[Avida-SVN] r3226 - in branches: . goings goings/source/cpu goings/source/main goings/support/config
goingssh at myxo.css.msu.edu
goingssh at myxo.css.msu.edu
Mon May 4 15:38:45 PDT 2009
Author: goingssh
Date: 2009-05-04 18:38:44 -0400 (Mon, 04 May 2009)
New Revision: 3226
Added:
branches/goings/
Modified:
branches/goings/Avida.sln
branches/goings/Avida.vcproj
branches/goings/source/cpu/cHardwareBase.cc
branches/goings/source/main/cAvidaConfig.h
branches/goings/source/main/cOrganism.cc
branches/goings/source/main/cOrganism.h
branches/goings/source/main/cWorld.cc
branches/goings/support/config/avida.cfg
Log:
Copied: branches/goings (from rev 3224, development)
Modified: branches/goings/Avida.sln
===================================================================
--- development/Avida.sln 2009-05-04 16:11:06 UTC (rev 3224)
+++ branches/goings/Avida.sln 2009-05-04 22:38:44 UTC (rev 3226)
@@ -1,6 +1,5 @@
-
-Microsoft Visual Studio Solution File, Format Version 9.00
-# Visual Studio 2005
+Microsoft Visual Studio Solution File, Format Version 10.00
+# Visual Studio 2008
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Avida", "Avida.vcproj", "{E1C1D683-833F-40D9-A952-CEC54FE40EFC}"
EndProject
Project("{54435603-DBB4-11D2-8724-00A0C9A8B90C}") = "Installer", "Installer\Installer.vdproj", "{9E776A2E-5D27-4900-9856-F5AF0C8FC84A}"
Modified: branches/goings/Avida.vcproj
===================================================================
--- development/Avida.vcproj 2009-05-04 16:11:06 UTC (rev 3224)
+++ branches/goings/Avida.vcproj 2009-05-04 22:38:44 UTC (rev 3226)
@@ -1,11 +1,12 @@
<?xml version="1.0" encoding="Windows-1252"?>
<VisualStudioProject
ProjectType="Visual C++"
- Version="8.00"
+ Version="9.00"
Name="Avida"
ProjectGUID="{E1C1D683-833F-40D9-A952-CEC54FE40EFC}"
RootNamespace="Avida"
Keyword="Win32Proj"
+ TargetFrameworkVersion="131072"
>
<Platforms>
<Platform
@@ -65,6 +66,8 @@
IgnoreDefaultLibraryNames="LIBCMT"
GenerateDebugInformation="true"
SubSystem="1"
+ RandomizedBaseAddress="1"
+ DataExecutionPrevention="0"
TargetMachine="1"
/>
<Tool
@@ -86,9 +89,6 @@
Name="VCAppVerifierTool"
/>
<Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
Name="VCPostBuildEventTool"
/>
</Configuration>
@@ -152,6 +152,8 @@
OptimizeReferences="2"
EnableCOMDATFolding="2"
LinkTimeCodeGeneration="1"
+ RandomizedBaseAddress="1"
+ DataExecutionPrevention="0"
TargetMachine="1"
/>
<Tool
@@ -173,9 +175,6 @@
Name="VCAppVerifierTool"
/>
<Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
Name="VCPostBuildEventTool"
/>
</Configuration>
@@ -297,6 +296,62 @@
>
</File>
<File
+ RelativePath=".\source\main\cBirthDemeHandler.cc"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthDemeHandler.h"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthGenomeSizeHandler.cc"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthGenomeSizeHandler.h"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthGlobalHandler.cc"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthGlobalHandler.h"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthGridLocalHandler.cc"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthGridLocalHandler.h"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthMateSelectHandler.cc"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthMateSelectHandler.h"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthNeighborhoodHandler.cc"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthNeighborhoodHandler.h"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthSelectionHandler.cc"
+ >
+ </File>
+ <File
+ RelativePath=".\source\main\cBirthSelectionHandler.h"
+ >
+ </File>
+ <File
RelativePath=".\source\tools\cBlockStruct.h"
>
</File>
Modified: branches/goings/source/cpu/cHardwareBase.cc
===================================================================
--- development/source/cpu/cHardwareBase.cc 2009-05-04 16:11:06 UTC (rev 3224)
+++ branches/goings/source/cpu/cHardwareBase.cc 2009-05-04 22:38:44 UTC (rev 3226)
@@ -530,6 +530,7 @@
if (ctx.GetRandom().P(m_organism->GetRevertPos())) revert = true;
if (ctx.GetRandom().P(m_organism->GetSterilizePos())) sterilize = true;
}
+ if (ctx.GetRandom().P(m_organism->GetRevertTaskLoss())) revert = true;
// Ideally, we won't have reversions and sterilizations turned on at the
// same time, but if we do, give revert the priority.
@@ -601,7 +602,26 @@
if (ctx.GetRandom().P(m_organism->GetRevertPos())) revert = true;
if (ctx.GetRandom().P(m_organism->GetSterilizePos())) sterilize = true;
}
+ // check if child has lost any tasks parent had AND not gained any new tasks
+ if (ctx.GetRandom().P(m_organism->GetRevertTaskLoss())) {
+ const tArray<int>& childtasks = test_info.GetTestPhenotype().GetCurTaskCount();
+ const tArray<int>& parenttasks = phenotype.GetCurTaskCount();
+ bool del = false;
+ bool added = false;
+ for (int i=0; i<childtasks.GetSize(); i++)
+ if (childtasks[i]>0 && parenttasks[i] == 0) {
+ added = true;
+ break;
+ }
+ else if (childtasks[i] == 0 && parenttasks[i] > 0)
+ del = true;
+ revert = (del && !added);
+ }
+
+
+ if (ctx.GetRandom().P(m_organism->GetRevertTaskLoss())) revert = true;
+
// Ideally, we won't have reversions and sterilizations turned on at the
// same time, but if we do, give revert the priority.
