[Avida-SVN] r1607 - in development/tests: . fitvalley_dynamic_mutrate fitvalley_dynamic_mutrate/config fitvalley_dynamic_mutrate/expected fitvalley_dynamic_mutrate/expected/data
jclune at myxo.css.msu.edu
jclune at myxo.css.msu.edu
Fri May 25 04:08:59 PDT 2007
Author: jclune
Date: 2007-05-25 07:08:58 -0400 (Fri, 25 May 2007)
New Revision: 1607
Added:
development/tests/fitvalley_dynamic_mutrate/
development/tests/fitvalley_dynamic_mutrate/config/
development/tests/fitvalley_dynamic_mutrate/config/10reproAs.org
development/tests/fitvalley_dynamic_mutrate/config/avida.cfg
development/tests/fitvalley_dynamic_mutrate/config/environment.cfg
development/tests/fitvalley_dynamic_mutrate/config/events-toggleEvery10.cfg
development/tests/fitvalley_dynamic_mutrate/config/instset-reprosA-B.cfg
development/tests/fitvalley_dynamic_mutrate/expected/
development/tests/fitvalley_dynamic_mutrate/expected/data/
development/tests/fitvalley_dynamic_mutrate/expected/data/average.dat
development/tests/fitvalley_dynamic_mutrate/expected/data/dominant.dat
development/tests/fitvalley_dynamic_mutrate/expected/data/instruction.dat
development/tests/fitvalley_dynamic_mutrate/test_list
Log:
added fitvalley_dynamic_mutrate test
Added: development/tests/fitvalley_dynamic_mutrate/config/10reproAs.org
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/config/10reproAs.org (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/config/10reproAs.org 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,10 @@
+repro #
+repro #
+repro #
+repro #
+repro #
+repro #
+repro #
+repro #
+repro #
+repro #
\ No newline at end of file
Added: development/tests/fitvalley_dynamic_mutrate/config/avida.cfg
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/config/avida.cfg (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/config/avida.cfg 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,264 @@
+#############################################################################
+# 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 0 # 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
+ # 3 = Clique
+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
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET - # 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 default-classic.org # Organism to seed the soup
+
+### DEME_GROUP ###
+# Demes and Germlines
+NUM_DEMES 1 # Number of independent groups in the population.
+DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline; 0=off
+DEMES_HAVE_MERIT 0 # Whether demes have merit; 0=no
+GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
+ # germline replication.
+GERMLINE_REPLACES_SOURCE 0 # Whether the source germline is updated
+ # on replication; 0=no.
+GERMLINE_RANDOM_PLACEMENT 0 # Whether the seed for a germline is placed
+ # randomly within the deme; 0=no.
+MAX_DEME_AGE 500 # The maximum age of a deme (in updates) to be
+ # used for age-based replication (default=500).
+
+### 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 0.0075 # 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
+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 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.
+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 the default bonus
+ # rather than the accumulated bonus of the parent?
+MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts (-1=none, 0= 1st in INST_SET.)
+MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned per INST (-1=penalty, 0= no effect.)
+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.
+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.
+
+### 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 after each cpu cycle.
+PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after 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 = 2^(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
+
+### 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
+
+### 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
Added: development/tests/fitvalley_dynamic_mutrate/config/environment.cfg
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/config/environment.cfg (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/config/environment.cfg 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,23 @@
+##############################################################################
+#
+# 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 file is currently setup to reward 9 tasks, all of which use the
+# "infinite" resource, which is undepletable.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+REACTION NOT not process:value=1.0:type=pow requisite:max_count=1
+REACTION NAND nand process:value=1.0:type=pow requisite:max_count=1
+REACTION AND and process:value=2.0:type=pow requisite:max_count=1
+REACTION ORN orn process:value=2.0:type=pow requisite:max_count=1
+REACTION OR or process:value=3.0:type=pow requisite:max_count=1
+REACTION ANDN andn process:value=3.0:type=pow requisite:max_count=1
+REACTION NOR nor process:value=4.0:type=pow requisite:max_count=1
+REACTION XOR xor process:value=4.0:type=pow requisite:max_count=1
+REACTION EQU equ process:value=5.0:type=pow requisite:max_count=1
Added: development/tests/fitvalley_dynamic_mutrate/config/events-toggleEvery10.cfg
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/config/events-toggleEvery10.cfg (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/config/events-toggleEvery10.cfg 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,51 @@
+#############################################################################
+#
+# 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/
+#
+##############################################################################
+
+#actions
+u 0 inject 10reproAs.org 0 100
+u 9:10:end ToggleRewardInstruction
+u 100 exit # exit
+
+# Print all of the standard data files...
