[Avida-SVN] r1609 - in development/tests: . bgs_dyn_mutrates_rank bgs_dyn_mutrates_rank/config bgs_dyn_mutrates_rank/expected bgs_dyn_mutrates_rank/expected/data
jclune at myxo.css.msu.edu
jclune at myxo.css.msu.edu
Fri May 25 04:51:30 PDT 2007
Author: jclune
Date: 2007-05-25 07:51:30 -0400 (Fri, 25 May 2007)
New Revision: 1609
Added:
development/tests/bgs_dyn_mutrates_rank/
development/tests/bgs_dyn_mutrates_rank/config/
development/tests/bgs_dyn_mutrates_rank/config/avida.cfg
development/tests/bgs_dyn_mutrates_rank/config/environment.77
development/tests/bgs_dyn_mutrates_rank/config/events-Test-RankSelection.cfg
development/tests/bgs_dyn_mutrates_rank/config/inst_set.divide
development/tests/bgs_dyn_mutrates_rank/config/org.div1
development/tests/bgs_dyn_mutrates_rank/config/org.div10
development/tests/bgs_dyn_mutrates_rank/config/org.div100
development/tests/bgs_dyn_mutrates_rank/config/org.div3
development/tests/bgs_dyn_mutrates_rank/config/org.div32
development/tests/bgs_dyn_mutrates_rank/expected/
development/tests/bgs_dyn_mutrates_rank/expected/data/
development/tests/bgs_dyn_mutrates_rank/expected/data/average.dat
development/tests/bgs_dyn_mutrates_rank/expected/data/count.dat
development/tests/bgs_dyn_mutrates_rank/expected/data/creature.final
development/tests/bgs_dyn_mutrates_rank/expected/data/detail-100.pop
development/tests/bgs_dyn_mutrates_rank/expected/data/divide_mut.dat
development/tests/bgs_dyn_mutrates_rank/expected/data/dominant.dat
development/tests/bgs_dyn_mutrates_rank/expected/data/historic-100.pop
development/tests/bgs_dyn_mutrates_rank/expected/data/instruction.dat
development/tests/bgs_dyn_mutrates_rank/expected/data/resource.dat
development/tests/bgs_dyn_mutrates_rank/expected/data/stats.dat
development/tests/bgs_dyn_mutrates_rank/expected/data/tasks.dat
development/tests/bgs_dyn_mutrates_rank/expected/data/time.dat
development/tests/bgs_dyn_mutrates_rank/test_list
Log:
adding bgs_dyn_mutrates_rank test
Added: development/tests/bgs_dyn_mutrates_rank/config/avida.cfg
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/avida.cfg (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/avida.cfg 2007-05-25 11:51:30 UTC (rev 1609)
@@ -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/bgs_dyn_mutrates_rank/config/environment.77
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/environment.77 (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/environment.77 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,92 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# this environmental setup rewards all one-, two- and three-input logic
+# operations available.
+#
+# 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=1.0:type=pow requisite:max_count=1
+REACTION ORN orn process:value=1.0:type=pow requisite:max_count=1
+REACTION OR or process:value=1.0:type=pow requisite:max_count=1
+REACTION ANDN andn process:value=1.0:type=pow requisite:max_count=1
+REACTION NOR nor process:value=1.0:type=pow requisite:max_count=1
+REACTION XOR xor process:value=1.0:type=pow requisite:max_count=1
+REACTION EQU equ process:value=1.0:type=pow requisite:max_count=1
+
+REACTION LOG3AA logic_3AA process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AB logic_3AB process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AC logic_3AC process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AD logic_3AD process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AE logic_3AE process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AF logic_3AF process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AG logic_3AG process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AH logic_3AH process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AI logic_3AI process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AJ logic_3AJ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AK logic_3AK process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AL logic_3AL process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AM logic_3AM process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AN logic_3AN process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AO logic_3AO process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AP logic_3AP process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AQ logic_3AQ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AR logic_3AR process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AS logic_3AS process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AT logic_3AT process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AU logic_3AU process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AV logic_3AV process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AW logic_3AW process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AX logic_3AX process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AY logic_3AY process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AZ logic_3AZ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BA logic_3BA process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BB logic_3BB process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BC logic_3BC process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BD logic_3BD process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BE logic_3BE process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BF logic_3BF process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BG logic_3BG process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BH logic_3BH process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BI logic_3BI process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BJ logic_3BJ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BK logic_3BK process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BL logic_3BL process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BM logic_3BM process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BN logic_3BN process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BO logic_3BO process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BP logic_3BP process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BQ logic_3BQ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BR logic_3BR process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BS logic_3BS process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BT logic_3BT process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BU logic_3BU process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BV logic_3BV process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BW logic_3BW process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BX logic_3BX process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BY logic_3BY process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BZ logic_3BZ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CA logic_3CA process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CB logic_3CB process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CC logic_3CC process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CD logic_3CD process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CE logic_3CE process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CF logic_3CF process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CG logic_3CG process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CH logic_3CH process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CI logic_3CI process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CJ logic_3CJ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CK logic_3CK process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CL logic_3CL process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CM logic_3CM process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CN logic_3CN process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CO logic_3CO process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CP logic_3CP process:value=1.0:type=pow requisite:max_count=1
Added: development/tests/bgs_dyn_mutrates_rank/config/events-Test-RankSelection.cfg
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/events-Test-RankSelection.cfg (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/events-Test-RankSelection.cfg 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,776 @@
+u 0 inject_range org.div1 1 180 # Inject all the begining
+u 0 inject_range org.div3 181 360 # Inject all the begining
+u 0 inject_range org.div10 361 540 # Inject all the begining
+u 0 inject_range org.div32 541 720 # Inject all the begining
+u 0 inject_range org.div100 721 900 # Inject all the begining
+
+u 10:1:end print_divide_mut_data
+u 20:1:end print_instruction_data
+#u 100:100:end print_deme_stats
+
+# Print all of the standard data files...
+u 0:1:end print_average_data # Save info about they average genotypes
+u 0:10:end print_dominant_data # Save info about most abundant genotypes
+u 0:10:end print_stats_data # Collect satistics about entire pop.
+u 0:10:end print_count_data # Count organisms, genotypes, species, etc.
+u 0:10:end print_tasks_data # Save organisms counts for each task.
+u 0:10:end print_time_data # Track time conversion (generations, etc.)