if (revert == true) {
Modified: branches/goings/source/main/cAvidaConfig.h
===================================================================
--- development/source/main/cAvidaConfig.h 2009-05-04 16:11:06 UTC (rev 3224)
+++ branches/goings/source/main/cAvidaConfig.h 2009-05-04 22:38:44 UTC (rev 3226)
@@ -419,6 +419,7 @@
CONFIG_ADD_VAR(REVERT_DETRIMENTAL, double, 0.0, " 0.0 to 1.0; Probability of reversion.");
CONFIG_ADD_VAR(REVERT_NEUTRAL, double, 0.0, "");
CONFIG_ADD_VAR(REVERT_BENEFICIAL, double, 0.0, "");
+ CONFIG_ADD_VAR(REVERT_TASKLOSS, double, 0.0, "should org be reverted if loses task(s) without gaining other(s)?");
CONFIG_ADD_VAR(STERILIZE_FATAL, double, 0.0, "Should any mutations clear (kill) the organism?");
CONFIG_ADD_VAR(STERILIZE_DETRIMENTAL, double, 0.0, "");
CONFIG_ADD_VAR(STERILIZE_NEUTRAL, double, 0.0, "");
Modified: branches/goings/source/main/cOrganism.cc
===================================================================
--- development/source/main/cOrganism.cc 2009-05-04 16:11:06 UTC (rev 3224)
+++ branches/goings/source/main/cOrganism.cc 2009-05-04 22:38:44 UTC (rev 3226)
@@ -640,6 +640,7 @@
bool cOrganism::GetRevertNeg() const { return m_world->GetConfig().REVERT_DETRIMENTAL.Get(); }
bool cOrganism::GetRevertNeut() const { return m_world->GetConfig().REVERT_NEUTRAL.Get(); }
bool cOrganism::GetRevertPos() const { return m_world->GetConfig().REVERT_BENEFICIAL.Get(); }
+bool cOrganism::GetRevertTaskLoss() const { return m_world->GetConfig().REVERT_TASKLOSS.Get(); }
bool cOrganism::GetSterilizeFatal() const { return m_world->GetConfig().STERILIZE_FATAL.Get(); }
bool cOrganism::GetSterilizeNeg() const { return m_world->GetConfig().STERILIZE_DETRIMENTAL.Get(); }
Modified: branches/goings/source/main/cOrganism.h
===================================================================
--- development/source/main/cOrganism.h 2009-05-04 16:11:06 UTC (rev 3224)
+++ branches/goings/source/main/cOrganism.h 2009-05-04 22:38:44 UTC (rev 3226)
@@ -366,6 +366,7 @@
bool GetRevertNeg() const;
bool GetRevertNeut() const;
bool GetRevertPos() const;
+ bool GetRevertTaskLoss() const;
bool GetSterilizeFatal() const;
bool GetSterilizeNeg() const;
Modified: branches/goings/source/main/cWorld.cc
===================================================================
--- development/source/main/cWorld.cc 2009-05-04 16:11:06 UTC (rev 3224)
+++ branches/goings/source/main/cWorld.cc 2009-05-04 22:38:44 UTC (rev 3226)
@@ -120,8 +120,9 @@
const bool revert_neg = m_conf->REVERT_DETRIMENTAL.Get() > 0.0;
const bool revert_neut = m_conf->REVERT_NEUTRAL.Get() > 0.0;
const bool revert_pos = m_conf->REVERT_BENEFICIAL.Get() > 0.0;
+ const bool revert_taskloss = m_conf->REVERT_TASKLOSS.Get() > 0.0;
const bool fail_implicit = m_conf->FAIL_IMPLICIT.Get() > 0;
- m_test_on_div = (revert_fatal || revert_neg || revert_neut || revert_pos || fail_implicit);
+ m_test_on_div = (revert_fatal || revert_neg || revert_neut || revert_pos || revert_taskloss || fail_implicit);
const bool sterilize_fatal = m_conf->STERILIZE_FATAL.Get() > 0.0;
const bool sterilize_neg = m_conf->STERILIZE_DETRIMENTAL.Get() > 0.0;
Modified: branches/goings/support/config/avida.cfg
===================================================================
--- development/support/config/avida.cfg 2009-05-04 16:11:06 UTC (rev 3224)
+++ branches/goings/support/config/avida.cfg 2009-05-04 22:38:44 UTC (rev 3226)
@@ -1,526 +1,527 @@
-#############################################################################
-# This file includes all the basic run-time defines for Avida.
-# For more information, see doc/config.html
-#############################################################################
-
-VERSION_ID 2.9.0 # Do not change this value.
-
-### GENERAL_GROUP ###
-# General Settings
-ANALYZE_MODE 0 # 0 = Disabled
- # 1 = Enabled
- # 2 = Interactive
-VIEW_MODE 1 # Initial viewer screen
-CLONE_FILE - # Clone file to load
-VERBOSITY 1 # 0 = No output at all
- # 1 = Normal output
- # 2 = Verbose output, detailing progress
- # 3 = High level of details, as available
- # 4 = Print Debug Information, as applicable
-
-### ARCH_GROUP ###
-# Architecture Variables
-WORLD_X 60 # Width of the Avida world
-WORLD_Y 60 # Height of the Avida world
-WORLD_Z 1 # Depth of the Avida world
-WORLD_GEOMETRY 2 # 1 = Bounded Grid
- # 2 = Torus
- # 3 = Clique
- # 4 = Hexagonal grid
- # 5 = Lattice
-RANDOM_SEED 0 # Random number seed (0 for based on time)
-HARDWARE_TYPE 0 # 0 = Original CPUs
- # 1 = New SMT CPUs
- # 2 = Transitional SMT
- # 3 = Experimental CPU
- # 4 = Gene Expression CPU
-SPECULATIVE 1 # Enable speculative execution
-TRACE_EXECUTION 0 # Trace the execution of all organisms in the population (default=off,SLOW!)
-BCAST_HOPS 1 # Number of hops to broadcast an alarm
-ALARM_SELF 0 # Does sending an alarm move sender IP to alarm label?
- # 0=no
- # 1=yes
-IO_EXPIRE 1 # Is the expiration functionality of '-expire' I/O instructions enabled?
-
-### CONFIG_FILE_GROUP ###
-# Configuration Files
-DATA_DIR data # Directory in which config files are found
-INST_SET - # File containing instruction set
-INST_SET_FORMAT 0 # Instruction set file format.
- # 0 = Default
- # 1 = New Style
-EVENT_FILE events.cfg # File containing list of events during run
-ANALYZE_FILE analyze.cfg # File used for analysis mode
-ENVIRONMENT_FILE environment.cfg # File that describes the environment
-START_CREATURE default-classic.org # Organism to seed the soup
-
-### DEME_GROUP ###
-# Demes and Germlines
-NUM_DEMES 1 # Number of independent groups in the
- # population (default=1).
-DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline (default=0).
-DEMES_PREVENT_STERILE 0 # Whether to prevent sterile demes from
- # replicating (default=0 or no).
-DEMES_RESET_RESOURCES 0 # Reset resources in demes on replication.
- # 0 = reset both demes
- # 1 = reset target deme
- # 2 = deme resources remain unchanged
-DEMES_REPLICATE_SIZE 1 # Number of identical organisms to create or copy from the
- # source deme to the target deme (default=1).
-LOG_DEMES_REPLICATE 0 # Log deme replications. 0/1 (off/on)
-DEMES_REPLICATE_LOG_START 0 # Update at which to start logging deme replications
-DEMES_PROB_ORG_TRANSFER 0.0 # Probablity of an organism being transferred from the
- # source deme to the target deme (default=0.0).
