[Avida-SVN] r1563 - in development/tests: avida_GA_lim_res/config optimize_task_lim_res/config string_match_embed3/config
goingssh at myxo.css.msu.edu
goingssh at myxo.css.msu.edu
Wed May 16 13:59:52 PDT 2007
Author: goingssh
Date: 2007-05-16 16:59:52 -0400 (Wed, 16 May 2007)
New Revision: 1563
Modified:
development/tests/avida_GA_lim_res/config/avida.cfg
development/tests/optimize_task_lim_res/config/avida.cfg
development/tests/optimize_task_lim_res/config/default-classic.org
development/tests/string_match_embed3/config/avida.cfg
Log:
Made tests faster with smaller pops
Modified: development/tests/avida_GA_lim_res/config/avida.cfg
===================================================================
--- development/tests/avida_GA_lim_res/config/avida.cfg 2007-05-16 20:47:00 UTC (rev 1562)
+++ development/tests/avida_GA_lim_res/config/avida.cfg 2007-05-16 20:59:52 UTC (rev 1563)
@@ -16,8 +16,8 @@
### ARCH_GROUP ###
# Architecture Variables
-WORLD_X 50 # Width of the Avida world
-WORLD_Y 40 # Height of the Avida world
+WORLD_X 15 # Width of the Avida world
+WORLD_Y 15 # 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
Modified: development/tests/optimize_task_lim_res/config/avida.cfg
===================================================================
--- development/tests/optimize_task_lim_res/config/avida.cfg 2007-05-16 20:47:00 UTC (rev 1562)
+++ development/tests/optimize_task_lim_res/config/avida.cfg 2007-05-16 20:59:52 UTC (rev 1563)
@@ -16,8 +16,8 @@
### ARCH_GROUP ###
# Architecture Variables
-WORLD_X 50 # Width of the Avida world
-WORLD_Y 50 # Height of the Avida world
+WORLD_X 15 # Width of the Avida world
+WORLD_Y 15 # 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
Modified: development/tests/optimize_task_lim_res/config/default-classic.org
===================================================================
--- development/tests/optimize_task_lim_res/config/default-classic.org 2007-05-16 20:47:00 UTC (rev 1562)
+++ development/tests/optimize_task_lim_res/config/default-classic.org 2007-05-16 20:59:52 UTC (rev 1563)
@@ -1,100 +1,130 @@
-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 #
-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 #
-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 #
-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 #
-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 #
-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 #
-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 #
+# Thu Mar 22 20:46:24 2007
+# Filename........: archive/103-aacrp.org
+# Update Output...: 20000
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+# Update Created..: 10008
+# Genotype ID.....: 854126
+# Parent Gen ID...: 846720
+# Tree Depth......: 229
+# Parent Distance.: 4
+#
+# Generation: 0
+# Merit...........: 100.000000
+# Gestation Time..: 237
+# Fitness.........: 0.421941
+# Errors..........: 5
+# Genome Size.....: 103
+# Copied Size.....: 103
+# Executed Size...: 100
+# Offspring.......: SELF
+#
+# Tasks Performed:
+# optimize 1 (0.941115)
+# optimize 1 (0.470749)
+
+
+h-alloc
+h-search
+set-flow
+nop-A
+mov-head
+nop-C
+IO
+sub
+nop-A
+push
+add
+IO
+dec
+nop-B
+if-n-equ
+add
+h-search
+if-label
+get-head
+nop-B
+nop-C
+h-copy
+h-copy
+h-copy
+dec
+swap-stk
+nop-B
+if-less
+h-search
+dec
+nop-B
+inc
+nop-C
+if-less
+swap
+if-n-equ
+h-search
+inc
+nop-C
+add
+h-alloc
+IO
+pop
+nop-A
+sub
+dec
+swap
+dec
+nop-B
+h-copy
+if-less
+h-alloc
+push
+nop-A
+inc
+nop-A
+h-divide
+nand
+inc
+sub
+h-search
+push
+if-less
+swap
+h-copy
+h-divide
+h-copy
+inc
+h-copy
+h-alloc
+nop-C
+push
+if-n-equ
+nop-C
+get-head
+nop-A
+get-head
+sub
+nand
+if-less
+shift-r
+shift-l
+pop
+inc
+pop
+sub
+add
+if-label
+IO
+nop-C
+pop
+swap
+h-search
+h-copy
+h-copy
+h-copy
+if-label
+nop-C
+nop-A
+h-divide
+mov-head
+nop-A
+nop-B
Modified: development/tests/string_match_embed3/config/avida.cfg
===================================================================
--- development/tests/string_match_embed3/config/avida.cfg 2007-05-16 20:47:00 UTC (rev 1562)
+++ development/tests/string_match_embed3/config/avida.cfg 2007-05-16 20:59:52 UTC (rev 1563)
@@ -1,183 +1,183 @@
-#############################################################################
-# This file includes all the basic run-time defines for Avida.