+u 0:10:end print_resource_data # Track resource abundance.
+
+# A few data files not printed by default
+# u 100:100:end print_totals_data # Total counts over entire run.
+# u 100:100:end print_tasks_exe_data # Num. times tasks have been executed.
+
+
+# Setup the exit time and full population data collection.
+u 100:100 detail_pop # Save current state of population.
+u 100:100 dump_historic_pop # Save ancestors of current population.
+
+u 100 print_dom creature.final
+u 100 exit # exit
+
+u 50:50 compete_demes 4
+
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Property changes on: development/tests/bgs_dyn_mutrates_rank/config/events-Test-RankSelection.cfg
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_rank/config/inst_set.divide
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/inst_set.divide (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/inst_set.divide 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,56 @@
+nop-A 1 # a
+nop-B 1 # b
+nop-C 1 # c
+if-n-equ 1 # d
+if-less 1 # e
+pop 1 # f
+push 1 # g
+swap-stk 1 # h
+swap 1 # i
+shift-r 1 # j
+shift-l 1 # k
+inc 1 # l
+dec 1 # m
+add 1 # n
+sub 1 # o
+nand 1 # p
+IO 1 # q Puts current contents of register and gets new.
+h-alloc 1 # r Allocate as much memory as organism can use.
+h-divide1 1
+h-divide3 1
+h-divide10 1
+h-divide32 1
+h-divide100 1
+h-copy 1 # t Combine h-read and h-write
+h-search 1 # u Search for matching template, set flow head & return info
+ # # if no template, move flow-head here, set size&offset=0.
+mov-head 1 # v Move ?IP? head to flow control.
+jmp-head 1 # w Move ?IP? head by fixed amount in CX. Set old pos in CX.
+get-head 1 # x Get position of specified head in CX.
+if-label 1 # y
+set-flow 1 # z Move flow-head to address in ?CX?
+
+#adv-head 1
+#jump-f 1
+#jump-b 1
+#call 1
+#return 1
+#if-bit-1 1
+#get 1
+#put 1
+#h-read 1
+#h-write 1
+#set-head 1
+#search-f 1
+#search-b 1
+
+
+# Works on multiple nops: pop push inc dec IO adv-head
+
+# What if we add a new head. Search will return the location of something,
+# and put the new head there. Then set-head will move another head to that
+# point. In the case of the copy loop, it only needs to be set once and
+# this will speed up the code quite a bit!
+
+# Search with no template returns current position (abs line number) in
+# genome.
Property changes on: development/tests/bgs_dyn_mutrates_rank/config/inst_set.divide
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_rank/config/org.div1
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/org.div1 (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/org.div1 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+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-divide1 # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Property changes on: development/tests/bgs_dyn_mutrates_rank/config/org.div1
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_rank/config/org.div10
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/org.div10 (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/org.div10 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+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-divide10 # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Property changes on: development/tests/bgs_dyn_mutrates_rank/config/org.div10
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_rank/config/org.div100
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/org.div100 (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/org.div100 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+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-divide100 # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Property changes on: development/tests/bgs_dyn_mutrates_rank/config/org.div100
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_rank/config/org.div3
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/org.div3 (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/org.div3 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+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-divide3 # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Property changes on: development/tests/bgs_dyn_mutrates_rank/config/org.div3
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_rank/config/org.div32
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/config/org.div32 (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/config/org.div32 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+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-divide32 # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Property changes on: development/tests/bgs_dyn_mutrates_rank/config/org.div32
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/average.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/average.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/average.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,120 @@
+# Avida Average Data
+# Fri May 25 07:54:14 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)
+
+0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 896.000000 896.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+1 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+2 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+3 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+4 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+5 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+6 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+7 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+8 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+9 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+10 97 389 0 0 100 100 97 179.2 0 0 0 0 0 0 0