-DEMES_ORGANISM_SELECTION 0 # How organisms are selected for transfer from
- # source to target during deme replication.
- # 0=random with replacement (default).
- # 1=sequential.
-DEMES_ORGANISM_PLACEMENT 0 # How organisms are placed during deme replication.
- # 0=cell-array middle (default).
- # 1=deme center.
- # 2=random placement.
- # 3=sequential.
-DEMES_ORGANISM_FACING 0 # How organisms are facing during deme replication.
- # 0=unchanged (default).
- # 1=northwest.
- # 2=random.
-DEMES_MAX_AGE 500 # The maximum age of a deme (in updates) to be
- # used for age-based replication (default=500).
-DEMES_MAX_BIRTHS 100 # The maximum number of births that can occur
- # within a deme; used with birth-count
- # replication (default=100).
-DEMES_MIM_EVENTS_KILLED_RATIO 0.7 # Minimum ratio of events killed required for event period to be a success.
-DEMES_MIM_SUCCESSFUL_EVENT_PERIODS 1 # Minimum number of consecutive event periods that must be a success.
-GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
- # germline replication (default=0.0075).
-GERMLINE_INS_MUT 0.05 # Prob. of an insertion mutation occuring
- # during germline replication (default=0.05).
-GERMLINE_DEL_MUT 0.05 # Prob. of a deletion mutation occuring
- # during germline replication (default=0.05).
-DEMES_REPLICATE_CPU_CYCLES 0.0 # Replicate a deme immediately after it has used
- # this number of cpu cycles, normalized
- # by number of orgs in deme (0 = OFF).
-DEMES_REPLICATE_TIME 0.0 # Replicate a deme immediately after it has used
- # this number of cpu cycles, normalized
- # by number of orgs in deme and organism merit (0 = OFF).
-DEMES_REPLICATE_BIRTHS 0 # Replicate a deme immediately after it has
- # produced this many offspring (0 = OFF).
-DEMES_REPLICATE_ORGS 0 # Replicate a deme immediately once it reaches a
- # certain number of organisms (0 = OFF).
-DEMES_REPLICATION_ONLY_RESETS 0 # Kin selection mode. Deme replication really:
- # 1=resets deme resources
- # 2=rests deme resources and re-injects organisms
-DEMES_MIGRATION_RATE 0.0 # Probability of an offspring being born in a different deme.
-DEMES_MIGRATION_METHOD 0 # How do we choose what demes an org may land in when it migrates?
- # 0=all other demes
- # 1=eight adjacent neighbors
- # 2=two adjacent demes in list
-DEMES_NUM_X 0 # Simulated number of demes in X dimension. Only used for migration.
-DEMES_SEED_METHOD 0 # Deme seeding method.
- # 0=maintain old consistency
- # 1=new method using genotypes
-DEMES_DIVIDE_METHOD 0 # Deme divide method. Only works with DEMES_SEED_METHOD 1
- # 0=replace and target demes
- # 1= replace target deme, reset source deme to founders
- # 2=replace target deme, leave source deme unchanged
-DEMES_DEFAULT_GERMLINE_PROPENSITY 0.0 # Default germline propensity of organisms in deme.
- # For use with DEMES_DIVIDE_METHOD 2.
-DEMES_FOUNDER_GERMLINE_PROPENSITY -1.0 # Default germline propensity of founder organisms in deme.
- # For use with DEMES_DIVIDE_METHOD 2.
- # <0 = OFF
-DEMES_PREFER_EMPTY 0 # Give empty demes preference as targets of deme replication?
-
-### 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)
- # 3 = Divide resets mother stats, but not state.
- # 4 = 3 + child inherits mother registers and stack values.
-EPIGENETIC_METHOD 0 # Inheritance of state information other than genome
- # 0 = none
- # 1 = offspring inherits registers and stacks of first thread
- # 1 = parent maintains registers and stacks of first thread
- #
- # 1 = offspring and parent keep state information
-INJECT_METHOD 0 # 0 = Leaves the parasite thread state untouched.
- # 1 = Resets the calling thread state on inject
-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).
-RESET_INPUTS_ON_DIVIDE 0 # Reset environment inputs of parent upon successful divide.
-REPRO_METHOD 1 # Replace existing organism: 1=yes
-
-### 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.
-MIN_GENOME_SIZE 0 # Minimum number of instructions allowed in a genome. 0 = OFF
-MAX_GENOME_SIZE 0 # Maximum number of instructions allowed in a genome. 0 = OFF
-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 0.0 # Required bonus to divide.
-IMPLICIT_REPRO_BONUS 0 # Call Inst_Repro to divide upon achieving this bonus. 0 = OFF
-IMPLICIT_REPRO_CPU_CYCLES 0 # Call Inst_Repro after this many cpu cycles. 0 = OFF
-IMPLICIT_REPRO_TIME 0 # Call Inst_Repro after this time used. 0 = OFF
-IMPLICIT_REPRO_END 0 # Call Inst_Repro after executing the last instruction in the genome.
-IMPLICIT_REPRO_ENERGY 0.0 # Call Inst_Repro if organism accumulates this amount of energy.
-
-### MUTATION_GROUP ###
-# Mutations
-POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
-COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
-COPY_INS_PROB 0.0 # Insertion rate (per copy)
-COPY_DEL_PROB 0.0 # Deletion rate (per copy)
-COPY_UNIFORM_PROB 0.0 # Uniform mutation probability (per copy)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-COPY_SLIP_PROB 0.0 # Slip rate (per copy)
-DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
-DIV_INS_PROB 0.0 # Insertion rate (per site, applied on divide)
-DIV_DEL_PROB 0.0 # Deletion rate (per site, applied on divide)
-DIV_UNIFORM_PROB 0.0 # Uniform mutation probability (per site, applied on divide)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-DIV_SLIP_PROB 0.0 # Slip rate
-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)
-DIVIDE_UNIFORM_PROB 0.0 # Uniform mutation probability (per divide)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
-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)
-SLIP_FILL_MODE 0 # Fill insertions from slip mutations with 0=duplication, 1=nop-X, 2=random, 3=scrambled
-PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
-SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
-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.
-MIGRATION_RATE 0.0 # Uniform probability of offspring migrating to a new deme.
-
-### 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 0 # 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.
- # 3 = DemeProbabalistic, each deme gets the same number of CPU cycles, which are awarded probabalistically within each deme.
- # 4 = ProbDemeProbabalistic, each deme gets CPU cycles proportional to its living population size, which are awarded probabalistically within each deme.
- # 5 = CONSTANT BURST: all organisms get default, in SLICING_BURST_SIZE chunks
-SLICING_BURST_SIZE 1 # Sets the scheduler burst size, when supported.
