_analyze/config/environment.9resource
branches/interrupt/tests/collect_specification_analyze/config/events-collect.cfg
branches/interrupt/tests/collect_specification_analyze/config/instset-destroy.cfg
branches/interrupt/tests/collect_specification_analyze/expected/
branches/interrupt/tests/collect_specification_analyze/expected/data/
branches/interrupt/tests/collect_specification_analyze/expected/data/executed.dat
branches/interrupt/tests/collect_specification_analyze/test_list
Removed:
branches/interrupt/tests/collect_specification_analyze/config/
branches/interrupt/tests/collect_specification_analyze/config/analyze-spec.cfg
branches/interrupt/tests/collect_specification_analyze/config/avida.cfg
branches/interrupt/tests/collect_specification_analyze/config/default-classic.org
branches/interrupt/tests/collect_specification_analyze/config/detail-200000.pop
branches/interrupt/tests/collect_specification_analyze/config/environment.9resource
branches/interrupt/tests/collect_specification_analyze/config/events-collect.cfg
branches/interrupt/tests/collect_specification_analyze/config/instset-destroy.cfg
branches/interrupt/tests/collect_specification_analyze/expected/
branches/interrupt/tests/collect_specification_analyze/expected/data/
branches/interrupt/tests/collect_specification_analyze/expected/data/executed.dat
branches/interrupt/tests/collect_specification_analyze/test_list
branches/interrupt/tests/interruptModel_quorumSensing/expected/
Modified:
branches/interrupt/documentation/analyze.html
branches/interrupt/source/actions/DriverActions.cc
branches/interrupt/source/actions/EnvironmentActions.cc
branches/interrupt/source/actions/PopulationActions.cc
branches/interrupt/source/actions/PrintActions.cc
branches/interrupt/source/actions/SaveLoadActions.cc
branches/interrupt/source/analyze/cAnalyzeGenotype.cc
branches/interrupt/source/analyze/cAnalyzeGenotype.h
branches/interrupt/source/classification/cClassificationManager.cc
branches/interrupt/source/classification/cClassificationManager.h
branches/interrupt/source/cpu/cHardwareCPU.cc
branches/interrupt/source/cpu/cHardwareCPU.h
branches/interrupt/source/drivers/cDefaultAnalyzeDriver.h
branches/interrupt/source/drivers/cDefaultRunDriver.h
branches/interrupt/source/drivers/cFallbackWorldDriver.h
branches/interrupt/source/drivers/cWorldDriver.h
branches/interrupt/source/main/cDeme.cc
branches/interrupt/source/main/cDeme.h
branches/interrupt/source/main/cDemePredicate.h
branches/interrupt/source/main/cGenomeUtil.cc
branches/interrupt/source/main/cGenomeUtil.h
branches/interrupt/source/main/cPhenotype.cc
branches/interrupt/source/main/cPopulation.cc
branches/interrupt/source/main/cPopulation.h
branches/interrupt/source/main/cStats.cc
branches/interrupt/source/main/cStats.h
branches/interrupt/source/main/cTaskLib.cc
branches/interrupt/source/main/cTaskLib.h
branches/interrupt/source/targets/avida-viewer/cTextViewerAnalyzeDriver.h
branches/interrupt/source/targets/avida-viewer/cTextViewerDriver.cc
branches/interrupt/source/targets/avida-viewer/cTextViewerDriver.h
branches/interrupt/source/targets/avida-viewer/cTextViewerDriver_Base.h
branches/interrupt/source/tools/tArray.h
branches/interrupt/source/tools/tArrayUtils.h
branches/interrupt/source/tools/tManagedPointerArray.h
branches/interrupt/source/tools/tSmartArray.h
branches/interrupt/source/utils/hist_map/Makefile
branches/interrupt/source/utils/process_map/Makefile
Log:
merged development r3250:3275 into interrupt branch. All tests pass. Remove expected results for test interruptModel_quorumSensing because I added a column to deme_repl.dat
Modified: branches/interrupt/documentation/analyze.html
===================================================================
--- branches/interrupt/documentation/analyze.html 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/documentation/analyze.html 2009-06-25 20:57:37 UTC (rev 3338)
@@ -644,11 +644,12 @@
</tr>
<tr>
<td><strong>total_task_performance_count</strong> (total # of tasks done)</td>
- <td><strong>inst.n</strong> (# of times instruction number n is done)</td>
+ <td><strong>inst.n</strong> (# of times instruction #n is done)</td>
<td><strong>r_tot.n</strong> (amount of resource n added to the organism's store in its lifetime)</td>
</tr>
<tr>
<td><strong>r_avail.n</strong> (amount of resource n in organism's store)</td>
+ <td><strong>r_spec.n</strong> (# of times specification #n is used)</td>
</tr>
</table>
</div>
@@ -658,6 +659,11 @@
</p>
<p>
+<b>A note on r_spec.n</b>: This counts nop specifications done by any and all "collect-type" instructions -- that is, any instruction that uses the helper function DoCollect. If more than one such instruction is included in the instruction set, r_spec.n will include specification counts for both instructions without any differentiation.
+For details on what the specification numbers mean, see cCodeLabel::AsIntUnique.
+</p>
+
+<p>
If a FIND_LINEAGE was done before the RECALCULATE (or RECALC), the parent
genotype for each regular genotype will be available, enabling the
additional formats:
Modified: branches/interrupt/source/actions/DriverActions.cc
===================================================================
--- branches/interrupt/source/actions/DriverActions.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/actions/DriverActions.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -40,6 +40,14 @@
void Process(cAvidaContext& ctx) { m_world->GetDriver().SetDone(); }
};
+class cActionPause : public cAction
+{
+public:
+ cActionPause(cWorld* world, const cString& args) : cAction(world, args) { ; }
+ static const cString GetDescription() { return "No Arguments"; }
+ void Process(cAvidaContext& ctx) { m_world->GetDriver().SetPause(); }
+};
+
class cActionExitAveLineageLabelGreater : public cAction
{
private:
@@ -197,6 +205,7 @@
action_lib->Register<cActionExitAveGeneration>("ExitAveGeneration");
action_lib->Register<cActionExitElapsedTime>("ExitElapsedTime");
action_lib->Register<cActionStopFastForward>("StopFastForward");
+ action_lib->Register<cActionPause>("Pause");
// @DMB - The following actions are DEPRECATED aliases - These will be removed in 2.7.
action_lib->Register<cActionExit>("exit");
Modified: branches/interrupt/source/actions/EnvironmentActions.cc
===================================================================
--- branches/interrupt/source/actions/EnvironmentActions.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/actions/EnvironmentActions.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -921,6 +921,29 @@
}
};
+class cActionSetFracDemeTreatable : public cAction {
+private:
+ double factionTreatable; // total number of unique event to create; they may overlab
+
+public:
+ cActionSetFracDemeTreatable(cWorld* world, const cString& args) : cAction(world, args), factionTreatable(0.0) {
+ cString largs(args);
+ if (largs.GetSize()) factionTreatable = largs.PopWord().AsDouble();
+ }
+
+ static const cString GetDescription() { return "Arguments: <double factionTreatable>"; }
+
+ void Process(cAvidaContext& ctx) {
+ cPopulation& pop = m_world->GetPopulation();
+ int numDemes = pop.GetNumDemes();
+ for(int i = 0; i < numDemes; i++) {
+ if(ctx.GetRandom().P(factionTreatable))
+ pop.GetDeme(i).setTreatable(true);
+ else
+ pop.GetDeme(i).setTreatable(false);
+ }
+ }
+};
class cActionSetConfig : public cAction
{
@@ -951,6 +974,7 @@
void RegisterEnvironmentActions(cActionLibrary* action_lib)
{
+ action_lib->Register<cActionSetFracDemeTreatable>("SetFracDemeTreatable");
action_lib->Register<cActionDelayedDemeEvent>("DelayedDemeEvent");
action_lib->Register<cActionDelayedDemeEventsPerSlots>("DelayedDemeEventsPerSlots");
action_lib->Register<cActionInjectResource>("InjectResource");
Modified: branches/interrupt/source/actions/PopulationActions.cc
===================================================================
--- branches/interrupt/source/actions/PopulationActions.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/actions/PopulationActions.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -30,6 +30,7 @@
#include "cGenome.h"
#include "cGenomeUtil.h"
#include "cHardwareManager.h"
+#include "cIntSum.h"
#include "cOrgMessagePredicate.h"
#include "cPopulation.h"
#include "cPopulationCell.h"
@@ -895,8 +896,183 @@
}
};
+/*
+ Randomly removes organisms proportional to number of a specific instruction in genome.
+ Proportion is based on instruction count weight and exponent.
+
+ Parameters:
+ 1. instruction type (string) default: "nand"
+ - The type of instruction in question.
+ 2. weight value multiplied by instruction count
+ 3. exponent applied to weighted instruction count
+ */
+class cAction_TherapyStructuralNumInst : public cAction {
+private:
+ cString m_inst;
+ double m_exprWeight;
+ double m_exponent;
+ int m_printUpdate;
+ cIntSum m_totalkilled;
+ cDoubleSum m_killProd;
+public:
+ cAction_TherapyStructuralNumInst(cWorld* world, const cString& args) : cAction(world, args), m_inst("nand"), m_exprWeight(1.0), m_exponent(1.0), m_printUpdate(100)
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_inst = largs.PopWord();
+ if (largs.GetSize()) m_exprWeight = largs.PopWord().AsDouble();
+ if (largs.GetSize()) m_exponent = largs.PopWord().AsDouble();
+ if (largs.GetSize()) m_printUpdate = largs.PopWord().AsInt();
+ m_totalkilled.Clear();
+ m_killProd.Clear();
+ }
+
+ static const cString GetDescription() { return "Arguments: [cString inst=nand] [double exprWeight=1.0] [double exponent=1.0(linear)]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ int totalkilled = 0;
+ cDoubleSum currentKillProb;
+ currentKillProb.Clear();
+
+ // for each deme in the population...
+ cPopulation& pop = m_world->GetPopulation();
+ const int numDemes = pop.GetNumDemes();
+ for (int demeCounter = 0; demeCounter < numDemes; ++demeCounter) {
+ cDeme& currentDeme = pop.GetDeme(demeCounter);
+
+ // if deme treatable?
+ if(currentDeme.IsTreatableNow() == false)
+ continue; //No, go to next deme
+
+ //Yes
+ for(int cellInDeme = 0; cellInDeme < currentDeme.GetSize(); ++cellInDeme) {
+ cPopulationCell& cell = currentDeme.GetCell(cellInDeme);
+
+ if (cell.IsOccupied() == false)
+ continue;
+
+ // count the number of target instructions in the genome
+ int count = cGenomeUtil::CountInst(cell.GetOrganism()->GetGenome(), m_world->GetHardwareManager().GetInstSet().GetInst(m_inst));
+
+ double killprob = min(pow(m_exprWeight*count,m_exponent), 100.0)/100.0;
+ // cout << count << " " << killprob << endl;
+ currentKillProb.Add(killprob);
+ // decide if it should be killed or not, based on the kill probability
+ if (ctx.GetRandom().P(killprob)) {
+ m_world->GetPopulation().KillOrganism(cell);
+ ++totalkilled;
+ }
+ }
+ }
+ m_totalkilled.Add(totalkilled);
+ m_killProd.Add(currentKillProb.Average());
+
+ const int update = m_world->GetStats().GetUpdate();
+ if(update % m_printUpdate == 0) {
+ cDataFile& df = m_world->GetDataFile("TherapyStructuralNumInst_kill.dat");
+ df.WriteComment("Number of organisms killed by structural therapy NumInst");
+ df.Write(update, "Update");
+ df.Write(m_totalkilled.Average(), "Mean organisms killed per update since last print");
+ df.Write(m_killProd.Average(), "Mean organism kill probablity");
+ df.Endl();
+ m_totalkilled.Clear();
+ m_killProd.Clear();
+ }
+ }
+};
+
/*
+ Randomly removes organisms proportional to minimum distance between two instances of the same instruction in its genome.
+ Proportion is based on instruction count weight and exponent.
+
+ Parameters:
+ 1. instruction type (string) default: "nand"
+ - The type of instruction in question.
+ 2. weight value multiplied by instruction count
+ 3. exponent applied to weighted instruction count
+ */
+class cAction_TherapyStructuralRatioDistBetweenNearest : public cAction {
+private:
+ cString m_inst;
+ double m_exprWeight;
+ double m_exponent;
+ int m_printUpdate;
+ cIntSum m_totalkilled;
+ cDoubleSum m_killProd;
+
+public:
+ cAction_TherapyStructuralRatioDistBetweenNearest(cWorld* world, const cString& args) : cAction(world, args), m_inst("nand"), m_exprWeight(1.0), m_exponent(1.0), m_printUpdate(100)
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_inst = largs.PopWord();
+ if (largs.GetSize()) m_exprWeight = largs.PopWord().AsDouble();
+ if (largs.GetSize()) m_exponent = largs.PopWord().AsDouble();
+ if (largs.GetSize()) m_printUpdate = largs.PopWord().AsInt();
+ m_totalkilled.Clear();
+ m_killProd.Clear();
+ }
+
+ static const cString GetDescription() { return "Arguments: [cString inst=nand] [double exprWeight=1.0] [double exponent=1.0(linear)] [int print=100]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ int totalkilled = 0;
+ cDoubleSum currentKillProb;
+ currentKillProb.Clear();
+ // for each deme in the population...
+ cPopulation& pop = m_world->GetPopulation();
+ const int numDemes = pop.GetNumDemes();
+
+ for (int demeCounter = 0; demeCounter < numDemes; ++demeCounter) {
+ cDeme& currentDeme = pop.GetDeme(demeCounter);
+
+ // if deme treatable?