+11 97 389 0.000556601 0 100 100 97 179.2 0.00111607 0.00111607 0 0.00223214 -0.00215342 0 0
+12 97 389 0.0381272 0 100 100 97 30.8966 0.0792411 0.0502232 0.0267857 0.152902 0.0257954 0 0
+13 97 389 0.164942 0 100 100 97 7.54622 0.319599 0.194878 0.128062 0.66147 -0.0318188 0 0
+14 97 389 0.242138 0 100 100 97 5.31361 0.256125 0.157016 0.183742 0.971047 -0.0151829 0 0
+15 97 389 0.249357 0 100 100 97 5.16092 0.0289532 0.0200445 0.18931 1 -0.0104307 0 0
+16 97 389 0.249357 0 100 100 97 5.16092 0 0 0.18931 1 -0.0104307 0 0
+17 97 389 0.249357 0 100 100 97 5.16092 0 0 0.18931 1 -0.0104307 0 0
+18 97 389 0.249357 0 100 100 97 5.16092 0 0 0.18931 1 -0.0104307 0 0
+19 97 389 0.249357 0 100 100 97 5.16092 0 0 0.18931 1 -0.0104307 0 0
+20 97 389 0.249357 0 100 100 97 5.16092 0 0 0.18931 1 -0.0104307 0 0
+21 97 389 0.249357 0 100 100 97 5.16092 0 0 0.18931 1 -0.0104307 0 0
+22 97 389 0.249357 0 100 100 97 5.16092 0 0 0.18931 1 -0.0104307 0 0
+23 97 389 0.249357 0 100 100 97 5.16092 0.00222717 0.00222717 0.18931 1.00445 -0.018337 0 0
+24 96.9955 388.987 0.249354 0 100 100 96.9955 5.04494 0.0155902 0.0100223 0.195991 1.03563 0.00517026 0 0
+25 96.9399 388.888 0.249273 0 100 100 96.9399 4.495 0.120133 0.0823137 0.232481 1.2525 0.00922104 0 0
+26 96.8756 388.73 0.249205 0 100 100 96.8756 3.65854 0.276667 0.156667 0.315556 1.67778 0.0434728 0 0
+27 96.8356 388.663 0.249142 0 100 100 96.8356 3.40909 0.195556 0.13 0.344444 1.90778 0.0515035 0 0
+28 96.8356 388.648 0.249152 0 100 100 96.8356 3.37079 0.0477778 0.03 0.351111 1.96111 0.0785301 0 0
+29 96.8356 388.648 0.249152 0 100 100 96.8356 3.35821 0.00444444 0.00222222 0.352222 1.96556 0.0689094 0 0
+30 96.8378 388.866 0.249046 0 100 100 96.8378 3.34572 0.00111111 0 0.354444 1.96667 0.0640394 0 0
+31 96.8422 389.739 0.24868 0 100 100 96.8422 3.34572 0.00222222 0.00111111 0.354444 1.96889 0.053943 0 0
+32 96.8444 390.181 0.248497 0 100 100 96.8444 3.33333 0.00111111 0 0.356667 1.97 0.0482526 0 0
+33 96.8467 390.619 0.248314 0 100 100 96.8467 3.32103 0.00111111 0 0.358889 1.97111 0.0451492 0 0
+34 96.8467 390.619 0.248314 0 100 100 96.8467 3.32103 0 0 0.358889 1.97111 0.0451492 0 0
+35 96.8467 390.619 0.248314 0 100 100 96.8467 3.32103 0.00111111 0.00111111 0.358889 1.97333 0.0420207 0 0
+36 96.8422 390.388 0.248404 0 100 100 96.8422 3.32103 0.00555556 0.00333333 0.36 1.98444 0.0515274 0 0
+37 96.8333 390.37 0.248392 0 100 100 96.8333 3.26087 0.0411111 0.0277778 0.368889 2.06222 0.0884813 0 0
+38 96.7822 390.271 0.248319 0 100 100 96.7822 3.14685 0.14 0.0844444 0.402222 2.30778 0.107572 0 0
+39 96.67 389.689 0.248306 0 100 100 96.67 3.02013 0.231111 0.154444 0.444444 2.65333 0.0957738 0 0
+40 96.6711 389.404 0.248444 0 100 100 96.6711 2.90323 0.163333 0.111111 0.495556 2.85222 0.0645978 0 0
+41 96.66 389.388 0.248426 0 100 100 96.66 2.85714 0.0633333 0.0422222 0.512222 2.92889 0.0403426 0 0
+42 96.6478 389.589 0.248271 0 100 100 96.6478 2.83019 0.0144444 0.00333333 0.517778 2.94556 0.0309077 0 0
+43 96.6478 389.589 0.248271 0 100 100 96.6478 2.83019 0.00222222 0.00222222 0.517778 2.94778 0.033999 0 0
+44 96.6478 389.589 0.248271 0 100 100 96.6478 2.83019 0 0 0.517778 2.94778 0.033999 0 0
+45 96.6478 389.589 0.248271 0 100 100 96.6478 2.83019 0 0 0.517778 2.94778 0.033999 0 0
+46 96.6544 389.814 0.248171 0 100 100 96.6544 2.83019 0.00222222 0.00111111 0.521111 2.95 0.0332359 0 0
+47 96.6544 389.814 0.248171 0 100 100 96.6544 2.83912 0.00111111 0.00111111 0.52 2.95222 0.0339138 0 0
+48 96.6567 390.477 0.247934 0 100 100 96.6567 2.83912 0.00111111 0 0.521111 2.95333 0.0266612 0 0
+49 96.6567 390.478 0.247934 0 100 100 96.6567 2.82132 0.0133333 0.01 0.523333 2.97889 0.00164156 0 0
+50 96.6467 390.459 0.247921 0 100 100 96.6467 2.77778 0.0644444 0.0411111 0.541111 3.10111 0.0361112 0 0
+51 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+52 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+53 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+54 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+55 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+56 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+57 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+58 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+59 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+60 96.9844 388.61 0.249568 0 100 100 96.9844 16.6667 0 0 0.46 3.27889 -0.343262 -1 0
+61 96.9844 388.606 0.249571 0 100 100 96.9844 16.6667 0.00333333 0.00333333 0.462222 3.28667 -0.335399 -1 0
+62 96.9844 388.589 0.249582 0 100 100 96.9844 13.8462 0.0555556 0.0433333 0.477778 3.39889 -0.329548 -1 0
+63 96.9822 388.528 0.249616 0 100 100 96.9822 7.31707 0.365556 0.28 0.531111 3.96667 -0.426185 -1 0
+64 96.9822 388.499 0.249634 0 100 100 96.9822 6 0.23 0.178889 0.565556 4.24667 -0.445957 -1 0
+65 96.9822 388.5 0.249634 0 100 100 96.9822 6 0.03 0.0277778 0.56 4.27667 -0.425134 -1 0
+66 96.9822 388.5 0.249634 0 100 100 96.9822 6 0 0 0.56 4.27667 -0.425134 -1 0
+67 96.9822 388.5 0.249634 0 100 100 96.9822 6 0 0 0.56 4.27667 -0.425134 -1 0
+68 96.9822 388.5 0.249634 0 100 100 96.9822 6 0 0 0.56 4.27667 -0.425134 -1 0
+69 96.9822 388.5 0.249634 0 100 100 96.9822 6 0 0 0.56 4.27667 -0.425134 -1 0
+70 96.9822 388.5 0.249634 0 100 100 96.9822 6 0 0 0.56 4.27667 -0.425134 -1 0
+71 96.9822 388.5 0.249634 0 100 100 96.9822 6 0 0 0.56 4.27667 -0.425134 -1 0
+72 96.9822 388.5 0.249634 0 100 100 96.9822 6 0 0 0.56 4.27667 -0.425134 -1 0