+u 10:1:end PrintAverageData # Save info about they average genotypes
+u 10:1:end PrintDominantData # Save info about most abundant genotypes
+u 10:1:end print_instruction_data
+
+#non standard
+#u 10:1:end print_deme_stats
+
+
+#less frequent
+#u 0:100:end PrintTasksData # Save organisms counts for each task.
+#u 50000:50000 SavePopulation # Save current state of population.
+#u 50000:50000 SaveHistoricPopulation # Save ancestors of current population.
+
+
+#defaults I am turning off
+#u 0:10:end PrintResourceData # Track resource abundance.
+#u 0:10:end PrintStatsData # Collect satistics about entire pop.
+#u 0:10:end PrintCountData # Count organisms, genotypes, species, etc.
+#u 0:10:end PrintTimeData # Track time conversion (generations, etc.)
+
+
+# A few data files not printed by default
+# u 0:100 PrintDominantGenotype # Save the most abundant genotypes
+# u 100:100:end PrintErrorData # Std. Error on averages.
+# u 100:100:end PrintVarianceData # Variance on averages.
+# u 100:100:end PrintTotalsData # Total counts over entire run.
+# u 100:100:end PrintTasksExeData # Num. times tasks have been executed.
+# u 100:100:end PrintTasksQualData # Task quality information
+
+# Setup the exit time and full population data collection.
Added: development/tests/fitvalley_dynamic_mutrate/config/instset-reprosA-B.cfg
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/config/instset-reprosA-B.cfg (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/config/instset-reprosA-B.cfg 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,3 @@
+nop-B 0 # has to be the first instruction for no good reason
+repro 1
+repro-B 1
Added: development/tests/fitvalley_dynamic_mutrate/expected/data/average.dat
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/expected/data/average.dat (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/expected/data/average.dat 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,110 @@
+# Avida Average Data
+# Fri May 25 07:11:17 2007
+# 1: Update
+# 2: Merit
+# 3: Gestation Time
+# 4: Fitness
+# 5: Repro Rate?
+# 6: Size
+# 7: Copied Size
+# 8: Executed Size
+# 9: Abundance
+# 10: Proportion of organisms that gave birth in this update
+# 11: Proportion of Breed True Organisms
+# 12: Genotype Depth
+# 13: Generation
+# 14: Neutral Metric
+# 15: Lineage Label
+# 16: True Replication Rate (based on births/update, time-averaged)
+