+ if(currentDeme.IsTreatableNow() == false)
+ continue; //No, go to next deme
+
+ //Yes
+ for(int cellInDeme = 0; cellInDeme < currentDeme.GetSize(); ++cellInDeme) {
+ cPopulationCell& cell = currentDeme.GetCell(cellInDeme);
+
+ if (cell.IsOccupied() == false)
+ continue;
+
+ // count the number of target instructions in the genome
+ const cGenome& genome = cell.GetOrganism()->GetGenome();
+ const double genomeSize = static_cast<double>(genome.GetSize());
+ int minDist = cGenomeUtil::MinDistBetween(genome, m_world->GetHardwareManager().GetInstSet().GetInst(m_inst));
+
+ int ratioNumerator = min(genomeSize, pow(m_exprWeight*minDist, m_exponent));
+ double killprob = (genomeSize - static_cast<double>(ratioNumerator))/genomeSize;
+ // cout<<minDist << " " << killprob<<endl;
+ currentKillProb.Add(killprob);
+ // decide if it should be killed or not, based on the kill probability
+ if (ctx.GetRandom().P(killprob)) {
+ m_world->GetPopulation().KillOrganism(cell);
+ ++totalkilled;
+ }
+ }
+ }
+ m_totalkilled.Add(totalkilled);
+ m_killProd.Add(currentKillProb.Average());
+
+ const int update = m_world->GetStats().GetUpdate();
+ if(update % m_printUpdate == 0) {
+ cDataFile& df = m_world->GetDataFile("TherapyStructuralRatioDistBetweenNearest_kill.dat");
+ df.WriteComment("Number of organisms killed by structural therapy RatioDistBetweenNearest");
+ df.Write(update, "Update");
+ df.Write(m_totalkilled.Average(), "Mean organisms killed per update since last print");
+ df.Write(m_killProd.Average(), "Mean organism kill probablity");
+ df.Endl();
+ m_totalkilled.Clear();
+ m_killProd.Clear();
+ }
+ }
+};
+
+
+/*
In avida.cfg, when BASE_MERIT_METHOD is set to 6 (Merit prop. to num times MERIT_BONUS_INST is in genome),
the merit is incremented by MERIT_BONUS_EFFECT if MERIT_BONUS_EFFECT is positive and decremented by
MERIT_BONUS_EFFECT if it is negative. For positive values the counting starts at 1, for negative values it starts
@@ -2892,16 +3068,17 @@
{
double level;
int target_cell;
+ cPopulation& pop = m_world->GetPopulation();
int res_id = m_world->GetPopulation().GetResourceCount().GetResourceCountID(m_resname);
assert(res_id != -1);
for(int i=0; i < m_numkills; i++) {
- target_cell = m_world->GetRandom().GetInt(0, m_world->GetPopulation().GetSize()-1);
- level = m_world->GetPopulation().GetResourceCount().GetSpatialResource(res_id).GetAmount(target_cell);
+ target_cell = m_world->GetRandom().GetInt(0, pop.GetSize()-1);
+ level = pop.GetResourceCount().GetSpatialResource(res_id).GetAmount(target_cell);
if(level > m_threshold) {
- m_world->GetPopulation().KillOrganism(m_world->GetPopulation().GetCell(target_cell));
+ pop.KillOrganism(pop.GetCell(target_cell));
m_world->GetStats().IncNumOrgsKilled();
}
}
@@ -2911,7 +3088,6 @@
-
/*
Kill a percentage of organisms in all demes
@@ -2920,7 +3096,7 @@
*/
class cActionKillDemePercent : public cAction
- {
+{
private:
double m_pctkills;
public:
@@ -2933,29 +3109,77 @@
assert(m_pctkills <= 1);
}
- static const cString GetDescription() { return "Arguments: [int pctkills=0.0]"; }
+ static const cString GetDescription() { return "Arguments: [double pctkills=0.0]"; }
void Process(cAvidaContext& ctx)
{
int target_cell;
-
- for (int d = 0; d < m_world->GetPopulation().GetNumDemes(); d++) {
- for (int c = 0; c < m_world->GetPopulation().GetDeme(d).GetWidth() * m_world->GetPopulation().GetDeme(d).GetHeight(); c++) {
- target_cell = m_world->GetPopulation().GetDeme(d).GetCellID(c);
+ cPopulation& pop = m_world->GetPopulation();
+
+ for (int d = 0; d < pop.GetNumDemes(); d++) {
+
+ cDeme &deme = pop.GetDeme(d);
+
+ if(deme.IsTreatableNow()) {
+
+ for (int c = 0; c < deme.GetWidth() * deme.GetHeight(); c++) {
+ target_cell = deme.GetCellID(c);
- if( m_world->GetRandom().GetDouble() < m_pctkills) {
- m_world->GetPopulation().KillOrganism(m_world->GetPopulation().GetCell(target_cell));
- m_world->GetStats().IncNumOrgsKilled();
- }
+ if(ctx.GetRandom().P(m_pctkills)) {
+ pop.KillOrganism(pop.GetCell(target_cell));
+ m_world->GetStats().IncNumOrgsKilled();
+ }
- } //End iterating through all cells
+ } //End iterating through all cells
+
+ } //End if deme is treatable
} //End iterating through all demes
} //End Process()
- };
+};
+/*
+ Set the ages at which treatable demes can be treated
+
+ Parameters:
+ - 1+ age numbers at which a deme may be treated (int)
+ */
+
+class cActionSetDemeTreatmentAges : public cAction
+{
+private:
+ std::set<int> treatment_ages;
+public:
+ static const cString GetDescription() { return "Arguments: <int treatment age>+"; }
+
+ cActionSetDemeTreatmentAges(cWorld* world, const cString& args) : cAction(world, args)
+ {
+ cString largs(args);
+ while (largs.GetSize()) {
+ treatment_ages.insert(largs.PopWord().AsInt());
+ }
+ }
+
+ void Process(cAvidaContext& ctx)
+ {
+ for (int d = 0; d < m_world->GetPopulation().GetNumDemes(); d++) {
+ cDeme& deme = m_world->GetPopulation().GetDeme(d);
+
+ if(deme.isTreatable()) {
+ for (std::set<int>::iterator it = treatment_ages.begin(); it != treatment_ages.end(); it++) {
+ deme.AddTreatmentAge(*it);
+ }
+ }
+
+ } //End iterating through demes
+
+ } //End Process()
+
+};
+
+
void RegisterPopulationActions(cActionLibrary* action_lib)
{
action_lib->Register<cActionInject>("Inject");
@@ -2975,6 +3199,12 @@
action_lib->Register<cActionKillInstLimit>("KillInstLimit");
action_lib->Register<cActionKillInstPair>("KillInstPair");
action_lib->Register<cActionKillProb>("KillProb");
+
+ // Theraputic deme actions
+ action_lib->Register<cAction_TherapyStructuralNumInst>("TherapyStructuralNumInst");
+ action_lib->Register<cAction_TherapyStructuralRatioDistBetweenNearest>("TherapyStructuralRatioDistBetweenNearest");
+
+
action_lib->Register<cActionToggleRewardInstruction>("ToggleRewardInstruction");
action_lib->Register<cActionToggleFitnessValley>("ToggleFitnessValley");
action_lib->Register<cActionKillProb>("KillRate");
@@ -3070,4 +3300,5 @@
action_lib->Register<cActionDisconnectCells>("disconnect_cells");
action_lib->Register<cActionSwapCells>("swap_cells");
action_lib->Register<cActionKillDemePercent>("KillDemePercent");
+ action_lib->Register<cActionSetDemeTreatmentAges>("SetDemeTreatmentAges");
}
Modified: branches/interrupt/source/actions/PrintActions.cc
===================================================================
--- branches/interrupt/source/actions/PrintActions.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/actions/PrintActions.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -102,6 +102,10 @@
STATS_OUT_FILE(PrintSleepData, sleep.dat );
STATS_OUT_FILE(PrintCompetitionData, competition.dat );
STATS_OUT_FILE(PrintDemeReplicationData, deme_repl.dat );
+STATS_OUT_FILE(PrintDemeTreatableReplicationData, deme_repl_treatable.dat );
+STATS_OUT_FILE(PrintDemeUntreatableReplicationData, deme_repl_untreatable.dat );
+STATS_OUT_FILE(PrintDemeTreatableCount, deme_treatable.dat );
+
STATS_OUT_FILE(PrintDemeCompetitionData, deme_compete.dat);
STATS_OUT_FILE(PrintDemeFoundersData, deme_founders.dat );
STATS_OUT_FILE(PrintPerDemeTasksData, per_deme_tasks.dat );
@@ -121,6 +125,7 @@
STATS_OUT_FILE(PrintCurrentTaskCounts, curr_task_counts.dat);
STATS_OUT_FILE(PrintGermlineData, germline.dat );
+STATS_OUT_FILE(PrintDemeResourceThresholdPredicate, deme_resourceThresholdPredicate.dat );
STATS_OUT_FILE(PrintPredicatedMessages, messages.dat );
STATS_OUT_FILE(PrintCellData, cell_data.dat );
STATS_OUT_FILE(PrintCurrentOpinions, opinions.dat );
@@ -139,6 +144,10 @@
STATS_OUT_FILE(PrintDirectReciprocityData, reciprocity.dat);
STATS_OUT_FILE(PrintStringMatchData, stringmatch.dat);
+// group formation
+STATS_OUT_FILE(PrintGroupsFormedData, groupformation.dat);
+
+
#define POP_OUT_FILE(METHOD, DEFAULT) /* 1 */ \
class cAction ## METHOD : public cAction { /* 2 */ \
private: /* 3 */ \
@@ -157,6 +166,7 @@
POP_OUT_FILE(PrintPhenotypeStatus, phenotype_status.dat);
POP_OUT_FILE(PrintDemeTestamentStats, deme_testament.dat );
POP_OUT_FILE(DumpDemeBoundaryData, deme_boundary ); // file name is dummy
+POP_OUT_FILE(PrintCurrentMeanDemeDensity, deme_currentMeanDensity.dat );
class cActionPrintData : public cAction
@@ -3041,7 +3051,9 @@
action_lib->Register<cActionPrintPhenotypeStatus>("PrintPhenotypeStatus");
action_lib->Register<cActionPrintDemeTestamentStats>("PrintDemeTestamentStats");
-
+ action_lib->Register<cActionPrintCurrentMeanDemeDensity>("PrintCurrentMeanDemeDensity");
+
+ action_lib->Register<cActionPrintDemeResourceThresholdPredicate>("PrintDemeResourceThresholdPredicate");
action_lib->Register<cActionPrintPredicatedMessages>("PrintPredicatedMessages");
action_lib->Register<cActionPrintCellData>("PrintCellData");
action_lib->Register<cActionPrintCurrentOpinions>("PrintCurrentOpinions");
@@ -3059,6 +3071,11 @@
action_lib->Register<cActionPrintDemeSpatialSleep>("PrintDemeSpatialSleepStats");
action_lib->Register<cActionPrintDemeResources>("PrintDemeResourceStats");
action_lib->Register<cActionPrintDemeReplicationData>("PrintDemeReplicationData");
+ action_lib->Register<cActionPrintDemeTreatableReplicationData>("PrintDemeTreatableReplicationData");
+ action_lib->Register<cActionPrintDemeUntreatableReplicationData>("PrintDemeUntreatableReplicationData");
+ action_lib->Register<cActionPrintDemeTreatableCount>("PrintDemeTreatableCount");
+
+
action_lib->Register<cActionPrintDemeCompetitionData>("PrintDemeCompetitionData");
action_lib->Register<cActionPrintDemeFoundersData>("PrintDemeFoundersData");
action_lib->Register<cActionPrintGermlineData>("PrintGermlineData");
@@ -3195,6 +3212,8 @@
action_lib->Register<cActionPrintStringMatchData>("PrintStringMatchData");
action_lib->Register<cActionPrintShadedAltruists>("PrintShadedAltruists");
+ // Group Formation
+ action_lib->Register<cActionPrintGroupsFormedData>("PrintGroupsFormedData");
action_lib->Register<cActionSetVerbose>("VERBOSE");
}
Modified: branches/interrupt/source/actions/SaveLoadActions.cc
===================================================================
--- branches/interrupt/source/actions/SaveLoadActions.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/actions/SaveLoadActions.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -130,6 +130,45 @@
/*
+ Sets up a population based on a dump file such as written out by
+ detail_pop. It is also possible to append a history file to the dump
+ file, in order to preserve the history of a previous run.
+
+ Parameters:
+ filename (string)
+ The name of the file to open.
+ update (int) *optional*
+ ??
+ */
+class cActionLoadStructuredPopulation : public cAction
+{
+private:
+ cString m_filename;
+ int m_update;
+
+public:
+ cActionLoadStructuredPopulation(cWorld* world, const cString& args) : cAction(world, args), m_filename(""), m_update(-1)
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ if (largs.GetSize()) m_update = largs.PopWord().AsInt();
+ }
+
+ static const cString GetDescription() { return "Arguments: <cString fname> [int update=-1]"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ // set the update if requested
+ if (m_update >= 0) m_world->GetStats().SetCurrentUpdate(m_update);
+
+ if (!m_world->GetPopulation().LoadStructuredPopulation(m_filename)) {
+ m_world->GetDriver().RaiseFatalException(-1, "failed to load structured population");
+ }
+ }
+};
+
+
+/*
Writes out a line of data for each genotype in the current population. The
line contains the genome as string, the number of organisms of that genotype,
and the genotype ID.
@@ -198,6 +237,29 @@
};
+class cActionSaveStructuredPopulation : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionSaveStructuredPopulation(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("detail-%d.spop", m_world->GetStats().GetUpdate());
+ m_world->GetPopulation().SaveStructuredPopulation(filename);
+ }
+};
+
+
/*
Like detail_pop, but for sexual populations.
Info for both parents is writen out.
@@ -339,9 +401,11 @@
action_lib->Register<cActionLoadClone>("LoadClone");
action_lib->Register<cActionLoadPopulation>("LoadPopulation");
+ action_lib->Register<cActionLoadStructuredPopulation>("LoadStructuredPopulation");
action_lib->Register<cActionDumpPopulation>("DumpPopulation");
action_lib->Register<cActionSavePopulation>("SavePopulation");
+ action_lib->Register<cActionSaveStructuredPopulation>("SaveStructuredPopulation");
action_lib->Register<cActionSaveSexPopulation>("SaveSexPopulation");
action_lib->Register<cActionSaveParasitePopulation>("SaveParasitePopulation");
action_lib->Register<cActionSaveHistoricPopulation>("SaveHistoricPopulation");
Modified: branches/interrupt/source/analyze/cAnalyzeGenotype.cc
===================================================================
--- branches/interrupt/source/analyze/cAnalyzeGenotype.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/analyze/cAnalyzeGenotype.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -82,6 +82,7 @@
, internal_task_qualities(0)
, rbins_total(0)
, rbins_avail(0)
+ , collect_spec_counts(0)
, fitness_ratio(0.0)
, efficiency_ratio(0.0)
, comp_merit_ratio(0.0)
@@ -136,6 +137,7 @@
, internal_task_qualities(0)
, rbins_total(0)
, rbins_avail(0)
+ , collect_spec_counts(0)
, fitness_ratio(0.0)
, efficiency_ratio(0.0)
, comp_merit_ratio(0.0)
@@ -179,6 +181,7 @@
, internal_task_qualities(_gen.internal_task_qualities)
, rbins_total(_gen.rbins_total)
, rbins_avail(_gen.rbins_avail)
+ , collect_spec_counts(_gen.collect_spec_counts)
, fitness_ratio(_gen.fitness_ratio)
, efficiency_ratio(_gen.efficiency_ratio)
, comp_merit_ratio(_gen.comp_merit_ratio)
@@ -331,6 +334,8 @@
("r_avail", &cAnalyzeGenotype::DescRAvail, &cAnalyzeGenotype::GetRBinAvail));
dcm->Add("prob_task", new tDataEntryOfType<cAnalyzeGenotype, double (int)>
("prob_task", &cAnalyzeGenotype::DescTaskProb, &cAnalyzeGenotype::GetTaskProbability, 5));
+ dcm->Add("r_spec", new tDataEntryOfType<cAnalyzeGenotype, int (int)>
+ ("r_spec", &cAnalyzeGenotype::DescRSpec, &cAnalyzeGenotype::GetRSpec));
// The remaining values should actually go in a separate list called
@@ -611,6 +616,7 @@
internal_task_qualities = likely_phenotype->GetLastInternalTaskQuality();
rbins_total = likely_phenotype->GetLastRBinsTotal();
rbins_avail = likely_phenotype->GetLastRBinsAvail();
+ collect_spec_counts = likely_phenotype->GetLastCollectSpecCounts();
// Setup a new parent stats if we have a parent to work with.
if (parent_genotype != NULL) {
Modified: branches/interrupt/source/analyze/cAnalyzeGenotype.h
===================================================================
--- branches/interrupt/source/analyze/cAnalyzeGenotype.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/analyze/cAnalyzeGenotype.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -159,6 +159,7 @@
tArray<double> internal_task_qualities;
tArray<double> rbins_total;
tArray<double> rbins_avail;
+ tArray<int> collect_spec_counts;
tArray<int> m_env_inputs;
// Group 3 : Stats requiring parental genotype (Also from test CPUs)
@@ -458,6 +459,12 @@
return rbins_avail[resource_id];
}
cString DescRAvail(int resource_id) const { return cStringUtil::Stringf("Resource %d Available", resource_id);}
+
+ int GetRSpec(int spec_id) const {
+ if (spec_id >= collect_spec_counts.GetSize() || spec_id < 0) return -1;
+ return collect_spec_counts[spec_id];
+ }
+ cString DescRSpec(int spec_id) const { return cStringUtil::Stringf("# times specification %d used", spec_id);}
// Comparisons... Compares a genotype to the "previous" one, which is
// passed in, in one specified phenotype.
Modified: branches/interrupt/source/classification/cClassificationManager.cc
===================================================================
--- branches/interrupt/source/classification/cClassificationManager.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/classification/cClassificationManager.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -718,10 +718,10 @@
return true;
}
-bool cClassificationManager::DumpHistoricSexSummary(ofstream& fp)
+bool cClassificationManager::DumpHistoricSexSummary(ofstream& fp, bool header)
{
m_genotype_ctl->ResetHistoric(0);
- DumpDetailSexHeading(fp);
+ if (header) DumpDetailSexHeading(fp);
for (int i = 0; i < m_genotype_ctl->GetHistoricCount(); i++) {
DumpDetailedSexEntry(m_genotype_ctl->Get(0), fp);
m_genotype_ctl->Next(0);
Modified: branches/interrupt/source/classification/cClassificationManager.h
===================================================================
--- branches/interrupt/source/classification/cClassificationManager.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/classification/cClassificationManager.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -158,7 +158,7 @@
bool DumpDetailedSummary(std::ofstream& fp, bool print_mut_steps = false);
bool DumpDetailedSexSummary(std::ofstream& fp);
bool DumpHistoricSummary(std::ofstream& fp, int back_dist, bool print_mut_steps = false);
- bool DumpHistoricSexSummary(std::ofstream& fp);
+ bool DumpHistoricSexSummary(std::ofstream& fp, bool header = true);
void DumpDetailedEntry(cGenotype* genotype, std::ofstream& fp, bool print_mut_steps = false);
void DumpDetailedSexEntry(cGenotype* genotype, std::ofstream& fp);
Modified: branches/interrupt/source/cpu/cHardwareCPU.cc
===================================================================
--- branches/interrupt/source/cpu/cHardwareCPU.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/cpu/cHardwareCPU.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -392,7 +392,10 @@
tInstLibEntry<tMethod>("and", &cHardwareCPU::Inst_And),
tInstLibEntry<tMethod>("order", &cHardwareCPU::Inst_Order),
tInstLibEntry<tMethod>("xor", &cHardwareCPU::Inst_Xor),
-
+
+ // treatable instructions
+ tInstLibEntry<tMethod>("nand-treatable", &cHardwareCPU::Inst_NandTreatable, nInstFlag::DEFAULT, "Nand BX by CX and place the result in ?BX?, fails if deme is treatable"),
+
tInstLibEntry<tMethod>("copy", &cHardwareCPU::Inst_Copy),
tInstLibEntry<tMethod>("read", &cHardwareCPU::Inst_ReadInst),
tInstLibEntry<tMethod>("write", &cHardwareCPU::Inst_WriteInst),
@@ -828,8 +831,10 @@
tInstLibEntry<tMethod>("if-donor", &cHardwareCPU::Inst_IfDonor, nInstFlag::STALL),
tInstLibEntry<tMethod>("prod-string", &cHardwareCPU::Inst_ProduceString, nInstFlag::STALL),
+ // Group formation instructions
+ tInstLibEntry<tMethod>("join-group", &cHardwareCPU::Inst_JoinGroup, nInstFlag::STALL),
+ tInstLibEntry<tMethod>("orgs-in-group", &cHardwareCPU::Inst_NumberOrgsInGroup, nInstFlag::STALL),
-
// Must always be the last instruction in the array
tInstLibEntry<tMethod>("NULL", &cHardwareCPU::Inst_Nop, 0, "True no-operation instruction: does nothing"),
};
@@ -2813,6 +2818,19 @@
return true;
}
+bool cHardwareCPU::Inst_NandTreatable(cAvidaContext& ctx)
+{
+/*
+ if(!m_organism->GetDeme()->isTreatable() && m_world->GetRandom().P(probFail))
+ return true;
+
+ const int dst = FindModifiedRegister(REG_BX);
+ const int op1 = REG_BX;
+ const int op2 = REG_CX;
+ GetRegister(dst) = ~(GetRegister(op1) & GetRegister(op2));
+ */return true;
+}
+
bool cHardwareCPU::Inst_Nor(cAvidaContext& ctx)
{
const int dst = FindModifiedRegister(REG_BX);
@@ -9659,3 +9677,41 @@
return true;
}
+//! An organism joins a group by setting it opinion to the group id.