+73 96.9822 388.5 0.249634 0 100 100 96.9822 6 0 0 0.56 4.27667 -0.425134 -1 0
+74 96.9822 388.498 0.249635 0 100 100 96.9822 5.88235 0.0188889 0.0155556 0.565556 4.31556 -0.433299 -1 0
+75 96.9822 388.452 0.249665 0 100 100 96.9822 5.11364 0.141111 0.0966667 0.598889 4.57333 -0.457407 -1 0
+76 96.9311 388.366 0.249586 0 100 100 96.9311 4.39024 0.264444 0.197778 0.658889 4.96222 -0.441105 -1 0
+77 96.9156 388.324 0.249572 0 100 100 96.9156 4.16667 0.196667 0.153333 0.676667 5.19667 -0.487411 -1 0
+78 96.9156 388.34 0.249562 0 100 100 96.9156 4.24528 0.0588889 0.0511111 0.663333 5.25444 -0.451579 -1 0
+79 96.9156 388.349 0.249556 0 100 100 96.9156 4.20561 0.0111111 0.00777778 0.663333 5.27 -0.44143 -1 0
+80 96.9156 388.349 0.249556 0 100 100 96.9156 4.20561 0 0 0.663333 5.27 -0.44143 -1 0
+81 96.9178 388.812 0.249366 0 100 100 96.9178 4.22535 0.00111111 0.00111111 0.663333 5.27222 -0.443092 -1 0
+82 96.92 389.248 0.249183 0 100 100 96.92 4.24528 0.00111111 0.00111111 0.663333 5.27333 -0.446338 -1 0
+83 96.92 389.248 0.249183 0 100 100 96.92 4.24528 0 0 0.663333 5.27333 -0.446338 -1 0
+84 96.92 389.248 0.249183 0 100 100 96.92 4.24528 0 0 0.663333 5.27333 -0.446338 -1 0
+85 96.92 389.248 0.249183 0 100 100 96.92 4.24528 0 0 0.663333 5.27333 -0.446338 -1 0
+86 96.92 389.249 0.249182 0 100 100 96.92 4.24528 0.00555556 0.00444444 0.668889 5.28556 -0.454676 -1 0
+87 96.92 389.247 0.249183 0 100 100 96.92 4.16667 0.05 0.0366667 0.674444 5.38 -0.43287 -1 0
+88 96.8578 389.118 0.249102 0 100 100 96.8578 4.09091 0.146667 0.122222 0.708889 5.64444 -0.405992 -1 0
+89 96.8633 388.887 0.24922 0 100 100 96.8633 3.9823 0.198889 0.153333 0.733333 5.94333 -0.413989 -1 0
+90 96.8522 388.857 0.24921 0 100 100 96.8522 3.94737 0.177778 0.146667 0.752222 6.16778 -0.431648 -1 0
+91 96.8522 388.872 0.2492 0 100 100 96.8522 3.82979 0.0666667 0.0488889 0.753333 6.23889 -0.433617 -1 0
+92 96.85 388.866 0.249199 0 100 100 96.85 3.81356 0.0166667 0.0155556 0.755556 6.25667 -0.422058 -1 0
+93 96.8522 389.088 0.24909 0 100 100 96.8522 3.82979 0.00555556 0.00444444 0.755556 6.26778 -0.415558 -1 0
+94 96.8544 389.528 0.248907 0 100 100 96.8544 3.81356 0.00111111 0 0.756667 6.26778 -0.421912 -1 0
+95 96.8544 389.528 0.248907 0 100 100 96.8544 3.81356 0 0 0.756667 6.26778 -0.421912 -1 0
+96 96.8567 389.969 0.248723 0 100 100 96.8567 3.79747 0.00111111 0 0.758889 6.26889 -0.419405 -1 0
+97 96.8567 389.969 0.248723 0 100 100 96.8567 3.79747 0 0 0.758889 6.26889 -0.419405 -1 0
+98 96.8567 390.406 0.248537 0 100 100 96.8567 3.81356 0.00111111 0.00111111 0.76 6.27 -0.414205 -1 0
+99 96.8567 390.402 0.248539 0 100 100 96.8567 3.78151 0.0177778 0.0133333 0.765556 6.30667 -0.456056 -1 0
+100 96.8844 390.631 0.248511 0 100 100 96.8844 3.68852 0.0733333 0.05 0.785556 6.44778 -0.403335 -1 0
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/count.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/count.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/count.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,30 @@
+# Avida count data
+# Fri May 25 07:54:14 2007
+# 1: update
+# 2: number of insts executed this update
+# 3: number of organisms
+# 4: number of different genotypes
+# 5: number of different threshold genotypes
+# 6: number of different species
+# 7: number of different threshold species
+# 8: number of different lineages
+# 9: number of births in this update
+# 10: number of deaths in this update
+# 11: number of breed true
+# 12: number of breed true organisms?
+# 13: number of no-birth organisms
+# 14: number of single-threaded organisms
+# 15: number of multi-threaded organisms
+# 16: number of modified organisms
+
+0 30 1 1 5 0 0 0 896 0 896 1 1 1 0 0
+10 26880 896 5 5 0 0 0 0 0 0 896 896 896 0 0
+20 26940 898 174 5 0 0 0 0 0 0 727 461 898 0 0
+30 27000 900 269 5 0 0 0 1 1 0 644 459 900 0 0
+40 27000 900 310 7 0 0 0 147 147 100 610 479 900 0 0
+50 27000 900 324 9 0 0 0 58 58 37 598 491 900 0 0
+60 27000 900 54 41 0 0 0 0 0 0 289 900 900 0 0
+70 27000 900 150 47 0 0 0 0 0 0 486 449 900 0 0
+80 27000 900 214 45 0 0 0 0 0 0 589 479 900 0 0
+90 27000 900 228 46 0 0 0 160 160 132 636 451 900 0 0
+100 27000 900 244 48 0 0 0 66 66 45 638 465 900 0 0
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/creature.final
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/creature.final (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/creature.final 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,202 @@
+# Fri May 25 07:54:18 2007
+# Filename........: creature.final
+# Update Output...: 100
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+# Update Created..: 0
+# Genotype ID.....: 5
+# Parent Gen ID...: -1
+# Tree Depth......: 0
+# Parent Distance.: -1
+#
+# Generation: 0
+# Merit...........: 97.000000
+# Gestation Time..: 389
+# Fitness.........: 0.249357
+# Errors..........: 0
+# Genome Size.....: 100
+# Copied Size.....: 100
+# Executed Size...: 97
+# Offspring.......: SELF
+#
+# Tasks Performed:
+# not 0 (0.000000)
+# nand 0 (0.000000)
+# and 0 (0.000000)
+# orn 0 (0.000000)
+# or 0 (0.000000)
+# andn 0 (0.000000)
+# nor 0 (0.000000)
+# xor 0 (0.000000)
+# equ 0 (0.000000)
+# logic_3AA 0 (0.000000)
+# logic_3AB 0 (0.000000)
+# logic_3AC 0 (0.000000)
+# logic_3AD 0 (0.000000)
+# logic_3AE 0 (0.000000)
+# logic_3AF 0 (0.000000)
+# logic_3AG 0 (0.000000)
+# logic_3AH 0 (0.000000)
+# logic_3AI 0 (0.000000)
+# logic_3AJ 0 (0.000000)
+# logic_3AK 0 (0.000000)
+# logic_3AL 0 (0.000000)
+# logic_3AM 0 (0.000000)
+# logic_3AN 0 (0.000000)