+10 4.940000 1.000000 4.940000 0.000000 10.000000 10.000000 1.000000 2.777778 30.000000 23.020000 46.340000 599.350000 32.739270 0.000000 0.000000
+11 7.71 1 7.71 0 10 10 1 1.88679 30 20.32 54.01 665.47 43.8709 0 0
+12 7.21 1 7.21 0 10 10 1 2.12766 30 20.38 57.39 723.55 34.8558 0 0
+13 8.51 1 8.51 0 10 10 1 2.22222 30 21.61 61.74 779.48 18.5263 0 0
+14 8.94 1 8.94 0 10 10 1 2.94118 30 23.84 63.45 848.91 29.1313 0 0
+15 8.97 1 8.97 0 10 10 1 3.84615 30 25.46 64.16 913.57 20.8541 0 0
+16 9.76 1 9.76 0 10 10 1 5 30 26.32 67.01 983.11 9.03803 0 0
+17 9.93 1 9.93 0 10 10 1 5.26316 30 26.67 67.48 1047.1 5.12836 0 0
+18 10.38 1 10.38 0 10 10 1 7.69231 30 27.43 65.93 1105.6 9.52459 0 0
+19 10.41 1 10.41 0 10 10 1 11.1111 30 28.11 65.74 1164.08 10.5635 0 0
+20 4.54 1 4.54 0 10 10 1 6.25 30 28.22 72.17 1223.04 17.4429 0 0
+21 4.74 1 4.74 0 10 10 1 10 30 28.3 71.35 1300.93 15.5676 0 0
+22 4.72 1 4.72 0 10 10 1 10 30 28.56 71.24 1353.07 18.863 0 0
+23 6.16 1 6.16 0 10 10 1 11.1111 30 28.51 72.06 1411.59 16.9252 0 0
+24 7.88 1 7.88 0 10 10 1 8.33333 30 28.45 73.7 1475.26 16.4072 0 0
+25 9.72 1 9.72 0 10 10 1 6.25 30 28 75.73 1539.96 3.35771 0 0
+26 10.38 1 10.38 0 10 10 1 7.14286 30 28.36 76.1 1603.79 -0.0723739 0 0
+27 10.02 1 10.02 0 10 10 1 6.66667 30 28.39 77.01 1671.22 -0.242498 0 0
+28 10.25 1 10.25 0 10 10 1 8.33333 30 28.37 76.77 1726.8 -10.3285 0 0
+29 9.93 1 9.93 0 10 10 1 7.69231 30 28.42 77.09 1782.43 -18.7316 0 0
+30 3.89 1 3.89 0 10 10 1 11.1111 30 28.66 79.17 1841.7 -14.3641 0 0
+31 3.87 1 3.87 0 10 10 1 11.1111 30 28.54 79.48 1898.8 -8.28483 0 0
+32 3.57 1 3.57 0 10 10 1 5.88235 30 28.58 80.38 1956.52 7.44933 0 0
+33 3.84 1 3.84 0 10 10 1 14.2857 30 28.4 79.6 2010.63 8.83179 0 0
+34 3.88 1 3.88 0 10 10 1 20 30 29.13 79.06 2071.47 0.779608 0 0
+35 3.9 1 3.9 0 10 10 1 20 30 29.16 79.06 2141.19 -0.34194 0 0
+36 3.7 1 3.7 0 10 10 1 10 30 28.76 79.21 2197.54 -8.62021 0 0
+37 3.89 1 3.89 0 10 10 1 25 30 28.91 79.07 2253.63 -32.1976 0 0
+38 3.74 1 3.74 0 10 10 1 14.2857 30 29.2 79.18 2308.4 -34.366 0 0
+39 3.69 1 3.69 0 10 10 1 14.2857 30 28.9 79.17 2369.49 -30.0365 0 0
+40 8.99 1 8.99 0 10 10 1 14.2857 30 29.09 80.13 2425.46 -28.2982 0 0
+41 9.74 1 9.74 0 10 10 1 16.6667 30 29.5 80.85 2489.94 -41.6096 0 0
+42 9.96 1 9.96 0 10 10 1 33.3333 30 29.4 81.05 2549.48 -39.0708 0 0
+43 10.18 1 10.18 0 10 10 1 25 30 29.73 81.29 2615.67 -44.409 0 0
+44 10.33 1 10.33 0 10 10 1 11.1111 30 29.49 82.07 2681.22 -37.8828 0 0
+45 10.53 1 10.53 0 10 10 1 12.5 30 29.41 82.46 2739.74 -30.4381 0 0