+bool cHardwareCPU::Inst_JoinGroup(cAvidaContext& ctx)
+{
+ int opinion;
+ // Check if the org is currently part of a group
+ assert(m_organism != 0);
+ if(m_organism->HasOpinion()) {
+ opinion = m_organism->GetOpinion().first;
+ // subtract org from group
+ m_world->GetPopulation().LeaveGroup(opinion);
+ }
+
+
+ // Call the set opinion instruction, which does all the dirty work.
+ Inst_SetOpinion(ctx);
+
+ // Add org to group count
+ opinion = m_organism->GetOpinion().first;
+ m_world->GetPopulation().JoinGroup(opinion);
+ return true;
+}
+
+//! Gets the number of organisms in the current organism's group
+//! and places the value in the ?CX? register
+bool cHardwareCPU::Inst_NumberOrgsInGroup(cAvidaContext& ctx)
+{
+ int num_orgs = 0;
+ assert(m_organism != 0);
+ const int num_org_reg = FindModifiedRegister(REG_CX);
+ int opinion;
+
+ if(m_organism->HasOpinion()) {
+ opinion = m_organism->GetOpinion().first;
+ num_orgs = m_world->GetPopulation().NumberOfOrganismsInGroup(opinion);
+ }
+ GetRegister(num_org_reg) = num_orgs;
+ return true;
+}
Modified: branches/interrupt/source/cpu/cHardwareCPU.h
===================================================================
--- branches/interrupt/source/cpu/cHardwareCPU.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/cpu/cHardwareCPU.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -470,6 +470,9 @@
bool Inst_Order(cAvidaContext& ctx);
bool Inst_Xor(cAvidaContext& ctx);
+ // Double Argument Math that are treatable
+ bool Inst_NandTreatable(cAvidaContext& ctx);
+
// Biological
bool Inst_Copy(cAvidaContext& ctx);
bool Inst_ReadInst(cAvidaContext& ctx);
@@ -944,8 +947,17 @@
bool Inst_GetNeighborhood(cAvidaContext& ctx);
//! Test if the current neighborhood has changed from that in the organism's memory.
bool Inst_IfNeighborhoodChanged(cAvidaContext& ctx);
+
+// -------- Group Formation Support --------
+public:
+ //! An organism joins a group by setting it opinion to the group id.
+ bool Inst_JoinGroup(cAvidaContext& ctx);
+ //! Returns the number of organisms in the current organism's group
+ bool Inst_NumberOrgsInGroup(cAvidaContext& ctx);
+
+
};
Modified: branches/interrupt/source/drivers/cDefaultAnalyzeDriver.h
===================================================================
--- branches/interrupt/source/drivers/cDefaultAnalyzeDriver.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/drivers/cDefaultAnalyzeDriver.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -61,6 +61,7 @@
// Driver Actions
void SignalBreakpoint() { return; }
void SetDone() { return; }
+ void SetPause() { return; }
void RaiseException(const cString& in_string);
void RaiseFatalException(int exit_code, const cString& in_string);
Modified: branches/interrupt/source/drivers/cDefaultRunDriver.h
===================================================================
--- branches/interrupt/source/drivers/cDefaultRunDriver.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/drivers/cDefaultRunDriver.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -57,6 +57,7 @@
// Driver Actions
void SignalBreakpoint() { return; }
void SetDone() { m_done = true; }
+ void SetPause() { return; }
void RaiseException(const cString& in_string);
void RaiseFatalException(int exit_code, const cString& in_string);
Modified: branches/interrupt/source/drivers/cFallbackWorldDriver.h
===================================================================
--- branches/interrupt/source/drivers/cFallbackWorldDriver.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/drivers/cFallbackWorldDriver.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -42,6 +42,7 @@
// Driver Actions
void SignalBreakpoint() { return; }
void SetDone() { return; }
+ void SetPause() { return; }
void RaiseException(const cString& in_string);
void RaiseFatalException(int exit_code, const cString& in_string);
Modified: branches/interrupt/source/drivers/cWorldDriver.h
===================================================================
--- branches/interrupt/source/drivers/cWorldDriver.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/drivers/cWorldDriver.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -49,6 +49,7 @@
// Driver Actions
virtual void SignalBreakpoint() = 0;
virtual void SetDone() = 0;
+ virtual void SetPause() = 0;
virtual void RaiseException(const cString& in_string) = 0;
virtual void RaiseFatalException(int exit_code, const cString& in_string) = 0;
Modified: branches/interrupt/source/main/cDeme.cc
===================================================================
--- branches/interrupt/source/main/cDeme.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cDeme.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -739,7 +739,9 @@
void cDeme::AddDemeResourceThresholdPredicate(cString resourceName, cString comparisonOperator, double threasholdValue) {
cDemeResourceThresholdPredicate* pred = new cDemeResourceThresholdPredicate(resourceName, comparisonOperator, threasholdValue);
deme_pred_list.Add(pred);
-
+
+ cString name = resourceName + " " + comparisonOperator + cStringUtil::Stringf(" %f", threasholdValue);
+ m_world->GetStats().AddDemeResourceThresholdPredicate(name);
}
void cDeme::AddEventReceivedCenterPred(int times) {
@@ -864,3 +866,19 @@
return 0;
}
+
+// Return whether or not this deme is treatable at the given age (updates). If a deme is not treatable,
+// this function will always return false.
+bool cDeme::IsTreatableAtAge(const int age) {
+
+ if(isTreatable()) {
+ if(treatment_ages.size() == 0) // implies treatable every update
+ return true;
+ set<int>::iterator it;
+ it = treatment_ages.find(age);
+ if(it != treatment_ages.end()) return true;
+ }
+
+ return false;
+
+} //End cDeme::IsTreatableAtAge()
Modified: branches/interrupt/source/main/cDeme.h
===================================================================
--- branches/interrupt/source/main/cDeme.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cDeme.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -24,6 +24,7 @@
#ifndef cDeme_h
#define cDeme_h
+#include <set>
#include <vector>
#include "cDemeCellEvent.h"
@@ -58,6 +59,8 @@
int width; //!< Width of this deme.
bool replicateDeme;
+ bool treatable;
+ std::set<int> treatment_ages;
// The following should be moved to cDemePhenotype / cPopulationPhenotype
int cur_birth_count; //!< Number of organisms that have been born into this deme since reset.
@@ -141,7 +144,7 @@
public:
- cDeme() : _id(0), width(0), replicateDeme(false), cur_birth_count(0), last_birth_count(0), cur_org_count(0), last_org_count(0), injected_count(0), birth_count_perslot(0),
+ cDeme() : _id(0), width(0), replicateDeme(false), treatable(false), 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),
MSG_sendFailed(0), MSG_dropped(0), MSG_SuccessfullySent(0), MSG_sent(0),
@@ -181,6 +184,7 @@
int GetOrgCount() const { return cur_org_count; }
int GetLastOrgCount() const { return last_org_count; }
+ double GetDensity() const { return static_cast<double>(cur_org_count) / static_cast<double>(GetSize()); }
void IncOrgCount() { cur_org_count++; }
void DecOrgCount() { cur_org_count--; }
@@ -199,6 +203,12 @@
bool TestReplication() const { return replicateDeme; }
void ReplicateDeme() { replicateDeme = true; }
+
+ bool isTreatable() const { return treatable; }
+ void setTreatable(bool value) { treatable = value; }
+ void AddTreatmentAge(const int age) { treatment_ages.insert(age); }
+ bool IsTreatableAtAge(const int age);
+ bool IsTreatableNow() { return IsTreatableAtAge(_age); }
int GetSlotFlowRate() const;
int GetEventsTotal() const { return eventsTotal; }
Modified: branches/interrupt/source/main/cDemePredicate.h
===================================================================
--- branches/interrupt/source/main/cDemePredicate.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cDemePredicate.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -98,7 +98,10 @@
void Reset() { previouslySatisfied = false; }
bool PreviouslySatisfied() { return previouslySatisfied; }
cString GetName() { return cString("cDemeResourceThreshold"); }
- void UpdateStats(cStats& stats) {;}
+ void UpdateStats(cStats& stats) {
+ cString name = demeResourceName + " " + compareOperator + cStringUtil::Stringf(" %f", resourceThresholdValue);
+ stats.IncDemeResourceThresholdPredicate(name);
+ }
};
#endif
Modified: branches/interrupt/source/main/cGenomeUtil.cc
===================================================================
--- branches/interrupt/source/main/cGenomeUtil.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cGenomeUtil.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -58,6 +58,43 @@
return count;
}
+// Returns minimum distance between two instance of inst respecting genome circularity.
+// If only one instance is found then lenght of genome is returned.
+int cGenomeUtil::MinDistBetween(const cGenome& genome, const cInstruction& inst) {
+ const int genomeSize = genome.GetSize();
+ int firstInstance(-1);
+ int secondInstance(-1);
+ int startIndex(0);
+ int minDist(genomeSize);
+
+ while(startIndex < genomeSize) {
+ firstInstance = FindInst(genome, inst, startIndex);
+ startIndex = firstInstance + 1;
+
+ if(startIndex >= genomeSize)
+ return minDist;
+
+ secondInstance = FindInst(genome, inst, startIndex);
+
+ if(firstInstance != -1 and secondInstance != -1) {
+ minDist = min(min(secondInstance-firstInstance, firstInstance+genomeSize-secondInstance), minDist);
+ } else if(secondInstance != -1) {
+ secondInstance = FindInst(genome, inst, 0);
+ if(firstInstance == secondInstance)
+ return minDist;
+ else {
+ assert(secondInstance < firstInstance);
+ minDist = min(secondInstance+genomeSize-firstInstance, minDist);
+ }
+ } else {
+ return minDist;
+ }
+ }
+ assert(false);
+ return -1;
+}
+
+
int cGenomeUtil::FindOverlap(const cGenome & gen1, const cGenome & gen2,
int offset)
{
Modified: branches/interrupt/source/main/cGenomeUtil.h
===================================================================
--- branches/interrupt/source/main/cGenomeUtil.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cGenomeUtil.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -43,6 +43,7 @@
// ========= Detection =========
static int FindInst(const cGenome& gen, const cInstruction& inst, int start_index = 0);
static int CountInst(const cGenome& gen, const cInstruction& inst);
+ static int MinDistBetween(const cGenome& gen, const cInstruction& inst);
static bool HasInst(const cGenome& gen, const cInstruction& inst)
{
Modified: branches/interrupt/source/main/cPhenotype.cc
===================================================================
--- branches/interrupt/source/main/cPhenotype.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cPhenotype.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -795,7 +795,7 @@
// 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;
Modified: branches/interrupt/source/main/cPopulation.cc
===================================================================
--- branches/interrupt/source/main/cPopulation.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cPopulation.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -62,6 +62,12 @@
#include "cTestCPU.h"
#include "cCPUTestInfo.h"
+#include "tArrayUtils.h"
+#include "tKVPair.h"
+#include "tHashTable.h"
+#include "tManagedPointerArray.h"
+
+
#include <fstream>
#include <vector>
#include <algorithm>
@@ -2776,6 +2782,22 @@
m_world->GetDataFileManager().Remove(m_filename);
}
+void cPopulation::PrintCurrentMeanDemeDensity(const cString& filename) {
+ cDoubleSum demeDensity;
+ demeDensity.Clear();
+ const int num_demes = deme_array.GetSize();
+ for (int deme_id = 0; deme_id < num_demes; ++deme_id) {
+ const cDeme & cur_deme = deme_array[deme_id];
+ demeDensity.Add(cur_deme.GetDensity());
+ }
+
+ cDataFile& df = m_world->GetDataFile(filename);
+ df.WriteTimeStamp();
+ df.Write(m_world->GetStats().GetUpdate(), "Update");
+ df.Write(demeDensity.Average(), "Current mean deme density");
+ df.Endl();
+}
+
// Print some stats about the energy sharing behavior of each deme
void cPopulation::PrintDemeEnergySharingStats() {
const int num_demes = deme_array.GetSize();
@@ -2795,7 +2817,7 @@
double amount_received = 0.0;
double amount_applied = 0.0;
- for (int deme_id = 0; deme_id < num_demes; deme_id++) {
+ for (int deme_id = 0; deme_id < num_demes; ++deme_id) {
const cDeme & cur_deme = deme_array[deme_id];
for (int i = 0; i < cur_deme.GetSize(); i++) {
@@ -4438,29 +4460,11 @@
return true;
}
-// This class is needed for the next function
-class cTmpGenotype {
-public:
- int id_num;
- int parent_id;
- int num_cpus;
- int total_cpus;
- double merit;
- int update_born;
- int update_dead;
-
- cGenotype *genotype;
-
- bool operator<( const cTmpGenotype rhs ) const {
- return id_num < rhs.id_num; }
-};
-
bool cPopulation::LoadDumpFile(cString filename, int update)
{
// set the update if requested
- if ( update >= 0 )
- m_world->GetStats().SetCurrentUpdate(update);
+ if (update >= 0) m_world->GetStats().SetCurrentUpdate(update);
// Clear out the population
for (int i = 0; i < cell_array.GetSize(); i++) KillOrganism(cell_array[i]);
@@ -4478,13 +4482,13 @@
// First, we read in all the genotypes and store them in a list
- vector<cTmpGenotype> genotype_vect;
+ vector<sTmpGenotype> genotype_vect;
for (int line_id = 0; line_id < input_file.GetNumLines(); line_id++) {
cString cur_line = input_file.GetLine(line_id);
// Setup the genotype for this line...
- cTmpGenotype tmp;
+ sTmpGenotype tmp;
tmp.id_num = cur_line.PopWord().AsInt();
tmp.parent_id = cur_line.PopWord().AsInt();
/*parent_dist =*/ cur_line.PopWord().AsInt();
@@ -4516,9 +4520,9 @@
sort( genotype_vect.begin(), genotype_vect.end() );
// set the parents correctly
- vector<cTmpGenotype>::const_iterator it = genotype_vect.begin();
+ vector<sTmpGenotype>::const_iterator it = genotype_vect.begin();
for ( ; it != genotype_vect.end(); it++ ){
- vector<cTmpGenotype>::const_iterator it2 = it;
+ vector<sTmpGenotype>::const_iterator it2 = it;
cGenotype *parent = 0;
// search backwards till we find the parent
if ( it2 != genotype_vect.begin() )
@@ -4580,6 +4584,193 @@
}
+bool cPopulation::SaveStructuredPopulation(const cString& filename)
+{
+ cDataFile& df = m_world->GetDataFile(filename);
+ df.WriteRawComment("#filetype genotype_data");
+ df.WriteRawComment("#format id parent_id parent2_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence cells");
+ df.WriteComment("");
+ df.WriteComment("Structured Population Dump");
+ df.WriteTimeStamp();
+
+ // Build up hash table of all current genotypes and the cells in which the organisms reside
+ tHashTable<int, tKVPair<cGenotype*, tArray<int> >* > genotype_map;
+
+ for (int i = 0; i < cell_array.GetSize(); i++) {
+ if (cell_array[i].IsOccupied()) {
+ cGenotype* genotype = cell_array[i].GetOrganism()->GetGenotype();
+ tKVPair<cGenotype*, tArray<int> >* map_entry = NULL;
+ if (genotype_map.Find(genotype->GetID(), map_entry)) {
+ map_entry->Value().Push(i);
+ } else {
+ map_entry = new tKVPair<cGenotype*, tArray<int> >(genotype, tArray<int>(0));
+ map_entry->Value().Push(i);
+ genotype_map.Add(genotype->GetID(), map_entry);
+ }
+ }
+ }
+
+ // Output all current genotypes
+
+ tArray<tKVPair<cGenotype*, tArray<int> >* > genotype_entries;
+ genotype_map.GetValues(genotype_entries);
+ for (int i = 0; i < genotype_entries.GetSize(); i++) {
+ cGenotype* genotype = genotype_entries[i]->Key();
+
+ df.Write(genotype->GetID(), "Genotype ID");
+ df.Write(genotype->GetAncestorID(0), "Parent 1 Genotype ID");
+ df.Write(genotype->GetAncestorID(1), "Parent 2 Genotype ID");
+ df.Write(genotype->GetParentDistance(), "Parent Distance");
+ df.Write(genotype->GetNumOrganisms(), "Number of currently living organisms");
+ df.Write(genotype->GetTotalOrganisms(), "Total number of organisms that ever existed");
+ df.Write(genotype->GetLength(), "Genome Length");
+ df.Write(genotype->GetMerit(), "Merit");
+ df.Write(genotype->GetGestationTime(), "Gestation Time");
+ df.Write(genotype->GetFitness(), "Fitness");
+ df.Write(genotype->GetUpdateBorn(), "Update Born");
+ df.Write(genotype->GetUpdateDeactivated(), "Update Deactivated");
+ df.Write(genotype->GetDepth(), "Phylogenetic Depth");
+ df.Write(genotype->GetGenome().AsString(), "Genome Sequence");
+
+ tArray<int>& cells = genotype_entries[i]->Value();
+ cString cellstr;
+ cellstr.Set("%d", cells[0]);
+ for (int cell_i = 1; cell_i < cells.GetSize(); cell_i++) {
+ cellstr.Set("%s,%d", (const char*)cellstr, cells[cell_i]);
+ }
+ df.Write(cellstr, "Occupied Cell IDs");
+ df.Endl();
+
+ delete genotype_entries[i];
+ }
+
+ // Output historic genotypes
+ m_world->GetClassificationManager().DumpHistoricSexSummary(df.GetOFStream(), false);
+
+ m_world->GetDataFileManager().Remove(filename);
+ return true;
+}
+
+
+bool cPopulation::LoadStructuredPopulation(const cString& filename)
+{
+ // @TODO - build in support for verifying population dimensions
+
+ cInitFile input_file(filename);
+ if (!input_file.WasOpened()) {
+ tConstListIterator<cString> err_it(input_file.GetErrors());
+ const cString* errstr = NULL;
+ while ((errstr = err_it.Next())) m_world->GetDriver().RaiseException(*errstr);
+ return false;
+ }
+
+ // Clear out the population
+ for (int i = 0; i < cell_array.GetSize(); i++) KillOrganism(cell_array[i]);
+
+ // First, we read in all the genotypes and store them in an array
+ tManagedPointerArray<sTmpGenotype> genotypes(input_file.GetNumLines());
+ const int update = m_world->GetStats().GetUpdate();
+
+ for (int line_id = 0; line_id < input_file.GetNumLines(); line_id++) {
+ cString cur_line = input_file.GetLine(line_id);
+
+ // Setup the genotype for this line...