+# logic_3AO 0 (0.000000)
+# logic_3AP 0 (0.000000)
+# logic_3AQ 0 (0.000000)
+# logic_3AR 0 (0.000000)
+# logic_3AS 0 (0.000000)
+# logic_3AT 0 (0.000000)
+# logic_3AU 0 (0.000000)
+# logic_3AV 0 (0.000000)
+# logic_3AW 0 (0.000000)
+# logic_3AX 0 (0.000000)
+# logic_3AY 0 (0.000000)
+# logic_3AZ 0 (0.000000)
+# logic_3BA 0 (0.000000)
+# logic_3BB 0 (0.000000)
+# logic_3BC 0 (0.000000)
+# logic_3BD 0 (0.000000)
+# logic_3BE 0 (0.000000)
+# logic_3BF 0 (0.000000)
+# logic_3BG 0 (0.000000)
+# logic_3BH 0 (0.000000)
+# logic_3BI 0 (0.000000)
+# logic_3BJ 0 (0.000000)
+# logic_3BK 0 (0.000000)
+# logic_3BL 0 (0.000000)
+# logic_3BM 0 (0.000000)
+# logic_3BN 0 (0.000000)
+# logic_3BO 0 (0.000000)
+# logic_3BP 0 (0.000000)
+# logic_3BQ 0 (0.000000)
+# logic_3BR 0 (0.000000)
+# logic_3BS 0 (0.000000)
+# logic_3BT 0 (0.000000)
+# logic_3BU 0 (0.000000)
+# logic_3BV 0 (0.000000)
+# logic_3BW 0 (0.000000)
+# logic_3BX 0 (0.000000)
+# logic_3BY 0 (0.000000)
+# logic_3BZ 0 (0.000000)
+# logic_3CA 0 (0.000000)
+# logic_3CB 0 (0.000000)
+# logic_3CC 0 (0.000000)
+# logic_3CD 0 (0.000000)
+# logic_3CE 0 (0.000000)
+# logic_3CF 0 (0.000000)
+# logic_3CG 0 (0.000000)
+# logic_3CH 0 (0.000000)
+# logic_3CI 0 (0.000000)
+# logic_3CJ 0 (0.000000)
+# logic_3CK 0 (0.000000)
+# logic_3CL 0 (0.000000)
+# logic_3CM 0 (0.000000)
+# logic_3CN 0 (0.000000)
+# logic_3CO 0 (0.000000)
+# logic_3CP 0 (0.000000)
+
+
+h-alloc
+h-search
+nop-C
+nop-A
+mov-head
+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
+h-copy
+if-label
+nop-C
+nop-A
+h-divide100
+mov-head
+nop-A
+nop-B
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/detail-100.pop
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/detail-100.pop (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/detail-100.pop 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,261 @@
+#filetype genotype_data
+#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
+
+# 1: ID
+# 2: parent ID
+# 3: parent distance
+# 4: number of orgranisms currently alive
+# 5: total number of organisms that ever existed
+# 6: length of genome
+# 7: merit
+# 8: gestation time
+# 9: fitness
+# 10: update born
+# 11: update deactivated
+# 12: depth in phylogentic tree
+# 13: genome of organism
+
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+1131 295 1 1 1 100 0 0 0 100 -1 3 rycazcccccccccccccccccccccccccccrccccccccccccccccccccccccccccccccccccccccccccccpcccccccceccyxCcatzab
+1132 1042 1 1 1 100 0 0 0 100 -1 2 rycazcccccccccccccccccccccccccccccccccbccccccccccccccccccccccccccccccscccccccccccccccccccccyxCcauzab
+816 647 1 1 3 100 97 388 0.25 64 -1 2 rycazcccccccccocccccccccccccaccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
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+1134 427 2 1 1 100 0 0 0 100 -1 2 rycazcccccccccccccccccccccccccccccccccccccccccccicccccccccccccccccccccccccccccccccccccccjccyxCcaumab
+1135 688 1 1 1 100 0 0 0 100 -1 2 rycazcccccckcccccccccccccccccccccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+1136 7 1 1 1 100 0 0 0 100 -1 2 rycazcccccccccscsccccccccccccccccccccccccccccccccDcccccccccccccccccccccccccccccccccccccccccyxCcatzab
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/divide_mut.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/divide_mut.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/divide_mut.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,105 @@
+# Avida divide mutation rate data
+# Fri May 25 07:54:15 2007
+# 1: Update
+# 2: Average divide mutation rate
+# 3: Variance in divide mutation rate
+# 4: Standard Deviation in divide mutation rate
+# 5: Skew in divide mutation rate
+# 6: Kurtosis in divide mutation rate
+# 7: Average log(divide mutation rate)
+# 8: Variance in log(divide mutation rate)
+# 9: Standard Deviation in log(divide mutation rate)
+# 10: Skew in log(divide mutation rate)
+# 11: Kurtosis in log(divide mutation rate)
+
+10 0.030000 -0.000000 nan -0.000000 0.000000 -3.506558 -0.000000 nan -0.000000 -0.000000
+11 0.0299337 1.96675e-06 0.00140241 -5.82818e-08 1.73485e-09 -3.50749 0.00430262 0.0655943 -0.0198103 0.0912481
+12 0.0267717 7.58256e-05 0.00870779 -1.58371e-06 3.99535e-08 -3.53608 0.101406 0.318443 -0.387601 1.58638
+13 0.0158633 0.000181666 0.0134783 5.30618e-08 3.7163e-08 -3.65273 0.48898 0.699271 -1.76534 7.06855
+14 0.00951718 0.000132772 0.0115227 1.60374e-06 4.25027e-08 -3.80058 0.933575 0.966217 -3.08857 11.9984
+15 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -3.934 1.29905 1.13976 -3.96843 15.1177
+16 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.05071 1.58957 1.26078 -4.50889 16.9653
+17 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.15367 1.82323 1.35027 -4.82402 18.0326
+18 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.24518 2.01311 1.41884 -4.98801 18.6144
+19 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.32703 2.16877 1.47267 -5.04997 18.8915
+20 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.4007 2.29739 1.51571 -5.04299 18.9769
+21 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.46734 2.40439 1.55061 -4.98963 18.9422
+22 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.52791 2.49395 1.57923 -4.90545 18.8333
+23 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.58321 2.56931 1.60291 -4.80127 18.6801
+24 0.00886353 0.000124009 0.011136 1.63333e-06 4.24349e-08 -4.6339 2.633 1.62265 -4.68466 18.5018
+25 0.008854 0.000123953 0.0111334 1.63435e-06 4.24559e-08 -4.68068 2.68746 1.63935 -4.56129 18.3137
+26 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.724 2.73399 1.65348 -4.43353 18.1186