-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
- # 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
-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 this default bonus
- # rather than the accumulated bonus of the parent? 0 = off
-MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
- # (-1 = none, 0 = First in INST_SET.)
-MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
- # per instruction (-1 = penalty, 0 = no effect.)
-FITNESS_METHOD 0 # 0 = default, >=1 = experimental
-FITNESS_COEFF_1 1.0 # 1st FITNESS_METHOD parameter
-FITNESS_COEFF_2 1.0 # 2nd FITNESS_METHOD parameter
-FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from
- # FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # (0 = off, 1 = on)
-FITNESS_VALLEY_START 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
- # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # get fitness 1 (lowest)
-FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
- # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # get fitness 1 (lowest)
-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.
-NO_CPU_CYCLE_TIME 0 # Don't count each CPU cycle as part of gestation time
-MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
-MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
-MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
-MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
-MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
-MIN_GB_DONATE_THRESHOLD -1 # threshold green beard donates only to orgs above this
- # donation attempt threshold; -1=no thresh
-DONATE_THRESH_QUANTA 10 # The size of steps between quanta donate thresholds
-MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
-PRECALC_PHENOTYPE 0 # 0 = Disabled
- # 1 = Assign precalculated merit at birth (unlimited resources only)
- # 2 = Assign precalculated gestation time
- # 3 = Assign precalculated merit AND gestation time.
- # Fitness will be evaluated for organism based on these settings.
-FASTFORWARD_UPDATES 0 # Fast-forward if the average generation has not changed in this many updates. (0 = off)
-FASTFORWARD_NUM_ORGS 0 # Fast-forward if population is equal to this
-
-### 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
-
-### ORGANISM_MESSAGING_GROUP ###
-# Organism Message-Based Communication
-MESSAGE_TYPE 0 # Messaging Style. 0=Receiver Facing, 1=Broadcast
-MESSAGE_BCAST_RADIUS 1 # Broadcast message radius (cells)
-ORGANISMS_REMEMBER_MESSAGES 1 # Does an organism remember all messages it has sent or received? 0=false, 1=true (default)
-MESSAGE_QUEUE_SIZE -1 # Maximum number of unretrieved messages an organism can store (-1 for no limit is the default)
-MESSAGE_QUEUE_BEHAVIOR_WHEN_FULL 0 # 0 = Drop incoming message (default), 1 = Drop oldest unretrieved message
-
-### 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 ###
-# Resource Hoarding Parameters
-USE_RESOURCE_BINS 0 # Enable resource bin use. This serves as a guard on most resource hoarding code.
-ABSORB_RESOURCE_FRACTION .0025 # Fraction of available environmental resource an organism absorbs with the collect instruction.
-MULTI_ABSORB_TYPE 0 # What to do if collect is called on a range of resources.
- # 0 = absorb a random resource in the range
- # 1 = absorb the first resource in the range
- # 2 = absorb the last resource in the range
- # 3 = absorb ABSORB_RESOURCE_FRACTION / (# of resources in range) of each resource in the range
-MAX_TOTAL_STORED -1 # Maximum total amount of all resources an organism can store.
- # <0 = no maximum
-USE_STORED_FRACTION 1.0 # The fraction of stored resource to use.
-ENV_FRACTION_THRESHOLD 1.0 # The fraction of available environmental resource to compare available stored resource to when deciding whether to use stored resource.
-RETURN_STORED_ON_DEATH 1 # Return an organism's stored resources to the world when it dies?
-
-### ANALYZE_GROUP ###
-# Analysis Settings
-MAX_CONCURRENCY -1 # Maximum number of analyze threads, -1 == use all available.
-ANALYZE_OPTION_1 # String variable accessible from analysis scripts
-ANALYZE_OPTION_2 # String variable accessible from analysis scripts
-
-### ENERGY_GROUP ###
-# Energy Settings
-ENERGY_ENABLED 0 # Enable Energy Model. 0/1 (off/on)
-ENERGY_GIVEN_ON_INJECT 0.0 # Energy given to organism upon injection.
-ENERGY_GIVEN_AT_BIRTH 0.0 # Energy given to offspring upon birth.
-FRAC_PARENT_ENERGY_GIVEN_TO_ORG_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring organism.
-FRAC_PARENT_ENERGY_GIVEN_TO_DEME_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring deme.
-FRAC_ENERGY_DECAY_AT_ORG_BIRTH 0.0 # Fraction of energy lost due to decay during organism reproduction.
-FRAC_ENERGY_DECAY_AT_DEME_BIRTH 0.0 # Fraction of energy lost due to decay during deme reproduction.
-NUM_INST_EXC_BEFORE_0_ENERGY 0 # Number of instructions executed before energy is exhausted.
-ENERGY_CAP -1.0 # Maximum amount of energy that can be stored in an organism. -1 means the cap is set to Max Double
-APPLY_ENERGY_METHOD 0 # When should rewarded energy be applied to current energy?
- # 0 = on divide
- # 1 = on completion of task
- # 2 = on sleep
-FRAC_ENERGY_TRANSFER 0.0 # Fraction of replaced organism's energy take by new resident
-LOG_SLEEP_TIMES 0 # Log sleep start and end times. 0/1 (off/on)
- # WARNING: may use lots of memory.
-FRAC_ENERGY_RELINQUISH 1.0 # Fraction of organisms energy to relinquish
-ENERGY_PASSED_ON_DEME_REPLICATION_METHOD 0 # Who get energy passed from a parent deme
- # 0 = Energy divided among organisms injected to offspring deme
- # 1 = Energy divided among cells in offspring deme
-INHERIT_EXE_RATE 0 # Inherit energy rate from parent? 0=no 1=yes
-ATTACK_DECAY_RATE 0.0 # Percent of cell's energy decayed by attack
-ENERGY_THRESH_LOW .33 # Threshold percent below which energy level is considered low. Requires ENERGY_CAP.
-ENERGY_THRESH_HIGH .75 # Threshold percent above which energy level is considered high. Requires ENERGY_CAP.
-
-### ENERGY_SHARING_GROUP ###
-# Energy Sharing Settings
-ENERGY_SHARING_METHOD 0 # Method for sharing energy. 0=receiver must actively receive/request, 1=energy pushed on receiver
-ENERGY_SHARING_PCT 0.0 # Percent of energy to share
-ENERGY_SHARING_INCREMENT 0.01 # Amount to change percent energy shared
-ENERGY_SHARING_LOSS 0.0 # Percent of shared energy lost in transfer
-
-### SECOND_PASS_GROUP ###
-# Tracking metrics known after the running experiment previously
-TRACK_CCLADES 0 # Enable tracking of coalescence clades
-TRACK_CCLADES_IDS coalescence.ids # File storing coalescence IDs
-
-### GX_GROUP ###
-# Gene Expression CPU Settings
-MAX_PROGRAMIDS 16 # Maximum number of programids an organism can create.