+46 10.63 1 10.63 0 10 10 1 11.1111 30 29.14 82.35 2802.37 -27.0746 0 0
+47 10.94 1 10.94 0 10 10 1 20 30 29.39 82.08 2871.24 -49.6555 0 0
+48 10.45 1 10.45 0 10 10 1 16.6667 30 29.64 82.55 2931.37 -37.8514 0 0
+49 10.95 1 10.95 0 10 10 1 50 30 29.72 82.15 2997.91 -37.621 0 0
+50 3.69 1 3.69 0 10 10 1 14.2857 30 29.79 86.79 3083 -36.6183 0 0
+51 3.96 1 3.96 0 10 10 1 25 30 29.7 87.02 3149.5 -35.5468 0 0
+52 3.97 1 3.97 0 10 10 1 33.3333 30 29.76 87.02 3205.63 -30.6727 0 0
+53 3.91 1 3.91 0 10 10 1 50 30 29.81 87.03 3265.05 -41.5333 0 0
+54 4 1 4 0 10 10 1 0 30 29.85 87 3310.71 -50.2496 0 0
+55 4 1 4 0 10 10 1 0 30 29.88 87 3365.44 -37.9134 0 0
+56 3.91 1 3.91 0 10 10 1 20 30 29.79 87.23 3420.36 -51.6309 0 0
+57 3.91 1 3.91 0 10 10 1 50 30 29.91 87.03 3477.17 -39.982 0 0
+58 4 1 4 0 10 10 1 0 30 29.86 87 3529.56 -44.6495 0 0
+59 4 1 4 0 10 10 1 0 30 29.87 87 3584.73 -33.7138 0 0
+60 7.86 1 7.86 0 10 10 1 50 30 29.86 87.02 3652.12 -52.9123 0 0
+61 8 1 8 0 10 10 1 0 30 29.94 87 3700.09 -43.136 0 0
+62 8 1 8 0 10 10 1 0 30 29.9 87 3763.51 -46.1924 0 0
+63 7.98 1 7.98 0 10 10 1 33.3333 30 29.91 87.06 3813.86 -35.8148 0 0
+64 8.63 1 8.63 0 10 10 1 20 30 29.86 87.64 3868.89 -37.9577 0 0
+65 8.63 1 8.63 0 10 10 1 16.6667 30 29.7 87.99 3917.15 -45.4008 0 0
+66 8.9 1 8.9 0 10 10 1 50 30 29.74 87.9 3965.81 -53.4735 0 0
+67 8.92 1 8.92 0 10 10 1 50 30 29.69 88.08 4014.37 -56.2306 0 0
+68 9.18 1 9.18 0 10 10 1 16.6667 30 29.64 88.4 4078.62 -58.0181 0 0
+69 9.43 1 9.43 0 10 10 1 33.3333 30 29.81 88.43 4152.84 -71.6437 0 0
+70 3.7 1 3.7 0 10 10 1 16.6667 30 29.78 88.77 4210.03 -72.0465 0 0
+71 3.97 1 3.97 0 10 10 1 33.3333 30 29.85 89.02 4266.1 -75.1942 0 0
+72 3.94 1 3.94 0 10 10 1 50 30 29.82 89.02 4322.03 -82.9647 0 0
+73 4 1 4 0 10 10 1 0 30 29.91 89 4383.22 -87.019 0 0
+74 4 1 4 0 10 10 1 0 30 29.86 89 4439.86 -86.7416 0 0
+75 3.97 1 3.97 0 10 10 1 50 30 29.82 89.01 4487.98 -94.947 0 0
+76 3.97 1 3.97 0 10 10 1 50 30 29.85 89.01 4541.12 -97.131 0 0
+77 3.94 1 3.94 0 10 10 1 33.3333 30 29.86 89.03 4596.2 -98.9793 0 0
+78 4 1 4 0 10 10 1 0 30 29.91 89 4662 -96.8521 0 0
+79 3.96 1 3.96 0 10 10 1 25 30 29.93 89.03 4718.65 -100.938 0 0
+80 7.93 1 7.93 0 10 10 1 50 30 29.92 89.01 4772.89 -99.3975 0 0
+81 7.87 1 7.87 0 10 10 1 33.3333 30 29.9 89.03 4816.03 -120.184 0 0
+82 8.24 1 8.24 0 10 10 1 50 30 29.91 89.24 4876.22 -124.076 0 0
+83 8.74 1 8.74 0 10 10 1 25 30 29.87 89.9 4943.05 -123.768 0 0
+84 9 1 9 0 10 10 1 0 30 29.91 90 5003.41 -128.059 0 0