+27 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.7641 2.77372 1.66545 -4.30489 17.9243
+28 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.80134 2.80772 1.67563 -4.17723 17.7342
+29 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.83599 2.83688 1.6843 -4.05185 17.5505
+30 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.86833 2.86192 1.69172 -3.92959 17.3742
+31 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.89858 2.88345 1.69807 -3.81102 17.2059
+32 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.92693 2.90197 1.70352 -3.69647 17.0459
+33 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.95356 2.9179 1.70818 -3.58614 16.8941
+34 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -4.97862 2.93159 1.71219 -3.48008 16.7503
+35 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.00225 2.94335 1.71562 -3.3783 16.6141
+36 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.02456 2.95343 1.71855 -3.28072 16.4852
+37 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.04566 2.96205 1.72106 -3.18725 16.3632
+38 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.06565 2.96939 1.72319 -3.09775 16.2477
+39 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.08461 2.97562 1.725 -3.01208 16.1382
+40 0.00882736 0.000123989 0.011135 1.64113e-06 4.25936e-08 -5.10269 2.98095 1.72654 -2.92967 16.034
+41 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.11981 2.98534 1.72781 -2.85119 15.9355
+42 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.13613 2.98897 1.72886 -2.77606 15.842
+43 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.15168 2.99194 1.72972 -2.70413 15.7531
+44 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.16652 2.99432 1.73041 -2.63523 15.6685
+45 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.1807 2.99618 1.73095 -2.56922 15.5879
+46 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.19427 2.99758 1.73135 -2.50596 15.5111
+47 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.20726 2.99858 1.73164 -2.44529 15.4378
+48 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.2197 2.99922 1.73183 -2.3871 15.3678
+49 0.00883743 0.000123921 0.011132 1.63793e-06 4.25229e-08 -5.23164 2.99955 1.73192 -2.33125 15.3008
+50 0.00882188 0.000123994 0.0111352 1.64328e-06 4.2628e-08 -5.24315 2.99959 1.73193 -2.27717 15.2363
+51 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.27098 3.02079 1.73804 -2.19983 15.3059
+52 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.29774 3.03972 1.74348 -2.12225 15.3629
+53 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.32348 3.05658 1.74831 -2.04484 15.409
+54 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.34828 3.07157 1.75259 -1.96793 15.4458
+55 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.37216 3.08484 1.75637 -1.8918 15.4745
+56 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.3952 3.09656 1.7597 -1.81667 15.496
+57 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.41742 3.10686 1.76263 -1.74271 15.5114
+58 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.43888 3.11587 1.76518 -1.67006 15.5214
+59 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.45961 3.12369 1.7674 -1.59883 15.5266
+60 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.47965 3.13044 1.76931 -1.5291 15.5276
+61 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.49903 3.13621 1.77093 -1.46093 15.5249
+62 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.5178 3.14106 1.7723 -1.39418 15.5188
+63 0.00317236 1.40375e-05 0.00374666 5.70109e-08 5.02507e-10 -5.53602 3.14505 1.77343 -1.3287 15.5096
+64 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.55363 3.14832 1.77435 -1.26525 15.4981
+65 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.5707 3.15089 1.77507 -1.20345 15.4844
+66 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.58725 3.15283 1.77562 -1.1433 15.4686
+67 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.6033 3.15419 1.776 -1.0848 15.451
+68 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.61888 3.15501 1.77624 -1.02791 15.4317
+69 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.63401 3.15535 1.77633 -0.972625 15.4111
+70 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.64871 3.15524 1.7763 -0.91891 15.3891
+71 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.66299 3.15471 1.77615 -0.866737 15.366
+72 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.67688 3.15381 1.7759 -0.816074 15.3418
+73 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.69038 3.15257 1.77555 -0.766887 15.3166
+74 0.00318792 1.41409e-05 0.00376043 5.70592e-08 5.03787e-10 -5.70352 3.15101 1.77511 -0.719142 15.2907
+75 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.71627 3.14919 1.7746 -0.673099 15.2641
+76 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.72871 3.1471 1.77401 -0.628269 15.2367
+77 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.74082 3.14476 1.77335 -0.584766 15.2087
+78 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.7526 3.14221 1.77263 -0.542693 15.1802
+79 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.76408 3.13947 1.77185 -0.501869 15.1513
+80 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.77528 3.13654 1.77103 -0.462257 15.1218
+81 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.7862 3.13344 1.77015 -0.423822 15.092
+82 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.79685 3.13018 1.76923 -0.386528 15.0617
+83 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.80725 3.12679 1.76827 -0.350341 15.0312