+ sTmpGenotype& tmp = genotypes[line_id];
+ tmp.id_num = cur_line.PopWord().AsInt();
+ tmp.parent_id = cur_line.PopWord().AsInt();
+ tmp.parent_id2 = cur_line.PopWord().AsInt();
+ /* parent_dist */ cur_line.PopWord();
+ tmp.num_cpus = cur_line.PopWord().AsInt();
+ tmp.total_cpus = cur_line.PopWord().AsInt();
+ /* length */ cur_line.PopWord();
+ tmp.merit = cur_line.PopWord().AsDouble();
+ /* gest_time */ cur_line.PopWord();
+ /* fitness */ cur_line.PopWord();
+ tmp.update_born = cur_line.PopWord().AsInt();
+ tmp.update_dead = cur_line.PopWord().AsInt();
+ /* depth */ cur_line.PopWord();
+ cString name = cStringUtil::Stringf("org-%d", tmp.id_num);
+ cGenome genome(cur_line.PopWord());
+
+ // Process resident cell ids
+ cString cellstr(cur_line.PopWord());
+ while (cellstr.GetSize()) tmp.cells.Push(cellstr.Pop(',').AsInt());
+ assert(tmp.cells.GetSize() == tmp.num_cpus);
+
+ // Don't allow birth or death times larger than the current update
+ if (update > tmp.update_born) tmp.update_born = update;
+ if (update > tmp.update_dead) tmp.update_dead = update;
+
+ tmp.genotype = m_world->GetClassificationManager().GetGenotypeLoaded(genome, tmp.update_born, tmp.id_num);
+ tmp.genotype->SetName(name);
+ }
+
+ // Sort genotypes in ascending order according to their id_num
+ tArrayUtils::QSort(genotypes);
+
+
+ // Set parents correctly
+ for (int gen_i = genotypes.GetSize() - 1; gen_i > 0; gen_i--) {
+ cGenotype* parent1 = NULL;
+ cGenotype* parent2 = NULL;
+
+ int pid = genotypes[gen_i].parent_id;
+ if (pid != -1) {
+ for (int p_i = gen_i + 1; p_i < genotypes.GetSize(); p_i++) {
+ if (genotypes[p_i].id_num == pid) {
+ parent1 = genotypes[p_i].genotype;
+ break;
+ }
+ }
+ }
+
+ pid = genotypes[gen_i].parent_id2;
+ if (pid != -1) {
+ for (int p_i = gen_i + 1; p_i < genotypes.GetSize(); p_i++) {
+ if (genotypes[p_i].id_num == pid) {
+ parent2 = genotypes[p_i].genotype;
+ break;
+ }
+ }
+ }
+
+ genotypes[gen_i].genotype->SetParent(parent1, parent2);
+ }
+
+
+ // Process genotypes, inject into organisms as necessary
+ for (int gen_i = genotypes.GetSize() - 1; gen_i > 0; gen_i--) {
+ sTmpGenotype& tmp = genotypes[gen_i];
+ if (tmp.num_cpus == 0) {
+ // historic organism - remove immediately, so that it gets transferred into
+ // the historic database. We change the update temporarily to the
+ // true death time of this organism, so that all stats are correct
+ m_world->GetStats().SetCurrentUpdate(tmp.update_dead);
+ m_world->GetClassificationManager().RemoveGenotype(*tmp.genotype);
+ m_world->GetStats().SetCurrentUpdate(update);
+ } else {
+ // otherwise, we insert as many organisms as we need
+ for (int cell_i = 0; cell_i < tmp.num_cpus; cell_i++) {
+ int cell_id = tmp.cells[cell_i];
+
+ InjectGenotype(cell_id, tmp.genotype);
+
+ cPhenotype& phenotype = GetCell(cell_id).GetOrganism()->GetPhenotype();
+ if (tmp.merit > 0) phenotype.SetMerit(cMerit(tmp.merit));
+ AdjustSchedule(GetCell(cell_id), phenotype.GetMerit());
+
+ LineageSetupOrganism(GetCell(cell_id).GetOrganism(), NULL, 0, tmp.genotype->GetParentGenotype());
+ }
+ }
+ }
+ sync_events = true;
+
+ return true;
+}
+
+
+
+
bool cPopulation::DumpMemorySummary(ofstream& fp)
{
if (fp.good() == false) return false;
@@ -5576,3 +5767,41 @@
}
}
+
+
+// Adds an organism to a group
+void cPopulation::JoinGroup(int group_id)
+{
+ map<int,int>::iterator it;
+ it=m_groups.find(group_id);
+ if (it == m_groups.end()) {
+ m_groups[group_id] = 0;
+ }
+ m_groups[group_id]++;
+
+}
+
+
+// Removes an organism from a group
+void cPopulation::LeaveGroup(int group_id)
+{
+ map<int,int>::iterator it;
+ it=m_groups.find(group_id);
+ if (it != m_groups.end()) {
+ m_groups[group_id]--;
+ }
+
+}
+
+// Identifies the number of organisms in a group
+int cPopulation::NumberOfOrganismsInGroup(int group_id)
+{
+ map<int,int>::iterator it;
+ it=m_groups.find(group_id);
+ int num_orgs = 0;
+ if (it != m_groups.end()) {
+ num_orgs = m_groups[group_id];
+ }
+ return num_orgs;
+
+}
Modified: branches/interrupt/source/main/cPopulation.h
===================================================================
--- branches/interrupt/source/main/cPopulation.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cPopulation.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -27,7 +27,9 @@
#define cPopulation_h
#include <fstream>
+#include <map>
+
#ifndef cBirthChamber_h
#include "cBirthChamber.h"
#endif
@@ -115,7 +117,10 @@
double fracOrgsCantSendMSG;
double fracOrgsCantReceiveMSG;
-
+
+ // Group formation information
+ std::map<int, int> m_groups; //<! Maps the group id to the number of orgs in the group
+
///////////////// Private Methods ////////////////////
void BuildTimeSlicer(cChangeList* change_list); // Build the schedule object
@@ -232,6 +237,7 @@
// Deme-related stats methods
void PrintDemeAllStats();
void PrintDemeTestamentStats(const cString& filename);
+ void PrintCurrentMeanDemeDensity(const cString& filename);
void PrintDemeEnergySharingStats();
void PrintDemeEnergyDistributionStats();
void PrintDemeOrganismEnergyDistributionStats();
@@ -274,6 +280,8 @@
bool SaveClone(std::ofstream& fp);
bool LoadClone(std::ifstream& fp);
bool LoadDumpFile(cString filename, int update);
+ bool SaveStructuredPopulation(const cString& filename);
+ bool LoadStructuredPopulation(const cString& filename);
bool DumpMemorySummary(std::ofstream& fp);
bool OK();
@@ -333,6 +341,39 @@
double getFracOrgsCantReceiveMSG() const { return fracOrgsCantReceiveMSG; }
void setFracOrgsCantSendMSG(double frac) { assert(1.0 >= frac && frac >= 0.0); fracOrgsCantSendMSG = frac; }
void setFracOrgsCantReceiveMSG(double frac) { assert(1.0 >= frac && frac >= 0.0); fracOrgsCantReceiveMSG = frac; }
+
+ // Adds an organism to a group
+ void JoinGroup(int group_id);
+ // Removes an organism from a group
+ void LeaveGroup(int group_id);
+ // Identifies the number of organisms in a group
+ int NumberOfOrganismsInGroup(int group_id);
+ // Get the group information
+ map<int, int> GetFormedGroups() { return m_groups; }
+
+private:
+ struct sTmpGenotype
+ {
+ public:
+ int id_num;
+ int parent_id;
+ int parent_id2;
+ int num_cpus;
+ int total_cpus;
+ double merit;
+ int update_born;
+ int update_dead;
+ tArray<int> cells;
+
+ cGenotype *genotype;
+
+ inline sTmpGenotype() : id_num(-1) { ; }
+ inline bool operator<(const sTmpGenotype& rhs) const { return id_num < rhs.id_num; }
+ inline bool operator>(const sTmpGenotype& rhs) const { return id_num > rhs.id_num; }
+ inline bool operator<=(const sTmpGenotype& rhs) const { return id_num <= rhs.id_num; }
+ inline bool operator>=(const sTmpGenotype& rhs) const { return id_num >= rhs.id_num; }
+ };
+
};
Modified: branches/interrupt/source/main/cStats.cc
===================================================================
--- branches/interrupt/source/main/cStats.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cStats.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -137,6 +137,8 @@
, m_spec_waste(0)
, num_orgs_killed(0)
, m_deme_num_repls(0)
+ , m_deme_num_repls_treatable(0)
+ , m_deme_num_repls_untreatable(0)
, m_donate_to_donor (0)
, m_donate_to_facing (0)
{
@@ -1446,7 +1448,30 @@
relative_pos_pred_sat.ElementAt(pos.first, pos.second)++;
}
+void cStats::AddDemeResourceThresholdPredicate(cString& name) {
+ demeResourceThresholdPredicateMap[name] = 0;
+}
+
+void cStats::IncDemeResourceThresholdPredicate(cString& name) {
+ ++demeResourceThresholdPredicateMap[name];
+}
+void cStats::PrintDemeResourceThresholdPredicate(const cString& filename)
+{
+ cDataFile& df = m_world->GetDataFile(filename);
+ df.WriteComment("Avida deme resource threshold predicate data");
+ df.WriteComment("Number of deme reproduced by a specific threshold since last update that data was printed");
+ df.WriteTimeStamp();
+
+ if(demeResourceThresholdPredicateMap.size() > 0) {
+ df.Write(GetUpdate(), "Update [update]");
+ for(map<cString, int>::iterator iter = demeResourceThresholdPredicateMap.begin(); iter != demeResourceThresholdPredicateMap.end(); ++iter) {
+ df.Write(iter->second, iter->first);
+ iter->second = 0;
+ }
+ df.Endl();
+ }
+}
/*! This method prints information contained within all active message predicates.
@@ -1504,6 +1529,23 @@
m_deme_births.Add(source_deme.GetBirthCount());
m_deme_merit.Add(source_deme.GetHeritableDemeMerit().GetDouble());
m_deme_generation.Add(source_deme.GetGeneration());
+ m_deme_density.Add(source_deme.GetDensity());
+
+ if(source_deme.isTreatable()) {
+ ++m_deme_num_repls_treatable;
+ m_deme_gestation_time_treatable.Add(source_deme.GetAge());
+ m_deme_births_treatable.Add(source_deme.GetBirthCount());
+ m_deme_merit_treatable.Add(source_deme.GetHeritableDemeMerit().GetDouble());
+ m_deme_generation_treatable.Add(source_deme.GetGeneration());
+ m_deme_density_treatable.Add(source_deme.GetDensity());
+ } else {
+ ++m_deme_num_repls_untreatable;
+ m_deme_gestation_time_untreatable.Add(source_deme.GetAge());
+ m_deme_births_untreatable.Add(source_deme.GetBirthCount());
+ m_deme_merit_untreatable.Add(source_deme.GetHeritableDemeMerit().GetDouble());
+ m_deme_generation_untreatable.Add(source_deme.GetGeneration());
+ m_deme_density_untreatable.Add(source_deme.GetDensity());
+ }
}
@@ -1551,7 +1593,8 @@
df.Write(m_deme_births.Average(), "Mean number of births within replicated demes [numbirths]");
df.Write(m_deme_merit.Average(), "Mean heritable merit of replicated demes [merit]");
df.Write(m_deme_generation.Average(), "Mean generation of replicated demes [generation]");
-
+ df.Write(m_deme_density.Average(), "Mean density of replicated demes [density]");
+
df.Endl();
m_deme_num_repls = 0;
@@ -1559,9 +1602,91 @@
m_deme_births.Clear();
m_deme_merit.Clear();
m_deme_generation.Clear();
+ m_deme_density.Clear();
}
+/*! Print statistics related to deme replication. Currently only prints the
+ number of deme replications since the last time PrintDemeReplicationData was
+ invoked.
+ */
+void cStats::PrintDemeTreatableReplicationData(const cString& filename)
+{
+ cDataFile& df = m_world->GetDataFile(filename);
+
+ df.WriteComment("Avida deme replication data for treatable deme");
+ df.WriteTimeStamp();
+ df.Write(GetUpdate(), "Update [update]");
+ df.Write(m_deme_num_repls_treatable, "Number of deme replications [numrepl]");
+ df.Write(m_deme_gestation_time_treatable.Average(), "Mean deme gestation time [gesttime]");
+ df.Write(m_deme_births_treatable.Average(), "Mean number of births within replicated demes [numbirths]");
+ df.Write(m_deme_merit_treatable.Average(), "Mean heritable merit of replicated demes [merit]");
+ df.Write(m_deme_generation_treatable.Average(), "Mean generation of replicated demes [generation]");
+ df.Write(m_deme_density_treatable.Average(), "Mean density of replicated demes [density]");
+
+ df.Endl();
+
+ m_deme_num_repls_treatable = 0;
+ m_deme_gestation_time_treatable.Clear();
+ m_deme_births_treatable.Clear();
+ m_deme_merit_treatable.Clear();
+ m_deme_generation_treatable.Clear();
+ m_deme_density_treatable.Clear();
+}
+/*! Print statistics related to deme replication. Currently only prints the
+ number of deme replications since the last time PrintDemeReplicationData was
+ invoked.
+ */
+void cStats::PrintDemeUntreatableReplicationData(const cString& filename)
+{
+ cDataFile& df = m_world->GetDataFile(filename);
+
+ df.WriteComment("Avida deme replication data for untreatable deme");
+ df.WriteTimeStamp();
+ df.Write(GetUpdate(), "Update [update]");
+ df.Write(m_deme_num_repls_untreatable, "Number of deme replications [numrepl]");
+ df.Write(m_deme_gestation_time_untreatable.Average(), "Mean deme gestation time [gesttime]");
+ df.Write(m_deme_births_untreatable.Average(), "Mean number of births within replicated demes [numbirths]");
+ df.Write(m_deme_merit_untreatable.Average(), "Mean heritable merit of replicated demes [merit]");
+ df.Write(m_deme_generation_untreatable.Average(), "Mean generation of replicated demes [generation]");
+ df.Write(m_deme_density_untreatable.Average(), "Mean density of replicated demes [density]");
+
+ df.Endl();
+
+ m_deme_num_repls_untreatable = 0;
+ m_deme_gestation_time_untreatable.Clear();
+ m_deme_births_untreatable.Clear();
+ m_deme_merit_untreatable.Clear();
+ m_deme_generation_untreatable.Clear();
+ m_deme_density_untreatable.Clear();
+}
+
+
+void cStats::PrintDemeTreatableCount(const cString& filename)
+{
+ cPopulation& pop = m_world->GetPopulation();
+ static const int numDemes = pop.GetNumDemes();
+ int treatable(0);
+ int untreatable(0);
+ for(int i = 0; i < numDemes; ++i) {
+ if(pop.GetDeme(i).isTreatable())
+ ++treatable;
+ else
+ ++untreatable;
+ }
+
+ cDataFile& df = m_world->GetDataFile(filename);
+
+ df.WriteComment("Avida deme replication data for untreatable deme");
+ df.WriteTimeStamp();
+ df.Write(GetUpdate(), "Update [update]");
+ df.Write(treatable, "Number demes treatable");
+ df.Write(untreatable, "Number demes untreatable");
+ df.Write(static_cast<double>(treatable)/static_cast<double>(untreatable), "Treatable:untreatable ratio");
+
+ df.Endl();
+}
+
void cStats::PrintGermlineData(const cString& filename)
{
cDataFile& df = m_world->GetDataFile(filename);
@@ -2476,4 +2601,40 @@
}
+/*
+ Print data regarding group formation.