+85 9.29 1 9.29 0 10 10 1 50 30 29.93 90.29 5065.68 -131.549 0 0
+86 9.49 1 9.49 0 10 10 1 50 30 29.9 90.49 5126.13 -135.311 0 0
+87 9.94 1 9.94 0 10 10 1 25 30 29.95 90.97 5187.19 -138.868 0 0
+88 10 1 10 0 10 10 1 0 30 29.93 91 5249.58 -144.988 0 0
+89 10 1 10 0 10 10 1 0 30 29.92 91 5303.02 -146.508 0 0
+90 3.8 1 3.8 0 10 10 1 25 30 29.88 92.92 5367.66 -117.422 0 0
+91 4 1 4 0 10 10 1 0 30 29.88 93 5423.62 -118.215 0 0
+92 4 1 4 0 10 10 1 50 30 29.91 93.01 5471.14 -118.305 0 0
+93 4 1 4 0 10 10 1 0 30 29.84 93 5522.01 -132.653 0 0
+94 4 1 4 0 10 10 1 50 30 29.88 93.01 5583.02 -137.256 0 0
+95 3.96 1 3.96 0 10 10 1 50 30 29.76 93.04 5649.66 -134.356 0 0
+96 4 1 4 0 10 10 1 50 30 29.8 93.01 5712.89 -117.478 0 0
+97 4 1 4 0 10 10 1 50 30 29.77 93.01 5768.84 -108.862 0 0
+98 4 1 4 0 10 10 1 0 30 29.89 93 5817.91 -115.148 0 0
+99 3.94 1 3.94 0 10 10 1 50 30 29.82 93.02 5878.23 -118.365 0 0
+100 8.09 1 8.09 0 10 10 1 33.3333 30 29.9 93.1 5938.06 -115.586 0 0
Added: development/tests/fitvalley_dynamic_mutrate/expected/data/dominant.dat
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/expected/data/dominant.dat (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/expected/data/dominant.dat 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,110 @@
+# Avida Dominant Data
+# Fri May 25 07:11:17 2007
+# 1: Update
+# 2: Average Merit of the Dominant Genotype
+# 3: Average Gestation Time of the Dominant Genotype
+# 4: Average Fitness of the Dominant Genotype
+# 5: Repro Rate?
+# 6: Size of Dominant Genotype
+# 7: Copied Size of Dominant Genotype
+# 8: Executed Size of Dominant Genotype
+# 9: Abundance of Dominant Genotype
+# 10: Number of Births
+# 11: Number of Dominant Breed True?
+# 12: Dominant Gene Depth
+# 13: Dominant Breed In
+# 14: Max Fitness?
+# 15: Genotype ID of Dominant Genotype
+# 16: Name of the Dominant Genotype
+
+10 4.154217 1.000000 4.154217 1.000000 10 10.000000 1.000000 10 399 322 42 3 8.000000 5263 010-aabpp
+11 9 1 9 1 10 10 1 7 77 64 51 6 10 6379 010-aacac
+12 8 1 8 1 10 10 1 9 46 38 56 1 10 7065 010-aacfz
+13 9 1 9 1 10 10 1 10 51 37 59 6 11 7896 010-aacmq
+14 10 1 10 1 10 10 1 23 263 234 62 7 10 8068 010-aacoj
+15 10 1 10 1 10 10 1 16 220 191 64 5 11 8591 010-aactr
+16 11 1 11 1 10 10 1 21 520 459 65 15 11 8783 010-aacvb
+17 10 1 10 1 10 10 1 23 380 346 66 13 11 9054 010-aacyc
+18 11 1 11 1 10 10 1 53 856 808 65 11 11 8783 010-aacvb
+19 11 1 11 1 10 10 1 67 1362 1297 65 1 11 8783 010-aacvb