+84 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.8174 3.12326 1.76728 -0.315228 15.0004
+85 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.82731 3.11963 1.76625 -0.281154 14.9693
+86 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.83699 3.11588 1.76519 -0.248088 14.938
+87 0.00321125 1.42951e-05 0.00378088 5.71135e-08 5.0562e-10 -5.84643 3.11206 1.7641 -0.216117 14.9065
+88 0.00321125 1.42951e-05 0.00378088 5.71135e-08 5.0562e-10 -5.85565 3.10816 1.763 -0.185087 14.8748
+89 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.8647 3.10414 1.76186 -0.154738 14.843
+90 0.00319569 1.41924e-05 0.00376728 5.70797e-08 5.04409e-10 -5.87355 3.10005 1.7607 -0.12528 14.811
+91 0.00320347 1.42438e-05 0.00377409 5.70978e-08 5.0502e-10 -5.88219 3.09592 1.75952 -0.0967943 14.7789
+92 0.00321125 1.42951e-05 0.00378088 5.71135e-08 5.0562e-10 -5.89062 3.09176 1.75834 -0.0692488 14.7468
+93 0.00321125 1.42951e-05 0.00378088 5.71135e-08 5.0562e-10 -5.89888 3.08754 1.75714 -0.0425037 14.7146
+94 0.00326347 1.58375e-05 0.00397964 9.7142e-08 1.63599e-09 -5.90691 3.0834 1.75596 -0.0166044 14.6831
+95 0.00326347 1.58375e-05 0.00397964 9.7142e-08 1.63599e-09 -5.91478 3.07923 1.75477 0.0085528 14.6516
+96 0.00326347 1.58375e-05 0.00397964 9.7142e-08 1.63599e-09 -5.92249 3.07502 1.75357 0.0329916 14.62
+97 0.00326347 1.58375e-05 0.00397964 9.7142e-08 1.63599e-09 -5.93003 3.07078 1.75236 0.0567348 14.5884
+98 0.00326347 1.58375e-05 0.00397964 9.7142e-08 1.63599e-09 -5.93742 3.06652 1.75115 0.0798045 14.5568
+99 0.00326347 1.58375e-05 0.00397964 9.7142e-08 1.63599e-09 -5.94467 3.06223 1.74992 0.102222 14.5253
+100 0.00326347 1.58375e-05 0.00397964 9.7142e-08 1.63599e-09 -5.95176 3.05794 1.7487 0.124008 14.4937
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/dominant.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/dominant.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/dominant.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,30 @@
+# Avida Dominant Data
+# Fri May 25 07:54:14 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
+
+0 0.000000 0.000000 0.000000 0.000000 100 0.000000 0.000000 1 0 0 0 0 0.000000 1 100-aaaaa
+10 0 0 0 0 100 0 0 180 0 0 0 0 0 1 100-aaaaa
+20 97 389 0.249357 0.00257069 100 100 97 178 0 0 0 0 0.249357 5 100-aaaae
+30 97 389 0.249357 0.00257069 100 100 97 172 0 0 0 0 0.252604 5 100-aaaae
+40 97 389 0.249357 0.00257069 100 100 97 169 21 21 0 0 0.252604 5 100-aaaae
+50 97 389 0.249357 0.00257069 100 100 97 168 10 9 0 0 0.252604 5 100-aaaae
+60 97 389 0.249357 0.00257069 100 100 97 336 0 0 0 0 0.251948 5 100-aaaae
+70 97 389 0.249357 0.00257069 100 100 97 322 0 0 0 0 0.252604 5 100-aaaae
+80 97 389 0.249357 0.00257069 100 100 97 304 0 0 0 0 0.252604 5 100-aaaae
+90 97 389 0.249357 0.00257069 100 100 97 286 60 56 0 0 0.253264 5 100-aaaae
+100 97 389 0.249357 0.00257069 100 100 97 285 20 19 0 0 0.253264 5 100-aaaae
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/historic-100.pop
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/historic-100.pop (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/historic-100.pop 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,39 @@
+#filetype genotype_data
+#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
+
+# 1: ID
+# 2: parent ID
+# 3: parent distance
+# 4: number of orgranisms currently alive
+# 5: total number of organisms that ever existed
+# 6: length of genome
+# 7: merit
+# 8: gestation time
+# 9: fitness
+# 10: update born
+# 11: update deactivated
+# 12: depth in phylogentic tree
+# 13: genome of organism
+
+758 3 1 0 1 100 97 388 0.25 63 100 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccccyxCcauzab
+1007 852 1 0 1 100 0 0 0 88 100 4 rycazccccccccctccccccccczccxcccccpcccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+725 7 1 0 2 100 97 388 0.25 63 91 2 rycazcccccccccccscccccccccccccccccchcccccccccccccDcccccccccccccccccccccccccccccccccccccccccyxCcatzab
+949 3 1 0 1 100 0 0 0 77 90 1 rycazcccccccccccccccwccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+748 488 2 0 2 100 97 386 0.251295 63 90 2 rycazcccccccccccccccecccpccccccccccccccccccccccccccccccccccccccccccjcccccccccccccccccccccccyxCcatzab
+797 3 1 0 2 100 97 389 0.249357 64 90 1 rycazccccccccacccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+588 200 1 0 10 100 97 385 0.251948 39 90 2 rycazccccccccccccccccccccccxcccccpcccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+366 2 1 0 12 100 97 389 0.249357 26 90 1 rycazcccccccccccccccccccccccccrccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+855 773 1 0 1 100 0 0 0 75 89 4 rycazcccccccccccccccccccccccccrccccuccccchcclcccccpccccccccccccccccccctccccccccccccccccccccyxCcatzab
+284 2 1 0 13 100 97 389 0.249357 26 89 1 rycazcccccccccccccccccccrccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+781 2 1 0 1 100 0 0 0 63 89 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccqcccccccccccccccccccccccyxCcatzab
+935 570 1 0 1 100 0 0 0 76 89 4 rycazcccccccccccccccccccccccccccrcccccdcccccccccccccccccccccccccccccccaccccccccpcccccccccccyxCcatzab
+909 509 1 0 1 100 0 0 0 76 89 3 rycazcccccccccgcccccccccccccccccccccccccccccccccgcccccccccccccccccccccccjcccccccccccxccccccyxCcatzab
+826 2 2 0 1 100 0 0 0 64 88 1 rycazccccccccccccccccccccccccdccccccccccccccCccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+814 2 1 0 1 100 0 0 0 64 87 1 rycazccccccccccccccccccccicccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+70 2 1 0 12 100 97 386 0.251295 13 86 1 rycazccccccccccxcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+834 570 2 0 1 100 0 0 0 64 77 4 rycazccccccccccccckcccccccccccccrcccccdcccccccccccccpccccccccccccccccccccccccccpcccccccccccyxCcatzab