+ */
+void cStats::PrintGroupsFormedData(const cString& filename)
+{
+ cDataFile& df = m_world->GetDataFile(filename);
+ df.WriteComment("The number of groups, average, max, and min number of orgs in groups");
+
+ map<int,int> groups = m_world->GetPopulation().GetFormedGroups();
+
+ map <int,int>::iterator itr;
+ double avg_size = 0.0;
+ double max_size = 0.0;
+ double min_size = 100000000000.0;
+ double active_groups = 0.0;
+
+ for(itr = groups.begin();itr!=groups.end();itr++) {
+ avg_size += itr->second;
+ if (itr->second > max_size) max_size = itr->second;
+ if (itr->second < min_size) min_size = itr->second;
+ if (itr->second > 0) active_groups++;
+ }
+
+ avg_size = avg_size / groups.size();
+ df.Write((double)groups.size(), "number of groups [num]");
+ df.Write(avg_size, "average size of groups [avg-size]");
+ df.Write(max_size, "max size of groups [max-size]");
+ df.Write(min_size, "min size of groups [min-size]");
+ df.Write(active_groups, "active groups [act-group]");
+
+
+ df.Endl();
+
+
+}
+
Modified: branches/interrupt/source/main/cStats.h
===================================================================
--- branches/interrupt/source/main/cStats.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cStats.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -320,6 +320,7 @@
// deme predicate stats
tMatrix<int> relative_pos_event_count;
tMatrix<int> relative_pos_pred_sat;
+ std::map<cString, int> demeResourceThresholdPredicateMap;
// Speculative Execution Stats
int m_spec_total;
@@ -775,11 +776,16 @@
void PrintCellVisitsData(const cString& filename);
void PrintExtendedTimeData(const cString& filename);
void PrintNumOrgsKilledData(const cString& filename);
+ void PrintGroupsFormedData(const cString& filename);
// deme predicate stats
void IncEventCount(int x, int y);
void IncPredSat(int cell_id);
void PrintPredSatFracDump(const cString& filename);
+
+ void AddDemeResourceThresholdPredicate(cString& name);
+ void IncDemeResourceThresholdPredicate(cString& name);
+ void PrintDemeResourceThresholdPredicate(const cString& filename);
void addOrgLocations(std::vector<std::pair<int, int> >);
void PrintDemeRepOrgLocation(const cString& filename);
@@ -827,6 +833,11 @@
void GermlineReplication(cGermline& source_germline, cGermline& target_germline);
//! Print statistics about deme replication.
void PrintDemeReplicationData(const cString& filename);
+
+ void PrintDemeTreatableReplicationData(const cString& filename);
+ void PrintDemeUntreatableReplicationData(const cString& filename);
+ void PrintDemeTreatableCount(const cString& filename);
+
//! Print statistics about germlines.
void PrintGermlineData(const cString& filename);
//! Accessor for average "generation" of germlines.
@@ -865,8 +876,24 @@
cDoubleSum m_deme_births; //!< Mean number of births in replicated demes.
cDoubleSum m_deme_merit; //!< Mean merit of replicated demes.
cDoubleSum m_deme_generation; //!< Mean generation of replicated demes.
+ cDoubleSum m_deme_density; //!< Mean density of replicated demes.
cDoubleSum m_germline_generation; //!< "Generation" accumulator of replicated germlines.
- t_founder_map m_deme_founders; //!< Data structure to track the founders of demes.
+
+ int m_deme_num_repls_treatable; //!< Number of deme replications in treatable demes since last PrintDemeReplicationData.
+ cDoubleSum m_deme_gestation_time_treatable; //!< Gestation time for treatable demes - mean age at deme replication.
+ cDoubleSum m_deme_births_treatable; //!< Mean number of births in replicated treatable demes.
+ cDoubleSum m_deme_merit_treatable; //!< Mean merit of replicated treatable demes.
+ cDoubleSum m_deme_generation_treatable; //!< Mean generation of replicated treatable demes.
+ cDoubleSum m_deme_density_treatable; //!< Mean density of replicated treatable demes.
+
+ int m_deme_num_repls_untreatable; //!< Number of deme replications in untreatable demes since last PrintDemeReplicationData.
+ cDoubleSum m_deme_gestation_time_untreatable; //!< Gestation time for untreatable demes - mean age at deme replication.
+ cDoubleSum m_deme_births_untreatable; //!< Mean number of births in replicated untreatable demes.
+ cDoubleSum m_deme_merit_untreatable; //!< Mean merit of replicated untreatable demes.
+ cDoubleSum m_deme_generation_untreatable; //!< Mean generation of replicated untreatable demes.
+ cDoubleSum m_deme_density_untreatable; //!< Mean density of replicated untreatable demes.
+
+ t_founder_map m_deme_founders; //!< Data structure to track the founders of demes.
// -------- Deme competition support --------
Modified: branches/interrupt/source/main/cTaskLib.cc
===================================================================
--- branches/interrupt/source/main/cTaskLib.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cTaskLib.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -438,6 +438,8 @@
if (name == "sg_path_traversal")
Load_SGPathTraversal(name, info, envreqs, errors);
+ if (name == "form-group")
+ Load_FormSpatialGroup(name, info, envreqs, errors);
// Make sure we have actually found a task
if (task_array.GetSize() == start_size) {
@@ -3383,3 +3385,35 @@
return bonus;
}
+
+
+void cTaskLib::Load_FormSpatialGroup(const cString& name, const cString& argstr, cEnvReqs& envreqs, tList<cString>* errors)
+{
+ cArgSchema schema;
+
+ // Integer Arguments
+ schema.AddEntry("group_size", 0, 1);
+
+ cArgContainer* args = cArgContainer::Load(argstr, schema, errors);
+ if (args) NewTask(name, "FormSpatialGroups", &cTaskLib::Task_FormSpatialGroup, 0, args);
+}
+
+double cTaskLib::Task_FormSpatialGroup(cTaskContext& ctx) const
+{
+ int ideal_group_size = ctx.GetTaskEntry()->GetArguments().GetInt(0);
+ double reward = 0.0;
+ int group_id = 0;
+ if (ctx.GetOrganism()->HasOpinion()) {
+ group_id = ctx.GetOrganism()->GetOpinion().first;
+ }
+ int orgs_in_group = m_world->GetPopulation().NumberOfOrganismsInGroup(group_id);
+
+ if (orgs_in_group < ideal_group_size) {
+ reward = orgs_in_group*orgs_in_group;
+ } else {
+ reward = ideal_group_size*ideal_group_size;
+ }
+ reward = reward / ideal_group_size;
+ return reward;
+}
+
Modified: branches/interrupt/source/main/cTaskLib.h
===================================================================
--- branches/interrupt/source/main/cTaskLib.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/main/cTaskLib.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -317,6 +317,10 @@
// reputation
double Task_CreatePerfectStrings(cTaskContext& ctx) const;
+
+ // group formation
+ void Load_FormSpatialGroup(const cString& name, const cString& argstr, cEnvReqs& envreqs, tList<cString>* errors);
+ double Task_FormSpatialGroup(cTaskContext& ctx) const;
};
Modified: branches/interrupt/source/targets/avida-viewer/cTextViewerAnalyzeDriver.h
===================================================================
--- branches/interrupt/source/targets/avida-viewer/cTextViewerAnalyzeDriver.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/targets/avida-viewer/cTextViewerAnalyzeDriver.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -49,6 +49,7 @@
// Driver Actions
void SignalBreakpoint() { return; }
void SetDone() { m_done = true; }
+ void SetPause() { return; }
void RaiseException(const cString& in_string);
void RaiseFatalException(int exit_code, const cString& in_string);
Modified: branches/interrupt/source/targets/avida-viewer/cTextViewerDriver.cc
===================================================================
--- branches/interrupt/source/targets/avida-viewer/cTextViewerDriver.cc 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/targets/avida-viewer/cTextViewerDriver.cc 2009-06-25 20:57:37 UTC (rev 3338)
@@ -43,7 +43,7 @@
cTextViewerDriver::cTextViewerDriver(cWorld* world)
- : cTextViewerDriver_Base(world)
+ : cTextViewerDriver_Base(world), m_pause(false), m_firstupdate(true)
{
m_view = new cView(world);
m_view->SetViewMode(world->GetConfig().VIEW_MODE.Get());
@@ -100,7 +100,17 @@
const int UD_size = ave_time_slice * population.GetNumOrganisms();
const double step_size = 1.0 / (double) UD_size;
-
+ if (m_pause) {
+ m_view->Pause();
+ m_pause = false;
+
+ // This is needed to have the top bar drawn properly; I'm not sure why...
+ if (m_firstupdate) {
+ m_view->Refresh();
+ m_firstupdate = false;
+ }
+ }
+
// Are we stepping through an organism?
if (m_view->GetStepOrganism() != -1) { // Yes we are!
// Keep the viewer informed about the organism we are stepping through...
@@ -111,10 +121,9 @@
m_view->NewUpdate();
// This is needed to have the top bar drawn properly; I'm not sure why...
- static bool first_update = true;
- if (first_update) {
+ if (m_firstupdate) {
m_view->Refresh();
- first_update = false;
+ m_firstupdate = false;
}
}
population.ProcessStep(ctx, step_size, next_id);
@@ -133,10 +142,9 @@
m_view->NewUpdate();
// This is needed to have the top bar drawn properly; I'm not sure why...
- static bool first_update = true;
- if (first_update) {
+ if (m_firstupdate) {
m_view->Refresh();
- first_update = false;
+ m_firstupdate = false;
}
}
Modified: branches/interrupt/source/targets/avida-viewer/cTextViewerDriver.h
===================================================================
--- branches/interrupt/source/targets/avida-viewer/cTextViewerDriver.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/targets/avida-viewer/cTextViewerDriver.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -32,6 +32,9 @@
class cTextViewerDriver : public cTextViewerDriver_Base
{
private:
+ bool m_pause;
+ bool m_firstupdate;
+
cTextViewerDriver(); // not implemented
public:
@@ -40,6 +43,8 @@
void Run();
+ void SetPause() { m_pause = true; }
+
// Driver Actions
void SignalBreakpoint();
void SetDone() { m_done = true; }
Modified: branches/interrupt/source/targets/avida-viewer/cTextViewerDriver_Base.h
===================================================================
--- branches/interrupt/source/targets/avida-viewer/cTextViewerDriver_Base.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/targets/avida-viewer/cTextViewerDriver_Base.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -43,6 +43,7 @@
cWorld* m_world;
cView_Base* m_view;
bool m_done; // This is set to true when run should finish.
+ bool m_pause;
std::stringstream out_stream;
std::stringstream err_stream;
Modified: branches/interrupt/source/tools/tArray.h
===================================================================
--- branches/interrupt/source/tools/tArray.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/tools/tArray.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -167,7 +167,19 @@
m_data[new_pos] = value;
return new_pos;
}
+
+ void Swap(int idx1, int idx2)
+ {
+ assert(idx1 >= 0); // Lower Bounds Error
+ assert(idx1 < m_size); // Upper Bounds Error
+ assert(idx2 >= 0); // Lower Bounds Error
+ assert(idx2 < m_size); // Upper Bounds Error
+ T v = m_data[idx1];
+ m_data[idx1] = m_data[idx2];
+ m_data[idx2] = v;
+ }
+
void SetAll(const T& value)
{
for (int i = 0; i < m_size; i++) m_data[i] = value;
Modified: branches/interrupt/source/tools/tArrayUtils.h
===================================================================
--- branches/interrupt/source/tools/tArrayUtils.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/tools/tArrayUtils.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -25,7 +25,9 @@
#ifndef tArrayUtils_h
#define tArrayUtils_h
-#include "tArray.h"
+template<typename T> class tArray;
+template<typename T> class tManagedPointerArray;
+template<typename T> class tSmartArray;
class tArrayUtils
@@ -39,7 +41,7 @@
public:
-
+
template<typename T> inline static void QSort(tArray<T>& array) { QSort(array, 0, array.GetSize() - 1); }
template<typename T> static void QSort(tArray<T>& array, int begin, int end)
{
@@ -58,7 +60,7 @@
if (array[l] > pivot)
l++;
else
- swap(array, l, r--);
+ array.Swap(l, r--);
}
if (array[l] > pivot && array[r] > pivot) {
@@ -66,18 +68,91 @@
} else if (array[l] > pivot && array[r] <= pivot) {
l++; r--;
} else if (array[l] <= pivot && array[r] > pivot) {
- swap(array, l++, r--);
+ array.Swap(l++, r--);
} else {
r = l - 1;
}
- swap(array, r--, begin);
+ array.Swap(r--, begin);
QSort(array, begin, r);
QSort(array, l, end);
}
+
+ template<typename T> inline static void QSort(tManagedPointerArray<T>& array) { QSort(array, 0, array.GetSize() - 1); }
+ template<typename T> static void QSort(tManagedPointerArray<T>& array, int begin, int end)
+ {
+ if (end < begin) return;
+ if (begin - end <= QUICKSORT_THRESHOLD) {
+ ISort(array, begin, end);
+ return;
+ }
- template<typename T> inline static void ISort(tArray<T>& array) { isort(array, 0, array.GetSize() - 1); }
+ T& pivot = array[begin];
+ int l = begin + 1;
+ int r = end;
+
+ while (l != r - 1) {
+ if (array[l] > pivot)
+ l++;
+ else
+ array.Swap(l, r--);
+ }
+
+ if (array[l] > pivot && array[r] > pivot) {
+ l = r + 1;
+ } else if (array[l] > pivot && array[r] <= pivot) {
+ l++; r--;
+ } else if (array[l] <= pivot && array[r] > pivot) {
+ array.Swap(l++, r--);
+ } else {
+ r = l - 1;
+ }
+
+ array.Swap(r--, begin);
+ QSort(array, begin, r);
+ QSort(array, l, end);
+ }
+
+ template<typename T> inline static void QSort(tSmartArray<T>& array) { QSort(array, 0, array.GetSize() - 1); }
+ template<typename T> static void QSort(tSmartArray<T>& array, int begin, int end)
+ {
+ if (end < begin) return;
+
+ if (begin - end <= QUICKSORT_THRESHOLD) {
+ ISort(array, begin, end);
+ return;
+ }
+
+ T pivot = array[begin];
+ int l = begin + 1;
+ int r = end;
+
+ while (l != r - 1) {
+ if (array[l] > pivot)
+ l++;
+ else
+ array.Swap(l, r--);
+ }
+
+ if (array[l] > pivot && array[r] > pivot) {
+ l = r + 1;
+ } else if (array[l] > pivot && array[r] <= pivot) {
+ l++; r--;
+ } else if (array[l] <= pivot && array[r] > pivot) {
+ array.Swap(l++, r--);
+ } else {
+ r = l - 1;
+ }
+
+ array.Swap(r--, begin);
+ QSort(array, begin, r);
+ QSort(array, l, end);
+ }
+
+
+
+ template<typename T> inline static void ISort(tArray<T>& array) { ISort(array, 0, array.GetSize() - 1); }
template<typename T> static void ISort(tArray<T>& array, int begin, int end)
{
T value;
@@ -95,16 +170,43 @@
array[j + 1] = value;
}
}
-
-
-private:
-
- template<typename T> inline static void swap(tArray<T>& array, int i, int j)
+
+ template<typename T> inline static void ISort(tManagedPointerArray<T>& array) { ISort(array, 0, array.GetSize() - 1); }
+ template<typename T> static void ISort(tManagedPointerArray<T>& array, int begin, int end)
{
- T v = array[i];
- array[i] = array[j];
- array[j] = v;
+ T value;
+ int j;
+
+ // for each entry
+ for (int i = begin + 1; i <= end; i++) {
+ // insert into array starting from the end of our sub-array
+ value = array[i];
+ j = i - 1;
+ while (j >= begin && array[j] < array[j + 1]) {
+ array.Swap(j, j + 1);
+ j--;
+ }
+ }
}
+
+ template<typename T> inline static void ISort(tSmartArray<T>& array) { ISort(array, 0, array.GetSize() - 1); }
+ template<typename T> static void ISort(tSmartArray<T>& array, int begin, int end)
+ {
+ T value;
+ int j;
+
+ // for each entry
+ for (int i = begin + 1; i <= end; i++) {
+ // insert into array starting from the end of our sub-array
+ value = array[i];
+ j = i - 1;
+ while (j >= begin && array[j] < value) {
+ array[j + 1] = array[j];
+ j--;
+ }
+ array[j + 1] = value;
+ }
+ }
};
#endif
Modified: branches/interrupt/source/tools/tManagedPointerArray.h
===================================================================
--- branches/interrupt/source/tools/tManagedPointerArray.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/tools/tManagedPointerArray.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -38,7 +38,7 @@
#include <cassert>
template <class T> class tManagedPointerArray
-{
+{
#if USE_tMemTrack
tMemTrack<tManagedPointerArray<T> > mt;
#endif
@@ -185,6 +185,21 @@
*m_data[m_size - 1] = value;
}
+ void Swap(int idx1, int idx2)
+ {
+ // Simple pointer swap, rather than deep copy
+
+ assert(idx1 >= 0); // Lower Bounds Error
+ assert(idx1 < m_size); // Upper Bounds Error
+ assert(idx2 >= 0); // Lower Bounds Error
+ assert(idx2 < m_size); // Upper Bounds Error
+
+ T* v = m_data[idx1];
+ m_data[idx1] = m_data[idx2];
+ m_data[idx2] = v;
+ }
+
+
void SetAll(const T& value)
{
for (int i = 0; i < m_size; i++) *m_data[i] = value;
Modified: branches/interrupt/source/tools/tSmartArray.h
===================================================================
--- branches/interrupt/source/tools/tSmartArray.h 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/tools/tSmartArray.h 2009-06-25 20:57:37 UTC (rev 3338)
@@ -171,7 +171,19 @@
}
+ void Swap(int idx1, int idx2)
+ {
+ assert(idx1 >= 0); // Lower Bounds Error
+ assert(idx1 < m_active); // Upper Bounds Error
+ assert(idx2 >= 0); // Lower Bounds Error
+ assert(idx2 < m_active); // Upper Bounds Error
+
+ T v = m_data[idx1];
+ m_data[idx1] = m_data[idx2];
+ m_data[idx2] = v;
+ }
+
void SetAll(const T& value)
{
for (int i = 0; i < m_active; i++) m_data[i] = value;
Modified: branches/interrupt/source/utils/hist_map/Makefile
===================================================================
--- branches/interrupt/source/utils/hist_map/Makefile 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/utils/hist_map/Makefile 2009-06-25 20:57:37 UTC (rev 3338)
@@ -30,7 +30,7 @@
SRC = hist_map.cc ../../tools/cFile.cc \
../../tools/cInitFile.cc ../../tools/cString.cc \
../../tools/cStringList.cc ../../tools/cStringIterator.cc \
- ../../tools/cStringUtil.cc
+ ../../tools/cStringUtil.cc ../../tools/cRCObject.cc
### List Object Files (for each source file there is a object file) ###########
OBJ = $(SRC:.cc=.o)
Modified: branches/interrupt/source/utils/process_map/Makefile
===================================================================
--- branches/interrupt/source/utils/process_map/Makefile 2009-06-25 20:34:47 UTC (rev 3337)
+++ branches/interrupt/source/utils/process_map/Makefile 2009-06-25 20:57:37 UTC (rev 3338)
@@ -30,7 +30,8 @@
SRC = process_map.cc ../../tools/cFile.cc \
../../tools/cInitFile.cc ../../tools/cString.cc \
../../tools/cStringList.cc ../../tools/cStringIterator.cc \
- ../../tools/cRandom.cc ../../tools/cStringUtil.o
+ ../../tools/cRandom.cc ../../tools/cStringUtil.o \
+ ../../tools/cRCObject.cc
### List Object Files (for each source file there is a object file) ###########
OBJ = $(SRC:.cc=.o)
Copied: branches/interrupt/tests/collect_specification_analyze (from rev 3275, development/tests/collect_specification_analyze)
Copied: branches/interrupt/tests/collect_specification_analyze/config (from rev 3275, development/tests/collect_specification_analyze/config)
Deleted: branches/interrupt/tests/collect_specification_analyze/config/analyze-spec.cfg
===================================================================
--- development/tests/collect_specification_analyze/config/analyze-spec.cfg 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/config/analyze-spec.cfg 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,16 +0,0 @@
-#############################################################################
-# This file is used to setup avida when it is in analysis-only mode (by
-# running "avida -a". It allows variety of methods to load organisms
-# (specifying the type of each) and analyze them once loaded.