+20 5 1 5 1 10 10 1 23 932 872 71 2 5 9569 010-aaddr
+21 5 1 5 1 10 10 1 61 1472 1411 71 0 5 9569 010-aaddr
+22 5 1 5 1 10 10 1 83 2160 2060 71 1 5 9569 010-aaddr
+23 8 1 8 1 10 10 1 42 376 364 73 1 8 9933 010-aadht
+24 8 1 8 1 10 10 1 61 2520 2390 73 1 11 9933 010-aadht
+25 10 1 10 1 10 10 1 53 675 642 75 5 11 10063 010-aadjl
+26 11 1 11 1 10 10 1 48 1020 958 76 9 11 10142 010-aadko
+27 11 1 11 1 10 10 1 24 1230 1157 76 5 11 10142 010-aadko
+28 11 1 11 1 10 10 1 43 929 879 76 10 11 10142 010-aadko
+29 11 1 11 1 10 10 1 30 1084 1014 76 9 11 10142 010-aadko
+30 4 1 4 1 10 10 1 46 704 677 79 1 4 10626 010-aadqr
+31 4 1 4 1 10 10 1 37 1151 1100 79 1 4 10626 010-aadqr
+32 4.09432 1 4.09432 1 10 10 1 24 1103 1061 79 0 4 10588 010-aadqe
+33 4 1 4 1 10 10 1 73 1207 1172 79 1 4 10626 010-aadqr
+34 4 1 4 1 10 10 1 94 2654 2585 79 0 4 10626 010-aadqr
+35 4 1 4 1 10 10 1 94 2819 2736 79 0 4 10626 010-aadqr
+36 4 1 4 1 10 10 1 79 2811 2691 79 1 4 10626 010-aadqr
+37 4 1 4 1 10 10 1 93 2749 2646 79 1 4 10626 010-aadqr
+38 4 1 4 1 10 10 1 85 2891 2814 79 0 4 10626 010-aadqr
+39 4 1 4 1 10 10 1 83 2689 2596 79 0 4 10626 010-aadqr
+40 8.96954 1 8.96954 1 10 10 1 43 588 575 80 10 10 11407 010-aadzd
+41 10 1 10 1 10 10 1 72 1011 995 81 1 10 11415 010-aadzi
+42 10 1 10 1 10 10 1 95 2524 2474 81 1 10 11415 010-aadzi
+43 10 1 10 1 10 10 1 71 2537 2511 81 0 11 11415 010-aadzi
+44 11 1 11 1 10 10 1 50 1396 1365 82 2 11 11546 010-aaeau
+45 11 1 11 1 10 10 1 69 1896 1858 82 1 11 11546 010-aaeau
+46 11 1 11 1 10 10 1 69 2371 2304 82 0 11 11546 010-aaeau
+47 11 1 11 1 10 10 1 93 2455 2411 82 0 11 11546 010-aaeau
+48 11 1 11 1 10 10 1 69 2591 2569 82 0 11 11546 010-aaeau
+49 11 1 11 1 10 10 1 95 2620 2596 82 0 11 11546 010-aaeau
+50 4 1 4 1 10 10 1 68 594 587 87 1 4 11793 010-aaedz
+51 4 1 4 1 10 10 1 94 2483 2457 87 0 4 11793 010-aaedz
+52 4 1 4 1 10 10 1 98 2968 2944 87 0 4 11793 010-aaedz
+53 4 1 4 1 10 10 1 97 2961 2943 87 0 4 11793 010-aaedz
+54 4 1 4 1 10 10 1 100 2965 2950 87 0 4 11793 010-aaedz
+55 4 1 4 1 10 10 1 100 2973 2961 87 0 4 11793 010-aaedz
+56 4 1 4 1 10 10 1 86 2868 2849 87 0 4 11793 010-aaedz
+57 4 1 4 1 10 10 1 97 2986 2977 87 0 4 11793 010-aaedz
+58 4 1 4 1 10 10 1 100 2979 2965 87 0 4 11793 010-aaedz
+59 4 1 4 1 10 10 1 100 2968 2955 87 0 4 11793 010-aaedz
+60 4.3998 1 4.3998 1 10 10 1 98 2970 2956 87 0 8 11793 010-aaedz
+61 4.72884 1 4.72884 1 10 10 1 100 2989 2983 87 0 8 11793 010-aaedz
+62 5.00294 1 5.00294 1 10 10 1 100 2991 2981 87 0 8 11793 010-aaedz