-MAX_PROGRAMID_AGE 2000 # Max number of CPU cycles a programid executes before it is removed.
-IMPLICIT_GENE_EXPRESSION 0 # Create executable programids from the genome without explicit allocation and copying?
-IMPLICIT_BG_PROMOTER_RATE 0.0 # Relative rate of non-promoter sites creating programids.
-IMPLICIT_TURNOVER_RATE 0.0 # Number of programids recycled per CPU cycle. 0 = OFF
-IMPLICIT_MAX_PROGRAMID_LENGTH 0 # Creation of an executable programid terminates after this many instructions. 0 = disabled
-
-### PROMOTER_GROUP ###
-# Promoters
-PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
- # Certain instructions must also be included.
-PROMOTER_INST_MAX 0 # Maximum number of instructions to execute before terminating. 0 = off
-PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating after each cpu cycle.
-PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after each instruction.
-PROMOTER_TO_REGISTER 0 # Place a promoter's base bit code in register BX when starting execution from it?
-TERMINATION_RESETS 0 # Does termination reset the thread's state?
-NO_ACTIVE_PROMOTER_EFFECT 0 # What happens when there are no active promoters?
- # 0 = Start execution at the beginning of the genome.
- # 1 = Kill the organism.
- # 2 = Stop the organism from executing any further instructions.
-PROMOTER_CODE_SIZE 24 # Size of a promoter code in bits. (Maximum value is 32)
-PROMOTER_EXE_LENGTH 3 # Length of promoter windows used to determine execution.
-PROMOTER_EXE_THRESHOLD 2 # Minimum number of bits that must be set in a promoter window to allow execution.
-INST_CODE_LENGTH 3 # Instruction binary code length (number of bits)
-INST_CODE_DEFAULT_TYPE 0 # Default value of instruction binary code value.
- # 0 = All zeros
- # 1 = Based off the instruction number
-CONSTITUTIVE_REGULATION 0 # Sense a new regulation value before each CPU cycle?
-
-### COLORS_GROUP ###
-# Output colors for when data files are printed in HTML mode.
-# There are two sets of these; the first are for lineages,
-# and the second are for mutation tests.
-COLOR_DIFF CCCCFF # Color to flag stat that has changed since parent.
-COLOR_SAME FFFFFF # Color to flag stat that has NOT changed since parent.
-COLOR_NEG2 FF0000 # Color to flag stat that is significantly worse than parent.
-COLOR_NEG1 FFCCCC # Color to flag stat that is minorly worse than parent.
-COLOR_POS1 CCFFCC # Color to flag stat that is minorly better than parent.
-COLOR_POS2 00FF00 # Color to flag stat that is significantly better than parent.
-COLOR_MUT_POS 00FF00 # Color to flag stat that has changed since parent.
-COLOR_MUT_NEUT FFFFFF # Color to flag stat that has changed since parent.
-COLOR_MUT_NEG FFFF00 # Color to flag stat that has changed since parent.
-COLOR_MUT_LETHAL FF0000 # Color to flag stat that has changed since parent.
-
-### BIOMIMETIC_GROUP ###
-# Biomimetic Features Settings
-BIOMIMETIC_REFRACTORY_PERIOD 0.0 # Number of updates affected by refractory period
-BIOMIMETIC_MOVEMENT_STEP 1 # Number of cells to move Avidian on move instruction
-BIOMIMETIC_MOVEMENT_LOG 0 # Log detailed movement information (WARNING: large data file)
-BIOMIMETIC_MOVEMENT_FACTOR 1.0 # Scale merit bonus due to movement (m<1.0 applies a cost)
-BIOMIMETIC_EVAL_ON_MOVEMENT 0 # Force task evaluation on each movement step
-BIOMIMETIC_K 0 # Carrying capacity in number of organisms
-
-### PHEROMONE_GROUP ###
-# Pheromone Settings
-PHEROMONE_ENABLED 0 # Enable pheromone usage. 0/1 (off/on)
-PHEROMONE_AMOUNT 1.0 # Amount of pheromone to add per drop
-PHEROMONE_DROP_MODE 0 # Where to drop pheromone
- # 0 = Half amount at src, half at dest
- # 1 = All at source
- # 2 = All at dest
-EXPLOIT_EXPLORE_PROB 0.00 # Probability of random exploration
- # instead of pheromone trail following
-LOG_PHEROMONE 0 # Log pheromone drops. 0/1 (off/on)
-PHEROMONE_LOG_START 0 # Update at which to start logging pheromone drops
-EXPLOIT_LOG_START 0 # Update at which to start logging exploit moves
-EXPLORE_LOG_START 0 # Update at which to start logging explore moves
-MOVETARGET_LOG_START 0 # Update at which to start logging movetarget moves
-LOG_INJECT 0 # Log injection of organisms. 0/1 (off/on)
-INJECT_LOG_START 0 # Update at which to start logging injection of
- # organisms
-
-### SYNCHRONIZATION_GROUP ###
-# Synchronization settings
-SYNC_FITNESS_WINDOW 100 # Number of updates over which to calculate fitness (default=100).
-SYNC_FLASH_LOSSRATE 0.0 # P() to lose a flash send (0.0==off).
-SYNC_TEST_FLASH_ARRIVAL -1 # CPU cycle at which an organism will receive a flash (off=-1, default=-1, analyze mode only.)
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.9.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 0 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 1 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+VERBOSITY 1 # 0 = No output at all
+ # 1 = Normal output
+ # 2 = Verbose output, detailing progress
+ # 3 = High level of details, as available
+ # 4 = Print Debug Information, as applicable
+
+### ARCH_GROUP ###
+# Architecture Variables
+WORLD_X 60 # Width of the Avida world
+WORLD_Y 60 # Height of the Avida world
+WORLD_Z 1 # Depth of the Avida world
+WORLD_GEOMETRY 2 # 1 = Bounded Grid
+ # 2 = Torus
+ # 3 = Clique
+ # 4 = Hexagonal grid
+ # 5 = Lattice
+RANDOM_SEED 0 # Random number seed (0 for based on time)
+HARDWARE_TYPE 0 # 0 = Original CPUs
+ # 1 = New SMT CPUs
+ # 2 = Transitional SMT
+ # 3 = Experimental CPU
+ # 4 = Gene Expression CPU
+SPECULATIVE 1 # Enable speculative execution
+TRACE_EXECUTION 0 # Trace the execution of all organisms in the population (default=off,SLOW!)
+BCAST_HOPS 1 # Number of hops to broadcast an alarm
+ALARM_SELF 0 # Does sending an alarm move sender IP to alarm label?
+ # 0=no
+ # 1=yes
+IO_EXPIRE 1 # Is the expiration functionality of '-expire' I/O instructions enabled?