-# For more information, see doc/config.html
-#############################################################################
-
-VERSION_ID 2.5.0 # Do not change this value.
-
-### GENERAL_GROUP ###
-# General Settings
-ANALYZE_MODE 0 # 0 = Disabled
- # 1 = Enabled
- # 2 = Interactive
-VIEW_MODE 0 # Initial viewer screen
-CLONE_FILE - # Clone file to load
-POPULATION_FILE - # Population file to load
-
-### ARCH_GROUP ###
-# Architecture Variables
-MAX_UPDATES -1 # Maximum updates to run experiment (-1 = no limit)
-MAX_GENERATIONS -1 # Maximum generations to run experiment (-1 = no limit)
-END_CONDITION_MODE 0 # End run when ...
- # 0 = MAX_UPDATES _OR_ MAX_GENERATIONS is reached
- # 1 = MAX_UPDATES _AND_ MAX_GENERATIONS is reached
-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, Stack-based CPUs
- # 2 = Newer -- Stacks, Memory, Threading
-
-### CONFIG_FILE_GROUP ###
-# Configuration Files
-DATA_DIR data # Directory in which config files are found
-INST_SET inst_set.default # File containing instruction set
-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 organism.default # Organism to seed the soup
-
-### REPRODUCTION_GROUP ###
-# Birth and Death
-BIRTH_METHOD 0 # 0 = Replace random organism in neighborhood
- # 1 = Replace oldest organism in neighborhood
- # 2 = Replace largest Age/Merit in neighborhood
- # 3 = Place only in empty cells in neighborhood
- # 4 = Replace random from population (Mass Action)
- # 5 = Replace oldest in entire population (like Tierra)
- # 6 = Replace random within deme
-PREFER_EMPTY 1 # Are empty cells given preference in offsping placement?
-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_PROB 1.0 # probability that recombination will happen when div-sex is used
-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 at random or with corresponding ones, by location
-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 # (Origianl CPU Only) Is a an allocate required before a divide? (0/1)
-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.
-DIE_PROB 0.0 # probability of death when 'die' instruction is executed
-
-### MUTATION_GROUP ###
-# Mutations
-POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
-COPY_MUT_PROB 0.0075 # 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
-
-### 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?
-
-### TIME_GROUP ###
-# Time Slicing
-AVE_TIME_SLICE 30 # Ave number of insts per org per update
-SLICING_METHOD 2 # 0 = CONSTANT: all organisms get default...
- # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
- # 2 = INTEGRATED: Perfectly integrated deterministic.
-SIZE_MERIT_METHOD 4 # 0 = off (merit is 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
-MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
-THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing -> 1 + (num_organism_threads-1) * THREAD_SLICING_METHOD.
- # 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
-BASE_SIZE_MERIT 100 # Base merit when size is *not* used
-DEFAULT_BONUS 1.0 # The bonus an organism gets before it has completed any tasks
-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
-MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
-
-### 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 #
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.5.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 0 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 0 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+POPULATION_FILE - # Population file to load
+
+### ARCH_GROUP ###
+# Architecture Variables
+MAX_UPDATES -1 # Maximum updates to run experiment (-1 = no limit)
+MAX_GENERATIONS -1 # Maximum generations to run experiment (-1 = no limit)
+END_CONDITION_MODE 0 # End run when ...
+ # 0 = MAX_UPDATES _OR_ MAX_GENERATIONS is reached
+ # 1 = MAX_UPDATES _AND_ MAX_GENERATIONS is reached
+WORLD_X 15 # Width of the Avida world
+WORLD_Y 15 # 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, Stack-based CPUs
+ # 2 = Newer -- Stacks, Memory, Threading
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET inst_set.default # File containing instruction set
+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 organism.default # Organism to seed the soup
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 0 # 0 = Replace random organism in neighborhood
+ # 1 = Replace oldest organism in neighborhood
+ # 2 = Replace largest Age/Merit in neighborhood
+ # 3 = Place only in empty cells in neighborhood
+ # 4 = Replace random from population (Mass Action)
+ # 5 = Replace oldest in entire population (like Tierra)
+ # 6 = Replace random within deme
+PREFER_EMPTY 1 # Are empty cells given preference in offsping placement?
+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_PROB 1.0 # probability that recombination will happen when div-sex is used
+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 at random or with corresponding ones, by location
+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 # (Origianl CPU Only) Is a an allocate required before a divide? (0/1)
+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.
+DIE_PROB 0.0 # probability of death when 'die' instruction is executed
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0075 # 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
+
+### 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?
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 2 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+SIZE_MERIT_METHOD 4 # 0 = off (merit is 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
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing -> 1 + (num_organism_threads-1) * THREAD_SLICING_METHOD.
+ # 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
+BASE_SIZE_MERIT 100 # Base merit when size is *not* used
+DEFAULT_BONUS 1.0 # The bonus an organism gets before it has completed any tasks
+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
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+
+### 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 #
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