-#
-# See the documentation in doc/analyze_mode.html for usage, or the file
-# doc/analyze_samples.html for guidelines on writing programs.
-#
-#############################################################################
-
-VERBOSE
-
-LOAD detail-200000.pop
-RECALCULATE 1
-DETAIL executed.dat inst.26 task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 sequence num_cpus length merit exe_length gest_time fitness r_spec.0 r_spec.1 r_spec.2 r_spec.3 r_spec.4 r_spec.5 r_spec.6 r_spec.7 r_spec.8 r_spec.9 r_spec.10 r_spec.11 r_spec.12
-PURGE_BATCH
Copied: branches/interrupt/tests/collect_specification_analyze/config/analyze-spec.cfg (from rev 3275, development/tests/collect_specification_analyze/config/analyze-spec.cfg)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/config/analyze-spec.cfg (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/config/analyze-spec.cfg 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,16 @@
+#############################################################################
+# This file is used to setup avida when it is in analysis-only mode (by
+# running "avida -a". It allows variety of methods to load organisms
+# (specifying the type of each) and analyze them once loaded.
+#
+# See the documentation in doc/analyze_mode.html for usage, or the file
+# doc/analyze_samples.html for guidelines on writing programs.
+#
+#############################################################################
+
+VERBOSE
+
+LOAD detail-200000.pop
+RECALCULATE 1
+DETAIL executed.dat inst.26 task.0 task.1 task.2 task.3 task.4 task.5 task.6 task.7 task.8 sequence num_cpus length merit exe_length gest_time fitness r_spec.0 r_spec.1 r_spec.2 r_spec.3 r_spec.4 r_spec.5 r_spec.6 r_spec.7 r_spec.8 r_spec.9 r_spec.10 r_spec.11 r_spec.12
+PURGE_BATCH
Deleted: branches/interrupt/tests/collect_specification_analyze/config/avida.cfg
===================================================================
--- development/tests/collect_specification_analyze/config/avida.cfg 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/config/avida.cfg 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,241 +0,0 @@
-#############################################################################
-# This file includes all the basic run-time defines for Avida.
-# For more information, see doc/config.html
-#############################################################################
-
-VERSION_ID 2.7.0 # Do not change this value.
-
-### GENERAL_GROUP ###
-# General Settings
-ANALYZE_MODE 1 # 0 = Disabled
- # 1 = Enabled
- # 2 = Interactive
-VIEW_MODE 1 # Initial viewer screen
-CLONE_FILE - # Clone file to load
-VERBOSITY 1 # Control output verbosity
-
-### ARCH_GROUP ###
-# Architecture Variables
-WORLD_X 60 # Width of the Avida world
-WORLD_Y 60 # Height of the Avida world
-WORLD_GEOMETRY 2 # 1 = Bounded Grid
- # 2 = Torus
-NUM_DEMES 0 # Number of independed groups in the population; 0=off
-RANDOM_SEED 0 # Random number seed (0 for based on time)
-HARDWARE_TYPE 0 # 0 = Original CPUs
- # 1 = New SMT CPUs
- # 2 = Transitional SMT
-
-### CONFIG_FILE_GROUP ###
-# Configuration Files
-DATA_DIR data # Directory in which config files are found
-INST_SET instset-destroy.cfg # File containing instruction set
-EVENT_FILE events-collect.cfg # File containing list of events during run
-ANALYZE_FILE analyze-spec.cfg # File used for analysis mode
-ENVIRONMENT_FILE environment.9resource # File that describes the environment
-START_CREATURE default-classic.org # Organism to seed the soup
-
-### REPRODUCTION_GROUP ###
-# Birth and Death
-BIRTH_METHOD 0 # Which organism should be replaced on birth?
- # 0 = Random organism in neighborhood
- # 1 = Oldest in neighborhood
- # 2 = Largest Age/Merit in neighborhood
- # 3 = None (use only empty cells in neighborhood)
- # 4 = Random from population (Mass Action)
- # 5 = Oldest in entire population
- # 6 = Random within deme
- # 7 = Organism faced by parent
- # 8 = Next grid cell (id+1)
- # 9 = Largest energy used in entire population
- # 10 = Largest energy used in neighborhood
-PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
-ALLOW_PARENT 1 # Allow births to replace the parent organism?
-DEATH_METHOD 2 # 0 = Never die of old age.
- # 1 = Die when inst executed = AGE_LIMIT (+deviation)
- # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
-AGE_LIMIT 20 # Modifies DEATH_METHOD
-AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
-ALLOC_METHOD 0 # (Orignal CPU Only)
- # 0 = Allocated space is set to default instruction.
- # 1 = Set to section of dead genome (Necrophilia)
- # 2 = Allocated space is set to random instruction.
-DIVIDE_METHOD 1 # 0 = Divide leaves state of mother untouched.
- # 1 = Divide resets state of mother
- # (after the divide, we have 2 children)
- # 2 = Divide resets state of current thread only
- # (does not touch possible parasite threads)
-GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
- # increased on divide.
- # 1 = Both the generation of the mother and child are
- # increased on divide (good with DIVIDE_METHOD 1).
-
-### RECOMBINATION_GROUP ###
-# Sexual Recombination and Modularity
-RECOMBINATION_PROB 1.0 # probability of recombination in div-sex
-MAX_BIRTH_WAIT_TIME -1 # Updates incipiant orgs can wait for crossover
-MODULE_NUM 0 # number of modules in the genome
-CONT_REC_REGS 1 # are (modular) recombination regions continuous
-CORESPOND_REC_REGS 1 # are (modular) recombination regions swapped randomly
- # or with corresponding positions?
-TWO_FOLD_COST_SEX 0 # 1 = only one recombined offspring is born.
- # 2 = both offspring are born
-SAME_LENGTH_SEX 0 # 0 = recombine with any genome
- # 1 = only recombine w/ same length
-
-### DIVIDE_GROUP ###
-# Divide Restrictions
-CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
-MIN_COPIED_LINES 0.5 # Code fraction which must be copied before divide.
-MIN_EXE_LINES 0.5 # Code fraction which must be executed before divide.
-REQUIRE_ALLOCATE 1 # (Original CPU Only) Require allocate before divide?
-REQUIRED_TASK -1 # Task ID required for successful divide.
-IMMUNITY_TASK -1 # Task providing immunity from the required task.
-REQUIRED_REACTION -1 # Reaction ID required for successful divide.
-REQUIRED_BONUS 0 # The bonus that an organism must accumulate to divide.
-
-### MUTATION_GROUP ###
-# Mutations
-POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
-COPY_MUT_PROB 0.0025 # Mutation rate (per copy)
-INS_MUT_PROB 0.0 # Insertion rate (per site, applied on divide)
-DEL_MUT_PROB 0.0 # Deletion rate (per site, applied on divide)
-DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
-DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
-DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
-DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
-PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
-SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
-INJECT_INS_PROB 0.0 # Insertion rate (per site, applied on inject)
-INJECT_DEL_PROB 0.0 # Deletion rate (per site, applied on inject)
-INJECT_MUT_PROB 0.0 # Mutation rate (per site, applied on inject)
-META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
-META_STD_DEV 0.0 # Standard deviation of meta mutation size.
-MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
- # 2 = Mutation rates inherited from parent.
-
-### REVERSION_GROUP ###
-# Mutation Reversion
-# These slow down avida a lot, and should be set to 0.0 normally.
-REVERT_FATAL 0.0 # Should any mutations be reverted on birth?
-REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
-REVERT_NEUTRAL 0.0 #
-REVERT_BENEFICIAL 0.0 #
-STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
-STERILIZE_DETRIMENTAL 0.0 #
-STERILIZE_NEUTRAL 0.0 #
-STERILIZE_BENEFICIAL 0.0 #
-FAIL_IMPLICIT 1 # Should copies that failed *not* due to mutations
- # be eliminated?
-NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness to be considered neutral.
-NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness to be considered neutral.
-
-### TIME_GROUP ###
-# Time Slicing
-AVE_TIME_SLICE 30 # Ave number of insts per org per update
-SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
- # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
- # 2 = INTEGRATED: Perfectly integrated deterministic.
-BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
- # 1 = Merit proportional to copied size
- # 2 = Merit prop. to executed size
- # 3 = Merit prop. to full size
- # 4 = Merit prop. to min of executed or copied size
- # 5 = Merit prop. to sqrt of the minimum size
-BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
-DEFAULT_BONUS 1.0 # Initial bonus before any tasks
-MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by the default bonus
- # rather than the accumulated bonus of the parent?
-MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
-THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
- # (num_threads-1) * THREAD_SLICING_METHOD + 1
- # 0 = One thread executed per time slice.
- # 1 = All threads executed each time slice.
-MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
-DONATE_SIZE 5.0 # Amount of merit donated with 'donate' command
-DONATE_MULT 10.0 # Multiple of merit given that the target receives.
-MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
-MAX_DONATE_EDIT_DIST -1 # Limit on edit distance for donate; -1=no max
-MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
-
-### PROMOTER_GROUP ###
-# Promoters
-PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
- # Certain instructions must also be included.
-PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating before executing each instruction.
-PROMOTER_BG_STRENGTH 0 # Probability of positions that are not promoter
- # instructions initiating execution (promoters are 1).
-REGULATION_STRENGTH 1 # Strength added or subtracted to a promoter by regulation.
-REGULATION_DECAY_FRAC 0.1 # Fraction of regulation that decays away.
- # (Max regulation = REGULATION_STRENGTH / REGULATION_DECAY_FRAC)
-
-### GENEOLOGY_GROUP ###
-# Geneology
-TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
- # 0=no, 1=yes, 2=yes,w/sexual population
-THRESHOLD 3 # Number of organisms in a genotype needed for it
- # to be considered viable.
-GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
-GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
- # this many updates. (0 = off)
-SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
-SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
-SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
-TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
-
-### LOG_GROUP ###
-# Log Files
-LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
-LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
-LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
-LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
-
-### LINEAGE_GROUP ###
-# Lineage
-# NOTE: This should probably be called "Clade"
-# This one can slow down avida a lot. It is used to get an idea of how
-# often an advantageous mutation arises, and where it goes afterwards.
-# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
-# 0 = manual creation (on inject, use successive integers as lineage labels).
-# 1 = when a child's (potential) fitness is higher than that of its parent.
-# 2 = when a child's (potential) fitness is higher than max in population.
-# 3 = when a child's (potential) fitness is higher than max in dom. lineage
-# *and* the child is in the dominant lineage, or (2)
-# 4 = when a child's (potential) fitness is higher than max in dom. lineage
-# (and that of its own lineage)
-# 5 = same as child's (potential) fitness is higher than that of the
-# currently dominant organism, and also than that of any organism
-# currently in the same lineage.
-# 6 = when a child's (potential) fitness is higher than any organism
-# currently in the same lineage.
-# 7 = when a child's (potential) fitness is higher than that of any
-# organism in its line of descent
-LOG_LINEAGES 0 #
-LINEAGE_CREATION_METHOD 0 #
-
-### ORGANISM_NETWORK_GROUP ###
-# Organism Network Communication
-NET_ENABLED 0 # Enable Network Communication Support
-NET_DROP_PROB 0.0 # Message drop rate
-NET_MUT_PROB 0.0 # Message corruption probability
-NET_MUT_TYPE 0 # Type of message corruption. 0 = Random Single Bit, 1 = Always Flip Last
-NET_STYLE 0 # Communication Style. 0 = Random Next, 1 = Receiver Facing
-
-### BUY_SELL_GROUP ###
-# Buying and Selling Parameters
-SAVE_RECEIVED 0 # Enable storage of all inputs bought from other orgs
-BUY_PRICE 0 # price offered by organisms attempting to buy
-SELL_PRICE 0 # price offered by organisms attempting to sell
-
-### HOARD_RESOURCE_GROUP ###
-USE_RESOURCE_BINS 1
-ABSORB_RESOURCE_FRACTION .0025
-MULTI_ABSORB_TYPE 0
-USE_STORED_FRACTION 0.0
-RETURN_STORED_ON_DEATH 1
-
-### ANALYZE_GROUP ###
-# Analysis Settings
-MT_CONCURRENCY 1 # Number of concurrent analyze threads
-ANALYZE_OPTION_1 # String variable accessible from analysis scripts
-ANALYZE_OPTION_2 # String variable accessible from analysis scripts
Copied: branches/interrupt/tests/collect_specification_analyze/config/avida.cfg (from rev 3275, development/tests/collect_specification_analyze/config/avida.cfg)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/config/avida.cfg (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/config/avida.cfg 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,241 @@
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.7.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 1 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 1 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+VERBOSITY 1 # Control output verbosity
+
+### ARCH_GROUP ###
+# Architecture Variables
+WORLD_X 60 # Width of the Avida world
+WORLD_Y 60 # Height of the Avida world
+WORLD_GEOMETRY 2 # 1 = Bounded Grid
+ # 2 = Torus
+NUM_DEMES 0 # Number of independed groups in the population; 0=off
+RANDOM_SEED 0 # Random number seed (0 for based on time)
+HARDWARE_TYPE 0 # 0 = Original CPUs
+ # 1 = New SMT CPUs
+ # 2 = Transitional SMT
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET instset-destroy.cfg # File containing instruction set
+EVENT_FILE events-collect.cfg # File containing list of events during run
+ANALYZE_FILE analyze-spec.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment.9resource # File that describes the environment
+START_CREATURE default-classic.org # Organism to seed the soup
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 0 # Which organism should be replaced on birth?