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET - # File containing instruction set
+INST_SET_FORMAT 0 # Instruction set file format.
+ # 0 = Default
+ # 1 = New Style
+EVENT_FILE events.cfg # File containing list of events during run
+ANALYZE_FILE analyze.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment.cfg # File that describes the environment
+START_CREATURE default-classic.org # Organism to seed the soup
+
+### DEME_GROUP ###
+# Demes and Germlines
+NUM_DEMES 1 # Number of independent groups in the
+ # population (default=1).
+DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline (default=0).
+DEMES_PREVENT_STERILE 0 # Whether to prevent sterile demes from
+ # replicating (default=0 or no).
+DEMES_RESET_RESOURCES 0 # Reset resources in demes on replication.
+ # 0 = reset both demes
+ # 1 = reset target deme
+ # 2 = deme resources remain unchanged
+DEMES_REPLICATE_SIZE 1 # Number of identical organisms to create or copy from the
+ # source deme to the target deme (default=1).
+LOG_DEMES_REPLICATE 0 # Log deme replications. 0/1 (off/on)
+DEMES_REPLICATE_LOG_START 0 # Update at which to start logging deme replications
+DEMES_PROB_ORG_TRANSFER 0.0 # Probablity of an organism being transferred from the
+ # source deme to the target deme (default=0.0).
+DEMES_ORGANISM_SELECTION 0 # How organisms are selected for transfer from
+ # source to target during deme replication.
+ # 0=random with replacement (default).
+ # 1=sequential.
+DEMES_ORGANISM_PLACEMENT 0 # How organisms are placed during deme replication.
+ # 0=cell-array middle (default).
+ # 1=deme center.
+ # 2=random placement.
+ # 3=sequential.
+DEMES_ORGANISM_FACING 0 # How organisms are facing during deme replication.
+ # 0=unchanged (default).
+ # 1=northwest.
+ # 2=random.
+DEMES_MAX_AGE 500 # The maximum age of a deme (in updates) to be
+ # used for age-based replication (default=500).
+DEMES_MAX_BIRTHS 100 # The maximum number of births that can occur
+ # within a deme; used with birth-count
+ # replication (default=100).
+DEMES_MIM_EVENTS_KILLED_RATIO 0.7 # Minimum ratio of events killed required for event period to be a success.
+DEMES_MIM_SUCCESSFUL_EVENT_PERIODS 1 # Minimum number of consecutive event periods that must be a success.
+GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
+ # germline replication (default=0.0075).
+GERMLINE_INS_MUT 0.05 # Prob. of an insertion mutation occuring
+ # during germline replication (default=0.05).
+GERMLINE_DEL_MUT 0.05 # Prob. of a deletion mutation occuring
+ # during germline replication (default=0.05).
+DEMES_REPLICATE_CPU_CYCLES 0.0 # Replicate a deme immediately after it has used
+ # this number of cpu cycles, normalized
+ # by number of orgs in deme (0 = OFF).
+DEMES_REPLICATE_TIME 0.0 # Replicate a deme immediately after it has used
+ # this number of cpu cycles, normalized
+ # by number of orgs in deme and organism merit (0 = OFF).
+DEMES_REPLICATE_BIRTHS 0 # Replicate a deme immediately after it has
+ # produced this many offspring (0 = OFF).
+DEMES_REPLICATE_ORGS 0 # Replicate a deme immediately once it reaches a
+ # certain number of organisms (0 = OFF).
+DEMES_REPLICATION_ONLY_RESETS 0 # Kin selection mode. Deme replication really:
+ # 1=resets deme resources
+ # 2=rests deme resources and re-injects organisms
+DEMES_MIGRATION_RATE 0.0 # Probability of an offspring being born in a different deme.
+DEMES_MIGRATION_METHOD 0 # How do we choose what demes an org may land in when it migrates?
+ # 0=all other demes
+ # 1=eight adjacent neighbors
+ # 2=two adjacent demes in list
+DEMES_NUM_X 0 # Simulated number of demes in X dimension. Only used for migration.
+DEMES_SEED_METHOD 0 # Deme seeding method.
+ # 0=maintain old consistency
+ # 1=new method using genotypes
+DEMES_DIVIDE_METHOD 0 # Deme divide method. Only works with DEMES_SEED_METHOD 1
+ # 0=replace and target demes
+ # 1= replace target deme, reset source deme to founders
+ # 2=replace target deme, leave source deme unchanged
+DEMES_DEFAULT_GERMLINE_PROPENSITY 0.0 # Default germline propensity of organisms in deme.
+ # For use with DEMES_DIVIDE_METHOD 2.
+DEMES_FOUNDER_GERMLINE_PROPENSITY -1.0 # Default germline propensity of founder organisms in deme.
+ # For use with DEMES_DIVIDE_METHOD 2.
+ # <0 = OFF
+DEMES_PREFER_EMPTY 0 # Give empty demes preference as targets of deme replication?
+
+### 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)
+ # 3 = Divide resets mother stats, but not state.
+ # 4 = 3 + child inherits mother registers and stack values.
+EPIGENETIC_METHOD 0 # Inheritance of state information other than genome
+ # 0 = none
+ # 1 = offspring inherits registers and stacks of first thread
+ # 1 = parent maintains registers and stacks of first thread
+ #
+ # 1 = offspring and parent keep state information
+INJECT_METHOD 0 # 0 = Leaves the parasite thread state untouched.
+ # 1 = Resets the calling thread state on inject
+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).
+RESET_INPUTS_ON_DIVIDE 0 # Reset environment inputs of parent upon successful divide.
+REPRO_METHOD 1 # Replace existing organism: 1=yes
+
+### 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.
+MIN_GENOME_SIZE 0 # Minimum number of instructions allowed in a genome. 0 = OFF
+MAX_GENOME_SIZE 0 # Maximum number of instructions allowed in a genome. 0 = OFF
+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 0.0 # Required bonus to divide.
+IMPLICIT_REPRO_BONUS 0 # Call Inst_Repro to divide upon achieving this bonus. 0 = OFF
+IMPLICIT_REPRO_CPU_CYCLES 0 # Call Inst_Repro after this many cpu cycles. 0 = OFF
+IMPLICIT_REPRO_TIME 0 # Call Inst_Repro after this time used. 0 = OFF
+IMPLICIT_REPRO_END 0 # Call Inst_Repro after executing the last instruction in the genome.
+IMPLICIT_REPRO_ENERGY 0.0 # Call Inst_Repro if organism accumulates this amount of energy.