+63 5.23444 1 5.23444 1 10 10 1 94 2988 2979 87 0 9 11793 010-aaedz
+64 9 1 9 1 10 10 1 56 786 777 88 0 10 11983 010-aaefn
+65 9 1 9 1 10 10 1 63 2019 1993 88 0 9 11983 010-aaefn
+66 9 1 9 1 10 10 1 90 2334 2312 88 0 9 11983 010-aaefn
+67 9 1 9 1 10 10 1 92 2705 2678 88 1 9 11983 010-aaefn
+68 9 1 9 1 10 10 1 60 2506 2476 88 0 10 11983 010-aaefn
+69 9 1 9 1 10 10 1 58 1891 1881 88 2 11 11983 010-aaefn
+70 4 1 4 1 10 10 1 67 726 719 89 1 4 12113 010-aaehc
+71 4 1 4 1 10 10 1 98 2832 2820 89 0 4 12113 010-aaehc
+72 4 1 4 1 10 10 1 98 2974 2956 89 0 4 12113 010-aaehc
+73 4 1 4 1 10 10 1 100 2983 2975 89 0 4 12113 010-aaehc
+74 4 1 4 1 10 10 1 100 2991 2978 89 1 4 12113 010-aaehc
+75 4 1 4 1 10 10 1 99 2987 2969 89 0 4 12113 010-aaehc
+76 4 1 4 1 10 10 1 99 2960 2946 89 0 4 12113 010-aaehc
+77 4 1 4 1 10 10 1 97 2990 2976 89 0 4 12113 010-aaehc
+78 4 1 4 1 10 10 1 100 2997 2988 89 0 4 12113 010-aaehc
+79 4 1 4 1 10 10 1 97 2980 2973 89 0 4 12113 010-aaehc
+80 4.39365 1 4.39365 1 10 10 1 99 2993 2985 89 0 8 12113 010-aaehc
+81 4.70976 1 4.70976 1 10 10 1 97 2922 2912 89 0 9 12113 010-aaehc
+82 4.93837 1 4.93837 1 10 10 1 76 2489 2481 89 1 9 12113 010-aaehc
+83 9 1 9 1 10 10 1 74 1023 1020 90 2 9 12253 010-aaeid
+84 9 1 9 1 10 10 1 100 2605 2597 90 0 9 12253 010-aaeid
+85 9 1 9 1 10 10 1 71 2524 2520 90 1 10 12253 010-aaeid
+86 9 1 9 1 10 10 1 51 1985 1978 90 1 10 12253 010-aaeid
+87 10 1 10 1 10 10 1 93 2267 2264 91 0 10 12276 010-aaeii
+88 10 1 10 1 10 10 1 100 2964 2957 91 0 10 12276 010-aaeii
+89 10 1 10 1 10 10 1 100 2948 2940 91 0 10 12276 010-aaeii
+90 4 1 4 1 10 10 1 86 841 835 93 1 4 12312 010-aaeit
+91 4 1 4 1 10 10 1 100 2965 2953 93 0 4 12312 010-aaeit
+92 4 1 4 1 10 10 1 99 2995 2986 93 0 4 12312 010-aaeit
+93 4 1 4 1 10 10 1 100 2967 2951 93 0 4 12312 010-aaeit
+94 4 1 4 1 10 10 1 99 2995 2984 93 0 4 12312 010-aaeit
+95 4 1 4 1 10 10 1 96 2984 2960 93 0 4 12312 010-aaeit
+96 4 1 4 1 10 10 1 99 2963 2943 93 0 4 12312 010-aaeit
+97 4 1 4 1 10 10 1 99 2954 2931 93 0 4 12312 010-aaeit
+98 4 1 4 1 10 10 1 100 2968 2957 93 0 4 12312 010-aaeit
+99 4 1 4 1 10 10 1 98 2988 2970 93 0 4 12312 010-aaeit
+100 4.3796 1 4.3796 1 10 10 1 90 2896 2886 93 0 9 12312 010-aaeit
Added: development/tests/fitvalley_dynamic_mutrate/expected/data/instruction.dat
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/expected/data/instruction.dat (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/expected/data/instruction.dat 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,98 @@