+ # 0 = Random organism in neighborhood
+ # 1 = Oldest in neighborhood
+ # 2 = Largest Age/Merit in neighborhood
+ # 3 = None (use only empty cells in neighborhood)
+ # 4 = Random from population (Mass Action)
+ # 5 = Oldest in entire population
+ # 6 = Random within deme
+ # 7 = Organism faced by parent
+ # 8 = Next grid cell (id+1)
+ # 9 = Largest energy used in entire population
+ # 10 = Largest energy used in neighborhood
+PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
+ALLOW_PARENT 1 # Allow births to replace the parent organism?
+DEATH_METHOD 2 # 0 = Never die of old age.
+ # 1 = Die when inst executed = AGE_LIMIT (+deviation)
+ # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
+AGE_LIMIT 20 # Modifies DEATH_METHOD
+AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
+ALLOC_METHOD 0 # (Orignal CPU Only)
+ # 0 = Allocated space is set to default instruction.
+ # 1 = Set to section of dead genome (Necrophilia)
+ # 2 = Allocated space is set to random instruction.
+DIVIDE_METHOD 1 # 0 = Divide leaves state of mother untouched.
+ # 1 = Divide resets state of mother
+ # (after the divide, we have 2 children)
+ # 2 = Divide resets state of current thread only
+ # (does not touch possible parasite threads)
+GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
+ # increased on divide.
+ # 1 = Both the generation of the mother and child are
+ # increased on divide (good with DIVIDE_METHOD 1).
+
+### RECOMBINATION_GROUP ###
+# Sexual Recombination and Modularity
+RECOMBINATION_PROB 1.0 # probability of recombination in div-sex
+MAX_BIRTH_WAIT_TIME -1 # Updates incipiant orgs can wait for crossover
+MODULE_NUM 0 # number of modules in the genome
+CONT_REC_REGS 1 # are (modular) recombination regions continuous
+CORESPOND_REC_REGS 1 # are (modular) recombination regions swapped randomly
+ # or with corresponding positions?
+TWO_FOLD_COST_SEX 0 # 1 = only one recombined offspring is born.
+ # 2 = both offspring are born
+SAME_LENGTH_SEX 0 # 0 = recombine with any genome
+ # 1 = only recombine w/ same length
+
+### DIVIDE_GROUP ###
+# Divide Restrictions
+CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
+MIN_COPIED_LINES 0.5 # Code fraction which must be copied before divide.
+MIN_EXE_LINES 0.5 # Code fraction which must be executed before divide.
+REQUIRE_ALLOCATE 1 # (Original CPU Only) Require allocate before divide?
+REQUIRED_TASK -1 # Task ID required for successful divide.
+IMMUNITY_TASK -1 # Task providing immunity from the required task.
+REQUIRED_REACTION -1 # Reaction ID required for successful divide.
+REQUIRED_BONUS 0 # The bonus that an organism must accumulate to divide.
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0025 # Mutation rate (per copy)
+INS_MUT_PROB 0.0 # Insertion rate (per site, applied on divide)
+DEL_MUT_PROB 0.0 # Deletion rate (per site, applied on divide)
+DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
+DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
+DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
+DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
+PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+INJECT_INS_PROB 0.0 # Insertion rate (per site, applied on inject)
+INJECT_DEL_PROB 0.0 # Deletion rate (per site, applied on inject)
+INJECT_MUT_PROB 0.0 # Mutation rate (per site, applied on inject)
+META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
+META_STD_DEV 0.0 # Standard deviation of meta mutation size.
+MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
+ # 2 = Mutation rates inherited from parent.
+
+### REVERSION_GROUP ###
+# Mutation Reversion
+# These slow down avida a lot, and should be set to 0.0 normally.
+REVERT_FATAL 0.0 # Should any mutations be reverted on birth?
+REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
+REVERT_NEUTRAL 0.0 #
+REVERT_BENEFICIAL 0.0 #
+STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
+STERILIZE_DETRIMENTAL 0.0 #
+STERILIZE_NEUTRAL 0.0 #
+STERILIZE_BENEFICIAL 0.0 #
+FAIL_IMPLICIT 1 # Should copies that failed *not* due to mutations
+ # be eliminated?
+NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness to be considered neutral.
+NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness to be considered neutral.
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
+ # 1 = Merit proportional to copied size
+ # 2 = Merit prop. to executed size
+ # 3 = Merit prop. to full size
+ # 4 = Merit prop. to min of executed or copied size
+ # 5 = Merit prop. to sqrt of the minimum size
+BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
+DEFAULT_BONUS 1.0 # Initial bonus before any tasks
+MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by the default bonus
+ # rather than the accumulated bonus of the parent?
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
+ # (num_threads-1) * THREAD_SLICING_METHOD + 1
+ # 0 = One thread executed per time slice.
+ # 1 = All threads executed each time slice.
+MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
+DONATE_SIZE 5.0 # Amount of merit donated with 'donate' command
+DONATE_MULT 10.0 # Multiple of merit given that the target receives.
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on edit distance for donate; -1=no max
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+
+### PROMOTER_GROUP ###
+# Promoters
+PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
+ # Certain instructions must also be included.
+PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating before executing each instruction.
+PROMOTER_BG_STRENGTH 0 # Probability of positions that are not promoter
+ # instructions initiating execution (promoters are 1).
+REGULATION_STRENGTH 1 # Strength added or subtracted to a promoter by regulation.
+REGULATION_DECAY_FRAC 0.1 # Fraction of regulation that decays away.
+ # (Max regulation = REGULATION_STRENGTH / REGULATION_DECAY_FRAC)
+
+### GENEOLOGY_GROUP ###
+# Geneology
+TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
+ # 0=no, 1=yes, 2=yes,w/sexual population
+THRESHOLD 3 # Number of organisms in a genotype needed for it
+ # to be considered viable.
+GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
+GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
+ # this many updates. (0 = off)
+SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
+SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
+SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
+TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
+
+### LOG_GROUP ###
+# Log Files
+LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
+LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
+LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
+LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
+
+### LINEAGE_GROUP ###
+# Lineage
+# NOTE: This should probably be called "Clade"
+# This one can slow down avida a lot. It is used to get an idea of how
+# often an advantageous mutation arises, and where it goes afterwards.
+# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
+# 0 = manual creation (on inject, use successive integers as lineage labels).
+# 1 = when a child's (potential) fitness is higher than that of its parent.
+# 2 = when a child's (potential) fitness is higher than max in population.
+# 3 = when a child's (potential) fitness is higher than max in dom. lineage
+# *and* the child is in the dominant lineage, or (2)
+# 4 = when a child's (potential) fitness is higher than max in dom. lineage
+# (and that of its own lineage)
+# 5 = same as child's (potential) fitness is higher than that of the
+# currently dominant organism, and also than that of any organism
+# currently in the same lineage.
+# 6 = when a child's (potential) fitness is higher than any organism
+# currently in the same lineage.
+# 7 = when a child's (potential) fitness is higher than that of any
+# organism in its line of descent
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
+
+### ORGANISM_NETWORK_GROUP ###
+# Organism Network Communication
+NET_ENABLED 0 # Enable Network Communication Support
+NET_DROP_PROB 0.0 # Message drop rate
+NET_MUT_PROB 0.0 # Message corruption probability
+NET_MUT_TYPE 0 # Type of message corruption. 0 = Random Single Bit, 1 = Always Flip Last
+NET_STYLE 0 # Communication Style. 0 = Random Next, 1 = Receiver Facing
+
+### BUY_SELL_GROUP ###
+# Buying and Selling Parameters
+SAVE_RECEIVED 0 # Enable storage of all inputs bought from other orgs
+BUY_PRICE 0 # price offered by organisms attempting to buy
+SELL_PRICE 0 # price offered by organisms attempting to sell
+
+### HOARD_RESOURCE_GROUP ###
+USE_RESOURCE_BINS 1
+ABSORB_RESOURCE_FRACTION .0025
+MULTI_ABSORB_TYPE 0
+USE_STORED_FRACTION 0.0
+RETURN_STORED_ON_DEATH 1
+
+### ANALYZE_GROUP ###
+# Analysis Settings
+MT_CONCURRENCY 1 # Number of concurrent analyze threads
+ANALYZE_OPTION_1 # String variable accessible from analysis scripts
+ANALYZE_OPTION_2 # String variable accessible from analysis scripts
Deleted: branches/interrupt/tests/collect_specification_analyze/config/default-classic.org
===================================================================
--- development/tests/collect_specification_analyze/config/default-classic.org 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/config/default-classic.org 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,100 +0,0 @@
-h-alloc # Allocate space for child
-h-search # Locate the end of the organism
-nop-C #
-nop-A #
-mov-head # Place write-head at beginning of offspring.
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
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-nop-C #
-nop-C #
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-nop-C #
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-nop-C #
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-nop-C #
-nop-C #
-nop-C #
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-nop-C #
-nop-C #
-nop-C #
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-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
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-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-nop-C #
-h-search # Mark the beginning of the copy loop
-h-copy # Do the copy
-if-label # If we're done copying....
-nop-C #
-nop-A #
-h-divide # ...divide!
-mov-head # Otherwise, loop back to the beginning of the copy loop.
-nop-A # End label.
-nop-B #
Copied: branches/interrupt/tests/collect_specification_analyze/config/default-classic.org (from rev 3275, development/tests/collect_specification_analyze/config/default-classic.org)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/config/default-classic.org (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/config/default-classic.org 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
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+nop-C #
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+nop-C #
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+nop-C #
+nop-C #
+nop-C #
+h-search # Mark the beginning of the copy loop
+h-copy # Do the copy
+if-label # If we're done copying....
+nop-C #
+nop-A #
+h-divide # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Deleted: branches/interrupt/tests/collect_specification_analyze/config/detail-200000.pop
===================================================================
--- development/tests/collect_specification_analyze/config/detail-200000.pop 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/config/detail-200000.pop 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,23 +0,0 @@
-#filetype genotype_data
-#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
-
-# 1: ID
-# 2: parent ID
-# 3: parent distance
-# 4: number of organisms currently alive
-# 5: total number of organisms that ever existed
-# 6: length of genome
-# 7: merit
-# 8: gestation time
-# 9: fitness
-# 10: update born
-# 11: update deactivated
-# 12: depth in phylogentic tree
-# 13: genome of organism
-
-4335143 4333347 -1 1043 887133 106 6907.63 1518 4.55048 99642 -1 393 rhuucavczebAqrjgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab
-4322574 4321310 -1 834 480241 102 6509.31 1436 4.53295 98644 -1 394 ArpucavczmnqrhAsnndlosimuqhcmptflqtlpwwaxkzunqqcdpqpclbtncogcAqchhmdfctpaoqcgqfmocloytpyaofahofycasvab
-4333347 4325270 -1 759 916175 106 6906.83 1518 4.54995 99498 -1 392 rhuucavczebAqrbgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab
-4329568 4327105 -1 574 584475 119 10590.8 2334 4.53763 99200 -1 410 rxuczaagvcjzjkcdqeadffpmxpmomtqodpdbzitgiyshebinlzsnnygunqtppqpdlceqnccptgcqcAAacycgfckaqfigfcqdetqcfbjpbapccecfycasvab
-4334827 4328326 -1 243 209369 112 9180.82 2045 4.4894 99619 -1 416 rxucajgvcczjkcAqkridrmbpmzAmtqodndhigftsuhebazfbylulnqtppqplceqncpbtgcqcAAacycgfckaqfigfcqdetqcfbjpbpccejycasvab
-4325402 4310669 -1 147 194622 107 8886.23 1966 4.51995 98865 -1 400 rxucavcczykfctfnfjmzpsqtodfpchzbxjheyitznruulnqtppqpclceuncptgcqcAAacycefckaqigfcqAetqcfbkpkapcceaAycasvrab
Copied: branches/interrupt/tests/collect_specification_analyze/config/detail-200000.pop (from rev 3275, development/tests/collect_specification_analyze/config/detail-200000.pop)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/config/detail-200000.pop (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/config/detail-200000.pop 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,23 @@
+#filetype genotype_data
+#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
+
+# 1: ID
+# 2: parent ID
+# 3: parent distance
+# 4: number of organisms currently alive
+# 5: total number of organisms that ever existed
+# 6: length of genome
+# 7: merit
+# 8: gestation time
+# 9: fitness
+# 10: update born
+# 11: update deactivated
+# 12: depth in phylogentic tree
+# 13: genome of organism
+
+4335143 4333347 -1 1043 887133 106 6907.63 1518 4.55048 99642 -1 393 rhuucavczebAqrjgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab
+4322574 4321310 -1 834 480241 102 6509.31 1436 4.53295 98644 -1 394 ArpucavczmnqrhAsnndlosimuqhcmptflqtlpwwaxkzunqqcdpqpclbtncogcAqchhmdfctpaoqcgqfmocloytpyaofahofycasvab
+4333347 4325270 -1 759 916175 106 6906.83 1518 4.54995 99498 -1 392 rhuucavczebAqrbgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab
+4329568 4327105 -1 574 584475 119 10590.8 2334 4.53763 99200 -1 410 rxuczaagvcjzjkcdqeadffpmxpmomtqodpdbzitgiyshebinlzsnnygunqtppqpdlceqnccptgcqcAAacycgfckaqfigfcqdetqcfbjpbapccecfycasvab
+4334827 4328326 -1 243 209369 112 9180.82 2045 4.4894 99619 -1 416 rxucajgvcczjkcAqkridrmbpmzAmtqodndhigftsuhebazfbylulnqtppqplceqncpbtgcqcAAacycgfckaqfigfcqdetqcfbjpbpccejycasvab
+4325402 4310669 -1 147 194622 107 8886.23 1966 4.51995 98865 -1 400 rxucavcczykfctfnfjmzpsqtodfpchzbxjheyitznruulnqtppqpclceuncptgcqcAAacycefckaqigfcqAetqcfbkpkapcceaAycasvrab
Deleted: branches/interrupt/tests/collect_specification_analyze/config/environment.9resource
===================================================================
--- development/tests/collect_specification_analyze/config/environment.9resource 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/config/environment.9resource 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,33 +0,0 @@
-##############################################################################
-#
-# This is the setup file for the task/resource system. From here, you can
-# setup the available resources (including their inflow and outflow rates) as
-# well as the reactions that the organisms can trigger by performing tasks.
-#
-# This environmental setup is that of a chemostat with 9 resources, each
-# with a unique task corresponding to them. All resources have a set inflow
-# of 100, and outflow rate of 0.01, setting their an equilibrium level at
-# 10,000. Given a maximum population size of 3600 and neighborhood size of
-# 9, the fraction of the resource absorbable in each reaction is simply
-# 9/3600 or 0.0025.
-#
-# For information on how to use this file, see: doc/environment.html
-# For other sample environments, see: source/support/config/
-#
-##############################################################################
-
-RESOURCE resNOT:inflow=100:outflow=0.01 resNAND:inflow=100:outflow=0.01
-RESOURCE resAND:inflow=100:outflow=0.01 resORN:inflow=100:outflow=0.01
-RESOURCE resOR:inflow=100:outflow=0.01 resANDN:inflow=100:outflow=0.01
-RESOURCE resNOR:inflow=100:outflow=0.01 resXOR:inflow=100:outflow=0.01
-RESOURCE resEQU:inflow=100:outflow=0.01
-
-REACTION NOT not process:resource=resNOT:value=1.0:frac=0.0025:max=25
-REACTION NAND nand process:resource=resNAND:value=1.0:frac=0.0025:max=25
-REACTION AND and process:resource=resAND:value=2.0:frac=0.0025:max=25
-REACTION ORN orn process:resource=resORN:value=2.0:frac=0.0025:max=25
-REACTION OR or process:resource=resOR:value=4.0:frac=0.0025:max=25
-REACTION ANDN andn process:resource=resANDN:value=4.0:frac=0.0025:max=25
-REACTION NOR nor process:resource=resNOR:value=8.0:frac=0.0025:max=25
-REACTION XOR xor process:resource=resXOR:value=8.0:frac=0.0025:max=25
-REACTION EQU equ process:resource=resEQU:value=16.0:frac=0.0025:max=25
Copied: branches/interrupt/tests/collect_specification_analyze/config/environment.9resource (from rev 3275, development/tests/collect_specification_analyze/config/environment.9resource)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/config/environment.9resource (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/config/environment.9resource 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,33 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This environmental setup is that of a chemostat with 9 resources, each
+# with a unique task corresponding to them. All resources have a set inflow
+# of 100, and outflow rate of 0.01, setting their an equilibrium level at
+# 10,000. Given a maximum population size of 3600 and neighborhood size of
+# 9, the fraction of the resource absorbable in each reaction is simply
+# 9/3600 or 0.0025.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+RESOURCE resNOT:inflow=100:outflow=0.01 resNAND:inflow=100:outflow=0.01
+RESOURCE resAND:inflow=100:outflow=0.01 resORN:inflow=100:outflow=0.01
+RESOURCE resOR:inflow=100:outflow=0.01 resANDN:inflow=100:outflow=0.01
+RESOURCE resNOR:inflow=100:outflow=0.01 resXOR:inflow=100:outflow=0.01
+RESOURCE resEQU:inflow=100:outflow=0.01
+
+REACTION NOT not process:resource=resNOT:value=1.0:frac=0.0025:max=25
+REACTION NAND nand process:resource=resNAND:value=1.0:frac=0.0025:max=25
+REACTION AND and process:resource=resAND:value=2.0:frac=0.0025:max=25
+REACTION ORN orn process:resource=resORN:value=2.0:frac=0.0025:max=25
+REACTION OR or process:resource=resOR:value=4.0:frac=0.0025:max=25
+REACTION ANDN andn process:resource=resANDN:value=4.0:frac=0.0025:max=25
+REACTION NOR nor process:resource=resNOR:value=8.0:frac=0.0025:max=25
+REACTION XOR xor process:resource=resXOR:value=8.0:frac=0.0025:max=25
+REACTION EQU equ process:resource=resEQU:value=16.0:frac=0.0025:max=25
Deleted: branches/interrupt/tests/collect_specification_analyze/config/events-collect.cfg
===================================================================
--- development/tests/collect_specification_analyze/config/events-collect.cfg 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/config/events-collect.cfg 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,38 +0,0 @@
-##############################################################################
-#
-# This is the setup file for the events system. From here, you can
-# configure any actions that you want to have happen during the course of
-# an experiment, including setting the times for data collection.