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
+COPY_INS_PROB 0.0 # Insertion rate (per copy)
+COPY_DEL_PROB 0.0 # Deletion rate (per copy)
+COPY_UNIFORM_PROB 0.0 # Uniform mutation probability (per copy)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+COPY_SLIP_PROB 0.0 # Slip rate (per copy)
+DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
+DIV_INS_PROB 0.0 # Insertion rate (per site, applied on divide)
+DIV_DEL_PROB 0.0 # Deletion rate (per site, applied on divide)
+DIV_UNIFORM_PROB 0.0 # Uniform mutation probability (per site, applied on divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+DIV_SLIP_PROB 0.0 # Slip rate
+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)
+DIVIDE_UNIFORM_PROB 0.0 # Uniform mutation probability (per divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
+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)
+SLIP_FILL_MODE 0 # Fill insertions from slip mutations with 0=duplication, 1=nop-X, 2=random, 3=scrambled
+PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+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.
+MIGRATION_RATE 0.0 # Uniform probability of offspring migrating to a new deme.
+
+### 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 #
+REVERT_TASKLOSS 1.0
+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 0 # 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.
+ # 3 = DemeProbabalistic, each deme gets the same number of CPU cycles, which are awarded probabalistically within each deme.
+ # 4 = ProbDemeProbabalistic, each deme gets CPU cycles proportional to its living population size, which are awarded probabalistically within each deme.
+ # 5 = CONSTANT BURST: all organisms get default, in SLICING_BURST_SIZE chunks
+SLICING_BURST_SIZE 1 # Sets the scheduler burst size, when supported.
+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
+ # 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
+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 this default bonus
+ # rather than the accumulated bonus of the parent? 0 = off
+MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
+ # (-1 = none, 0 = First in INST_SET.)
+MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
+ # per instruction (-1 = penalty, 0 = no effect.)
+FITNESS_METHOD 0 # 0 = default, >=1 = experimental
+FITNESS_COEFF_1 1.0 # 1st FITNESS_METHOD parameter
+FITNESS_COEFF_2 1.0 # 2nd FITNESS_METHOD parameter
+FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from
+ # FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # (0 = off, 1 = on)
+FITNESS_VALLEY_START 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+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.
+NO_CPU_CYCLE_TIME 0 # Don't count each CPU cycle as part of gestation time
+MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
+MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
+MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
+MIN_GB_DONATE_THRESHOLD -1 # threshold green beard donates only to orgs above this
+ # donation attempt threshold; -1=no thresh
+DONATE_THRESH_QUANTA 10 # The size of steps between quanta donate thresholds
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+PRECALC_PHENOTYPE 0 # 0 = Disabled
+ # 1 = Assign precalculated merit at birth (unlimited resources only)
+ # 2 = Assign precalculated gestation time
+ # 3 = Assign precalculated merit AND gestation time.
+ # Fitness will be evaluated for organism based on these settings.
+FASTFORWARD_UPDATES 0 # Fast-forward if the average generation has not changed in this many updates. (0 = off)
+FASTFORWARD_NUM_ORGS 0 # Fast-forward if population is equal to this
+
+### 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
+
+### ORGANISM_MESSAGING_GROUP ###
+# Organism Message-Based Communication
+MESSAGE_TYPE 0 # Messaging Style. 0=Receiver Facing, 1=Broadcast
+MESSAGE_BCAST_RADIUS 1 # Broadcast message radius (cells)
+ORGANISMS_REMEMBER_MESSAGES 1 # Does an organism remember all messages it has sent or received? 0=false, 1=true (default)
+MESSAGE_QUEUE_SIZE -1 # Maximum number of unretrieved messages an organism can store (-1 for no limit is the default)
+MESSAGE_QUEUE_BEHAVIOR_WHEN_FULL 0 # 0 = Drop incoming message (default), 1 = Drop oldest unretrieved message
+
+### 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 ###
+# Resource Hoarding Parameters
+USE_RESOURCE_BINS 0 # Enable resource bin use. This serves as a guard on most resource hoarding code.
+ABSORB_RESOURCE_FRACTION .0025 # Fraction of available environmental resource an organism absorbs with the collect instruction.
+MULTI_ABSORB_TYPE 0 # What to do if collect is called on a range of resources.
+ # 0 = absorb a random resource in the range
+ # 1 = absorb the first resource in the range
+ # 2 = absorb the last resource in the range
+ # 3 = absorb ABSORB_RESOURCE_FRACTION / (# of resources in range) of each resource in the range
+MAX_TOTAL_STORED -1 # Maximum total amount of all resources an organism can store.
+ # <0 = no maximum
+USE_STORED_FRACTION 1.0 # The fraction of stored resource to use.
+ENV_FRACTION_THRESHOLD 1.0 # The fraction of available environmental resource to compare available stored resource to when deciding whether to use stored resource.
+RETURN_STORED_ON_DEATH 1 # Return an organism's stored resources to the world when it dies?
+
+### ANALYZE_GROUP ###
+# Analysis Settings
+MAX_CONCURRENCY -1 # Maximum number of analyze threads, -1 == use all available.
+ANALYZE_OPTION_1 # String variable accessible from analysis scripts
+ANALYZE_OPTION_2 # String variable accessible from analysis scripts
+
+### ENERGY_GROUP ###
+# Energy Settings
+ENERGY_ENABLED 0 # Enable Energy Model. 0/1 (off/on)
+ENERGY_GIVEN_ON_INJECT 0.0 # Energy given to organism upon injection.
+ENERGY_GIVEN_AT_BIRTH 0.0 # Energy given to offspring upon birth.
+FRAC_PARENT_ENERGY_GIVEN_TO_ORG_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring organism.
+FRAC_PARENT_ENERGY_GIVEN_TO_DEME_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring deme.
+FRAC_ENERGY_DECAY_AT_ORG_BIRTH 0.0 # Fraction of energy lost due to decay during organism reproduction.
+FRAC_ENERGY_DECAY_AT_DEME_BIRTH 0.0 # Fraction of energy lost due to decay during deme reproduction.
+NUM_INST_EXC_BEFORE_0_ENERGY 0 # Number of instructions executed before energy is exhausted.
+ENERGY_CAP -1.0 # Maximum amount of energy that can be stored in an organism. -1 means the cap is set to Max Double
+APPLY_ENERGY_METHOD 0 # When should rewarded energy be applied to current energy?
+ # 0 = on divide
+ # 1 = on completion of task
+ # 2 = on sleep
+FRAC_ENERGY_TRANSFER 0.0 # Fraction of replaced organism's energy take by new resident
+LOG_SLEEP_TIMES 0 # Log sleep start and end times. 0/1 (off/on)
+ # WARNING: may use lots of memory.