+# Avida instruction execution data
+# Fri May 25 07:11:17 2007
+# 1: Update
+# 2: nop-B
+# 3: repro
+# 4: repro-B
+
+10 0 65 35
+11 0 85 15
+12 0 51 49
+13 0 52 48
+14 0 85 15
+15 0 94 6
+16 0 84 16
+17 0 79 21
+18 0 91 9
+19 0 98 2
+20 0 67 33
+21 0 93 7
+22 0 98 2
+23 0 100 0
+24 0 78 22
+25 0 74 26
+26 0 26 74
+27 0 2 98
+28 0 11 89
+29 0 7 93
+30 0 11 89
+31 0 4 96
+32 0 2 98
+33 0 0 100
+34 0 2 98
+35 0 1 99
+36 0 1 99
+37 0 0 100
+38 0 2 98
+39 0 1 99
+40 0 0 100
+41 0 0 100
+42 0 0 100
+43 0 0 100
+44 0 0 100
+45 0 0 100
+46 0 2 98
+47 0 0 100
+48 0 9 91
+49 0 0 100
+50 0 0 100
+51 0 1 99
+52 0 1 99
+53 0 0 100
+54 0 0 100
+55 0 0 100
+56 0 10 90
+57 0 0 100
+58 0 0 100
+59 0 0 100
+60 0 0 100
+61 0 0 100
+62 0 0 100
+63 0 0 100
+64 0 0 100
+65 0 10 90
+66 0 0 100
+67 0 0 100
+68 0 0 100
+69 0 0 100
+70 0 2 98
+71 0 0 100
+72 0 0 100
+73 0 0 100
+74 0 0 100
+75 0 0 100
+76 0 0 100
+77 0 0 100
+78 0 0 100
+79 0 0 100
+80 0 0 100
+81 0 0 100
+82 0 0 100
+83 0 1 99
+84 0 0 100
+85 0 0 100
+86 0 0 100
+87 0 0 100
+88 0 0 100
+89 0 0 100
+90 0 100 0
+91 0 100 0
+92 0 100 0
+93 0 100 0
+94 0 100 0
+95 0 100 0
+96 0 100 0
+97 0 100 0
+98 0 100 0
+99 0 100 0
+100 0 91 9
Added: development/tests/fitvalley_dynamic_mutrate/test_list
===================================================================
--- development/tests/fitvalley_dynamic_mutrate/test_list (rev 0)
+++ development/tests/fitvalley_dynamic_mutrate/test_list 2007-05-25 11:08:58 UTC (rev 1607)
@@ -0,0 +1,37 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+args = -s 1 -set CHILD_SIZE_RANGE 1 -set DIVIDE_INS_PROB 0 -set DIVIDE_DEL_PROB 0 -set INST_SET instset-reprosA-B.cfg -set START_CREATURE 10reproAs.org -set BASE_MERIT_METHOD 6 -set WORLD_X 10 -set WORLD_Y 10 -set MERIT_BONUS_INST 2 -set COPY_MUT_PROB .1 -set MERIT_BONUS_EFFECT 1 -set EVENT_FILE events-toggleEvery10.cfg -v2 -set META_COPY_MUT .5 -set META_STD_DEV .1 -set MUT_RATE_SOURCE 2 -set NUM_DEMES 1 -set FITNESS_VALLEY 1 -set FITNESS_VALLEY_START 5 -set FITNESS_VALLEY_STOP 6
+
+ ; Command line arguments to pass to the application
+app = %(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 = Jeff Clune ; Who created the test
+email = jclune at 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.
+;
+; app
+; builddir
+; cpus
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
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