-#
-# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
-#
-# This file is currently setup to record key information every 100 updates.
-#
-# For information on how to use this file, see: doc/events.html
-# For other sample event configurations, see: support/config/
-#
-##############################################################################
-
-# Print all of the standard data files...
-u 0:100:end PrintAverageData # Save info about they average genotypes
-u 0:100:end PrintDominantData # Save info about most abundant genotypes
-u 0:100:end PrintStatsData # Collect satistics about entire pop.
-u 0:100:end PrintCountData # Count organisms, genotypes, species, etc.
-u 0:100:end PrintTasksData # Save organisms counts for each task.
-u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
-u 0:100:end PrintResourceData # Track resource abundance.
-
-u 100:100:end PrintTasksQualData # Task quality information
-u 0:100:end PrintInternalTasksData
-u 0:100:end PrintInternalTasksQualData
-
-# Setup the full population data collection.
-u 50000:50000 SavePopulation # Save current state of population.
-u 50000:50000 SaveHistoricPopulation # Save ancestors of current population.
-
-# Start the ecological period
-u 100000 ZeroMuts # Set all mutation rates to 0, starting eco phase
-
-# Do final population data collection and exit
-u 200000 PrintDominantGenotype
-u 200000 exit # exit
Copied: branches/interrupt/tests/collect_specification_analyze/config/events-collect.cfg (from rev 3275, development/tests/collect_specification_analyze/config/events-collect.cfg)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/config/events-collect.cfg (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/config/events-collect.cfg 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,38 @@
+##############################################################################
+#
+# This is the setup file for the events system. From here, you can
+# configure any actions that you want to have happen during the course of
+# an experiment, including setting the times for data collection.
+#
+# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
+#
+# This file is currently setup to record key information every 100 updates.
+#
+# For information on how to use this file, see: doc/events.html
+# For other sample event configurations, see: support/config/
+#
+##############################################################################
+
+# Print all of the standard data files...
+u 0:100:end PrintAverageData # Save info about they average genotypes
+u 0:100:end PrintDominantData # Save info about most abundant genotypes
+u 0:100:end PrintStatsData # Collect satistics about entire pop.
+u 0:100:end PrintCountData # Count organisms, genotypes, species, etc.
+u 0:100:end PrintTasksData # Save organisms counts for each task.
+u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
+u 0:100:end PrintResourceData # Track resource abundance.
+
+u 100:100:end PrintTasksQualData # Task quality information
+u 0:100:end PrintInternalTasksData
+u 0:100:end PrintInternalTasksQualData
+
+# Setup the full population data collection.
+u 50000:50000 SavePopulation # Save current state of population.
+u 50000:50000 SaveHistoricPopulation # Save ancestors of current population.
+
+# Start the ecological period
+u 100000 ZeroMuts # Set all mutation rates to 0, starting eco phase
+
+# Do final population data collection and exit
+u 200000 PrintDominantGenotype
+u 200000 exit # exit
Deleted: branches/interrupt/tests/collect_specification_analyze/config/instset-destroy.cfg
===================================================================
--- development/tests/collect_specification_analyze/config/instset-destroy.cfg 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/config/instset-destroy.cfg 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,53 +0,0 @@
-nop-A 1 # a
-nop-B 1 # b
-nop-C 1 # c
-if-n-equ 1 # d
-if-less 1 # e
-pop 1 # f
-push 1 # g
-swap-stk 1 # h
-swap 1 # i
-shift-r 1 # j
-shift-l 1 # k
-inc 1 # l
-dec 1 # m
-add 1 # n
-sub 1 # o
-nand 1 # p
-IO 1 # q Puts current contents of register and gets new.
-h-alloc 1 # r Allocate as much memory as organism can use.
-h-divide 1 # s Cuts off everything between the read and write heads
-h-copy 1 # t Combine h-read and h-write
-h-search 1 # u Search for matching template, set flow head & return info
- # # if no template, move flow-head here, set size&offset=0.
-mov-head 1 # v Move ?IP? head to flow control.
-jmp-head 1 # w Move ?IP? head by fixed amount in CX. Set old pos in CX.
-get-head 1 # x Get position of specified head in CX.
-if-label 1 # y
-set-flow 1 # z Move flow-head to address in ?CX?
-destroy 1
-
-#adv-head 1
-#jump-f 1
-#jump-b 1
-#call 1
-#return 1
-#if-bit-1 1
-#get 1
-#put 1
-#h-read 1
-#h-write 1
-#set-head 1
-#search-f 1
-#search-b 1
-
-
-# Works on multiple nops: pop push inc dec IO adv-head
-
-# What if we add a new head. Search will return the location of something,
-# and put the new head there. Then set-head will move another head to that
-# point. In the case of the copy loop, it only needs to be set once and
-# this will speed up the code quite a bit!
-
-# Search with no template returns current position (abs line number) in
-# genome.
\ No newline at end of file
Copied: branches/interrupt/tests/collect_specification_analyze/config/instset-destroy.cfg (from rev 3275, development/tests/collect_specification_analyze/config/instset-destroy.cfg)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/config/instset-destroy.cfg (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/config/instset-destroy.cfg 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,53 @@
+nop-A 1 # a
+nop-B 1 # b
+nop-C 1 # c
+if-n-equ 1 # d
+if-less 1 # e
+pop 1 # f
+push 1 # g
+swap-stk 1 # h
+swap 1 # i
+shift-r 1 # j
+shift-l 1 # k
+inc 1 # l
+dec 1 # m
+add 1 # n
+sub 1 # o
+nand 1 # p
+IO 1 # q Puts current contents of register and gets new.
+h-alloc 1 # r Allocate as much memory as organism can use.
+h-divide 1 # s Cuts off everything between the read and write heads
+h-copy 1 # t Combine h-read and h-write
+h-search 1 # u Search for matching template, set flow head & return info
+ # # if no template, move flow-head here, set size&offset=0.
+mov-head 1 # v Move ?IP? head to flow control.
+jmp-head 1 # w Move ?IP? head by fixed amount in CX. Set old pos in CX.
+get-head 1 # x Get position of specified head in CX.
+if-label 1 # y
+set-flow 1 # z Move flow-head to address in ?CX?
+destroy 1
+
+#adv-head 1
+#jump-f 1
+#jump-b 1
+#call 1
+#return 1
+#if-bit-1 1
+#get 1
+#put 1
+#h-read 1
+#h-write 1
+#set-head 1
+#search-f 1
+#search-b 1
+
+
+# Works on multiple nops: pop push inc dec IO adv-head
+
+# What if we add a new head. Search will return the location of something,
+# and put the new head there. Then set-head will move another head to that
+# point. In the case of the copy loop, it only needs to be set once and
+# this will speed up the code quite a bit!
+
+# Search with no template returns current position (abs line number) in
+# genome.
\ No newline at end of file
Copied: branches/interrupt/tests/collect_specification_analyze/expected (from rev 3275, development/tests/collect_specification_analyze/expected)
Copied: branches/interrupt/tests/collect_specification_analyze/expected/data (from rev 3275, development/tests/collect_specification_analyze/expected/data)
Deleted: branches/interrupt/tests/collect_specification_analyze/expected/data/executed.dat
===================================================================
--- development/tests/collect_specification_analyze/expected/data/executed.dat 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/expected/data/executed.dat 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,41 +0,0 @@
-#filetype genotype_data
-#format inst task task task task task task task task task sequence num_cpus length merit exe_length gest_time fitness r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec
-
-# Legend:
-# 1: # Times destroy Executed
-# 2: Not
-# 3: Nand
-# 4: And
-# 5: OrNot
-# 6: Or
-# 7: AndNot
-# 8: Nor
-# 9: Xor
-# 10: Equals
-# 11: Genome Sequence
-# 12: Number of CPUs
-# 13: Genome Length
-# 14: Merit
-# 15: Executed Length
-# 16: Gestation Time
-# 17: Fitness
-# 18: # times specification 0 used
-# 19: # times specification 1 used
-# 20: # times specification 2 used
-# 21: # times specification 3 used
-# 22: # times specification 4 used
-# 23: # times specification 5 used
-# 24: # times specification 6 used
-# 25: # times specification 7 used
-# 26: # times specification 8 used
-# 27: # times specification 9 used
-# 28: # times specification 10 used
-# 29: # times specification 11 used
-# 30: # times specification 12 used
-
-112 0 0 0 37 0 74 0 36 36 rhuucavczebAqrjgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab 1043 106 102 102 1518 0.0671937 75 0 37 0 0 0 0 0 0 0 0 0 0
-37 0 35 0 0 0 70 0 0 68 ArpucavczmnqrhAsnndlosimuqhcmptflqtlpwwaxkzunqqcdpqpclbtncogcAqchhmdfctpaoqcgqfmocloytpyaofahofycasvab 834 102 99 99 1436 0.0689415 37 0 0 0 0 0 0 0 0 0 0 0 0
-112 0 0 0 37 0 74 0 36 36 rhuucavczebAqrbgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab 759 106 102 102 1518 0.0671937 75 0 37 0 0 0 0 0 0 0 0 0 0
-114 56 0 0 0 116 0 164 0 0 rxuczaagvcjzjkcdqeadffpmxpmomtqodpdbzitgiyshebinlzsnnygunqtppqpdlceqnccptgcqcAAacycgfckaqfigfcqdetqcfbjpbapccecfycasvab 574 119 116 116 2334 0.0497001 57 0 0 0 0 0 57 0 0 0 0 0 0
-110 54 0 0 0 108 0 157 0 0 rxucajgvcczjkcAqkridrmbpmzAmtqodndhigftsuhebazfbylulnqtppqplceqncpbtgcqcAAacycgfckaqfigfcqdetqcfbjpbpccejycasvab 243 112 106 106 2045 0.0518337 56 0 0 0 0 0 54 0 0 0 0 0 0
-159 52 51 153 0 51 0 0 0 0 rxucavcczykfctfnfjmzpsqtodfpchzbxjheyitznruulnqtppqpclceuncptgcqcAAacycefckaqigfcqAetqcfbkpkapcceaAycasvrab 147 107 99 99 1966 0.0503561 107 0 0 0 0 0 52 0 0 0 0 0 0
Copied: branches/interrupt/tests/collect_specification_analyze/expected/data/executed.dat (from rev 3275, development/tests/collect_specification_analyze/expected/data/executed.dat)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/expected/data/executed.dat (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/expected/data/executed.dat 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,41 @@
+#filetype genotype_data
+#format inst task task task task task task task task task sequence num_cpus length merit exe_length gest_time fitness r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec r_spec
+
+# Legend:
+# 1: # Times destroy Executed
+# 2: Not
+# 3: Nand
+# 4: And
+# 5: OrNot
+# 6: Or
+# 7: AndNot
+# 8: Nor
+# 9: Xor
+# 10: Equals
+# 11: Genome Sequence
+# 12: Number of CPUs
+# 13: Genome Length
+# 14: Merit
+# 15: Executed Length
+# 16: Gestation Time
+# 17: Fitness
+# 18: # times specification 0 used
+# 19: # times specification 1 used
+# 20: # times specification 2 used
+# 21: # times specification 3 used
+# 22: # times specification 4 used
+# 23: # times specification 5 used
+# 24: # times specification 6 used
+# 25: # times specification 7 used
+# 26: # times specification 8 used
+# 27: # times specification 9 used
+# 28: # times specification 10 used
+# 29: # times specification 11 used
+# 30: # times specification 12 used
+
+112 0 0 0 37 0 74 0 36 36 rhuucavczebAqrjgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab 1043 106 102 102 1518 0.0671937 75 0 37 0 0 0 0 0 0 0 0 0 0
+37 0 35 0 0 0 70 0 0 68 ArpucavczmnqrhAsnndlosimuqhcmptflqtlpwwaxkzunqqcdpqpclbtncogcAqchhmdfctpaoqcgqfmocloytpyaofahofycasvab 834 102 99 99 1436 0.0689415 37 0 0 0 0 0 0 0 0 0 0 0 0
+112 0 0 0 37 0 74 0 36 36 rhuucavczebAqrbgjkslAdpsomfuhhpawxxeyrspgigtcszuuqqcppqpclAtncogcAqchhmdfctkaoqcgqfmoclythyamfomhAbycasvab 759 106 102 102 1518 0.0671937 75 0 37 0 0 0 0 0 0 0 0 0 0
+114 56 0 0 0 116 0 164 0 0 rxuczaagvcjzjkcdqeadffpmxpmomtqodpdbzitgiyshebinlzsnnygunqtppqpdlceqnccptgcqcAAacycgfckaqfigfcqdetqcfbjpbapccecfycasvab 574 119 116 116 2334 0.0497001 57 0 0 0 0 0 57 0 0 0 0 0 0
+110 54 0 0 0 108 0 157 0 0 rxucajgvcczjkcAqkridrmbpmzAmtqodndhigftsuhebazfbylulnqtppqplceqncpbtgcqcAAacycgfckaqfigfcqdetqcfbjpbpccejycasvab 243 112 106 106 2045 0.0518337 56 0 0 0 0 0 54 0 0 0 0 0 0
+159 52 51 153 0 51 0 0 0 0 rxucavcczykfctfnfjmzpsqtodfpchzbxjheyitznruulnqtppqpclceuncptgcqcAAacycefckaqigfcqAetqcfbkpkapcceaAycasvrab 147 107 99 99 1966 0.0503561 107 0 0 0 0 0 52 0 0 0 0 0 0
Deleted: branches/interrupt/tests/collect_specification_analyze/test_list
===================================================================
--- development/tests/collect_specification_analyze/test_list 2009-06-02 21:33:05 UTC (rev 3275)
+++ branches/interrupt/tests/collect_specification_analyze/test_list 2009-06-25 20:57:37 UTC (rev 3338)
@@ -1,37 +0,0 @@
-;--- Begin Test Configuration File (test_list) ---
-[main]
-; Command line arguments to pass to the application
-args = -s 4927 -a
-
-app = %(default_app)s ; Application path to test
-nonzeroexit = disallow ; Exit code handling (disallow, allow, or require)
- ; disallow - treat non-zero exit codes as failures
- ; allow - all exit codes are acceptable
- ; require - treat zero exit codes as failures, useful
- ; for creating tests for app error checking
-createdby = blw ; Who created the test
-email = blwalker at egr.msu.edu ; Email address for the test's creator
-
-[consistency]
-enabled = yes ; Is this test a consistency test?
-long = no ; Is this test a long test?
-
-[performance]
-enabled = no ; Is this test a performance test?
-long = no ; Is this test a long test?
-
-; The following variables can be used in constructing setting values by calling
-; them with %(variable_name)s. For example see 'app' above.
-;
-; builddir
-; cpus
-; default_app
-; mode
-; perf_repeat
-; perf_user_margin
-; perf_wall_margin
-; svn
-; svnmetadir
-; svnversion
-; testdir
-;--- End Test Configuration File ---
Copied: branches/interrupt/tests/collect_specification_analyze/test_list (from rev 3275, development/tests/collect_specification_analyze/test_list)
===================================================================
--- branches/interrupt/tests/collect_specification_analyze/test_list (rev 0)
+++ branches/interrupt/tests/collect_specification_analyze/test_list 2009-06-25 20:57:37 UTC (rev 3338)
@@ -0,0 +1,37 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+; Command line arguments to pass to the application
+args = -s 4927 -a
+
+app = %(default_app)s ; Application path to test
+nonzeroexit = disallow ; Exit code handling (disallow, allow, or require)
+ ; disallow - treat non-zero exit codes as failures
+ ; allow - all exit codes are acceptable
+ ; require - treat zero exit codes as failures, useful
+ ; for creating tests for app error checking
+createdby = blw ; Who created the test
+email = blwalker at egr.msu.edu ; Email address for the test's creator
+
+[consistency]
+enabled = yes ; Is this test a consistency test?
+long = no ; Is this test a long test?
+
+[performance]
+enabled = no ; Is this test a performance test?
+long = no ; Is this test a long test?
+
+; The following variables can be used in constructing setting values by calling
+; them with %(variable_name)s. For example see 'app' above.
+;
+; builddir
+; cpus
+; default_app
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
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