+FRAC_ENERGY_RELINQUISH 1.0 # Fraction of organisms energy to relinquish
+ENERGY_PASSED_ON_DEME_REPLICATION_METHOD 0 # Who get energy passed from a parent deme
+ # 0 = Energy divided among organisms injected to offspring deme
+ # 1 = Energy divided among cells in offspring deme
+INHERIT_EXE_RATE 0 # Inherit energy rate from parent? 0=no 1=yes
+ATTACK_DECAY_RATE 0.0 # Percent of cell's energy decayed by attack
+ENERGY_THRESH_LOW .33 # Threshold percent below which energy level is considered low. Requires ENERGY_CAP.
+ENERGY_THRESH_HIGH .75 # Threshold percent above which energy level is considered high. Requires ENERGY_CAP.
+
+### ENERGY_SHARING_GROUP ###
+# Energy Sharing Settings
+ENERGY_SHARING_METHOD 0 # Method for sharing energy. 0=receiver must actively receive/request, 1=energy pushed on receiver
+ENERGY_SHARING_PCT 0.0 # Percent of energy to share
+ENERGY_SHARING_INCREMENT 0.01 # Amount to change percent energy shared
+ENERGY_SHARING_LOSS 0.0 # Percent of shared energy lost in transfer
+
+### SECOND_PASS_GROUP ###
+# Tracking metrics known after the running experiment previously
+TRACK_CCLADES 0 # Enable tracking of coalescence clades
+TRACK_CCLADES_IDS coalescence.ids # File storing coalescence IDs
+
+### GX_GROUP ###
+# Gene Expression CPU Settings
+MAX_PROGRAMIDS 16 # Maximum number of programids an organism can create.
+MAX_PROGRAMID_AGE 2000 # Max number of CPU cycles a programid executes before it is removed.
+IMPLICIT_GENE_EXPRESSION 0 # Create executable programids from the genome without explicit allocation and copying?
+IMPLICIT_BG_PROMOTER_RATE 0.0 # Relative rate of non-promoter sites creating programids.
+IMPLICIT_TURNOVER_RATE 0.0 # Number of programids recycled per CPU cycle. 0 = OFF
+IMPLICIT_MAX_PROGRAMID_LENGTH 0 # Creation of an executable programid terminates after this many instructions. 0 = disabled
+
+### PROMOTER_GROUP ###
+# Promoters
+PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
+ # Certain instructions must also be included.
+PROMOTER_INST_MAX 0 # Maximum number of instructions to execute before terminating. 0 = off
+PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating after each cpu cycle.
+PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after each instruction.
+PROMOTER_TO_REGISTER 0 # Place a promoter's base bit code in register BX when starting execution from it?
+TERMINATION_RESETS 0 # Does termination reset the thread's state?
+NO_ACTIVE_PROMOTER_EFFECT 0 # What happens when there are no active promoters?
+ # 0 = Start execution at the beginning of the genome.
+ # 1 = Kill the organism.
+ # 2 = Stop the organism from executing any further instructions.
+PROMOTER_CODE_SIZE 24 # Size of a promoter code in bits. (Maximum value is 32)
+PROMOTER_EXE_LENGTH 3 # Length of promoter windows used to determine execution.
+PROMOTER_EXE_THRESHOLD 2 # Minimum number of bits that must be set in a promoter window to allow execution.
+INST_CODE_LENGTH 3 # Instruction binary code length (number of bits)
+INST_CODE_DEFAULT_TYPE 0 # Default value of instruction binary code value.
+ # 0 = All zeros
+ # 1 = Based off the instruction number
+CONSTITUTIVE_REGULATION 0 # Sense a new regulation value before each CPU cycle?
+
+### COLORS_GROUP ###
+# Output colors for when data files are printed in HTML mode.
+# There are two sets of these; the first are for lineages,
+# and the second are for mutation tests.
+COLOR_DIFF CCCCFF # Color to flag stat that has changed since parent.
+COLOR_SAME FFFFFF # Color to flag stat that has NOT changed since parent.
+COLOR_NEG2 FF0000 # Color to flag stat that is significantly worse than parent.
+COLOR_NEG1 FFCCCC # Color to flag stat that is minorly worse than parent.
+COLOR_POS1 CCFFCC # Color to flag stat that is minorly better than parent.
+COLOR_POS2 00FF00 # Color to flag stat that is significantly better than parent.
+COLOR_MUT_POS 00FF00 # Color to flag stat that has changed since parent.
+COLOR_MUT_NEUT FFFFFF # Color to flag stat that has changed since parent.
+COLOR_MUT_NEG FFFF00 # Color to flag stat that has changed since parent.
+COLOR_MUT_LETHAL FF0000 # Color to flag stat that has changed since parent.
+
+### BIOMIMETIC_GROUP ###
+# Biomimetic Features Settings
+BIOMIMETIC_REFRACTORY_PERIOD 0.0 # Number of updates affected by refractory period
+BIOMIMETIC_MOVEMENT_STEP 1 # Number of cells to move Avidian on move instruction
+BIOMIMETIC_MOVEMENT_LOG 0 # Log detailed movement information (WARNING: large data file)
+BIOMIMETIC_MOVEMENT_FACTOR 1.0 # Scale merit bonus due to movement (m<1.0 applies a cost)
+BIOMIMETIC_EVAL_ON_MOVEMENT 0 # Force task evaluation on each movement step
+BIOMIMETIC_K 0 # Carrying capacity in number of organisms
+
+### PHEROMONE_GROUP ###
+# Pheromone Settings
+PHEROMONE_ENABLED 0 # Enable pheromone usage. 0/1 (off/on)
+PHEROMONE_AMOUNT 1.0 # Amount of pheromone to add per drop
+PHEROMONE_DROP_MODE 0 # Where to drop pheromone
+ # 0 = Half amount at src, half at dest
+ # 1 = All at source
+ # 2 = All at dest
+EXPLOIT_EXPLORE_PROB 0.00 # Probability of random exploration
+ # instead of pheromone trail following
+LOG_PHEROMONE 0 # Log pheromone drops. 0/1 (off/on)
+PHEROMONE_LOG_START 0 # Update at which to start logging pheromone drops
+EXPLOIT_LOG_START 0 # Update at which to start logging exploit moves
+EXPLORE_LOG_START 0 # Update at which to start logging explore moves
+MOVETARGET_LOG_START 0 # Update at which to start logging movetarget moves
+LOG_INJECT 0 # Log injection of organisms. 0/1 (off/on)
+INJECT_LOG_START 0 # Update at which to start logging injection of
+ # organisms
+
+### SYNCHRONIZATION_GROUP ###
+# Synchronization settings
+SYNC_FITNESS_WINDOW 100 # Number of updates over which to calculate fitness (default=100).
+SYNC_FLASH_LOSSRATE 0.0 # P() to lose a flash send (0.0==off).
+SYNC_TEST_FLASH_ARRIVAL -1 # CPU cycle at which an organism will receive a flash (off=-1, default=-1, analyze mode only.)
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