+726 284 1 0 1 100 0 0 0 63 75 2 rycazcccccccccccccccccccrcccccccccccccccccccccccccccccccccccbccccccccccccccccccccccccccccccyxCcatzab
+312 2 2 0 1 100 0 0 0 26 40 1 rycazcccccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccxccccccyxCcatzab
+6 2 3 0 1 100 95 385 0.246753 12 39 1 rycazccccccccccccccccccqccccccccccccccccccccccccccccccCccwcccccccccccccccccccccccccccccccccyxCcatzab
+150 2 1 0 1 100 97 389 0.249357 14 39 1 rycazcccccccccccccccccccccccccccrccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+167 3 1 0 1 100 97 388 0.25 14 38 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccczcccccccccccccccccccccccccyxCcauzab
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/instruction.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/instruction.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/instruction.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,115 @@
+# Avida instruction execution data
+# Fri May 25 07:54:15 2007
+# 1: Update
+# 2: nop-A
+# 3: nop-B
+# 4: nop-C
+# 5: if-n-equ
+# 6: if-less
+# 7: pop
+# 8: push
+# 9: swap-stk
+# 10: swap
+# 11: shift-r
+# 12: shift-l
+# 13: inc
+# 14: dec
+# 15: add
+# 16: sub
+# 17: nand
+# 18: IO
+# 19: h-alloc
+# 20: h-divide1
+# 21: h-divide3
+# 22: h-divide10
+# 23: h-divide32
+# 24: h-divide100
+# 25: h-copy
+# 26: h-search
+# 27: mov-head
+# 28: jmp-head
+# 29: get-head
+# 30: if-label
+# 31: set-flow
+
+20 0 0 76330 0 0 0 0 0 0 0 0 0 0 0 0 0 0 898 180 180 179 180 179 89800 1796 89800 0 0 89800 0
+21 0 0 76330 0 0 0 0 0 0 0 0 0 0 0 0 0 0 898 180 180 179 180 179 89800 1796 89800 0 0 89800 0
+22 0 0 76330 0 0 0 0 0 0 0 0 0 0 0 0 0 0 898 180 180 179 180 179 89800 1796 89800 0 0 89800 0
+23 0 0 76330 0 0 0 0 0 0 0 0 0 0 0 0 0 0 898 180 180 179 180 179 89800 1796 89800 0 0 89800 0
+24 0 0 76304 0 0 0 0 0 0 0 0 0 0 0 0 2 2 898 180 180 179 180 179 89800 1796 89800 0 0 89802 2
+25 0 0 76271 0 0 0 0 2 2 0 3 2 2 0 0 8 2 899 180 180 179 180 180 89900 1804 89900 0 0 89900 2
+26 1 2 76100 4 2 4 6 5 4 8 4 4 11 5 4 12 9 900 180 179 180 181 180 90000 1811 90006 0 7 90002 7
+27 1 3 76000 4 2 4 7 11 5 12 4 4 10 8 8 15 9 900 180 179 180 181 180 90000 1814 90006 0 8 90002 9
+28 1 3 75971 5 2 6 7 14 5 11 6 4 10 8 11 16 8 900 180 179 180 181 180 90000 1814 90006 0 7 90000 9
+29 1 3 75971 5 2 6 7 14 5 11 6 4 10 8 11 16 8 900 180 179 180 181 180 90000 1814 90006 0 7 90000 9
+30 1 3 75971 5 2 6 7 14 5 11 6 4 10 8 11 16 8 900 180 179 180 181 180 90000 1814 90006 0 7 90000 9
+31 379 3 75970 5 2 6 7 13 5 11 204 4 10 7 11 17 8 900 180 179 180 181 180 90000 1814 90004 20 7 89800 9
+32 579 3 75970 5 2 6 7 13 5 11 204 4 10 7 11 17 8 900 180 179 180 181 180 90000 1814 90004 20 207 89600 9
+33 757 5 75960 5 2 6 7 13 5 11 206 4 10 29 11 19 8 900 180 179 180 181 180 90000 1814 90004 20 207 89600 9
+34 757 5 75960 5 2 6 7 13 5 11 206 4 10 29 11 19 8 900 180 179 180 181 180 90000 1814 90004 20 207 89600 9
+35 757 5 75960 5 2 6 7 13 5 11 206 4 10 29 11 19 8 900 180 179 180 181 180 90000 1814 90004 20 207 89600 9
+36 657 5 75951 5 2 6 7 13 6 11 206 4 10 29 11 20 8 900 180 179 180 181 180 90000 1815 90003 20 107 89699 9
+37 657 5 75922 7 2 6 6 14 6 12 207 6 10 29 11 23 6 900 180 179 180 181 180 90000 1817 90004 20 107 89698 10
+38 661 8 75808 7 1 8 8 15 10 12 211 5 15 30 14 22 10 900 180 179 180 181 180 90000 1819 89998 20 108 89696 8
+39 477 14 75606 8 3 11 11 19 12 11 107 6 18 26 16 21 7 900 180 179 180 181 180 90000 1824 90000 22 112 89802 13
+40 380 16 75470 8 5 19 11 23 15 17 105 14 25 25 21 24 9 900 180 178 180 182 180 90000 1824 89998 22 16 89900 12
+41 380 18 75430 10 5 19 11 24 17 16 104 14 28 27 22 24 11 900 180 179 180 181 180 90000 1824 89999 22 17 89902 11
+42 290 18 75402 14 5 20 10 24 17 18 106 14 26 29 22 25 13 900 180 179 180 181 180 90000 1825 89999 12 18 89902 10
+43 290 18 75402 14 5 20 10 24 17 18 106 14 26 29 22 25 13 900 180 179 180 181 180 90000 1825 89999 12 18 89902 10
+44 290 18 75402 14 5 20 10 24 17 18 106 14 26 29 22 25 13 900 180 179 180 181 180 90000 1825 89999 12 18 89902 10
+45 290 18 75402 14 5 20 10 24 17 18 106 14 26 29 22 25 13 900 180 179 180 181 180 90000 1825 89999 12 18 89902 10
+46 290 18 75404 14 5 20 10 24 17 18 106 14 26 29 22 25 15 900 180 179 180 181 180 90000 1824 89999 12 18 89902 10
+47 290 18 75404 14 5 20 10 24 17 18 106 14 26 29 22 25 15 900 180 179 180 181 180 90000 1824 89999 12 18 89902 10
+48 490 218 75598 14 5 22 10 24 17 18 106 14 26 29 22 25 15 900 180 179 180 181 180 90000 1824 89999 12 18 89702 10
+49 490 218 75600 14 5 22 10 24 17 18 106 14 26 29 21 25 15 900 180 179 180 181 180 90000 1824 89999 12 18 89702 10
+50 491 217 75557 13 6 24 11 25 17 20 108 17 28 28 20 29 15 900 180 177 182 181 180 90000 1824 90001 11 19 89704 11
+51 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+52 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+53 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+54 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+55 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+56 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+57 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+58 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+59 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+60 0 14 75993 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89948 0 4 89951 14
+61 0 14 75990 0 14 10 7 2 8 6 0 0 44 2 0 42 7 900 0 196 254 30 420 90000 1800 89947 0 5 89950 14
+62 0 15 75945 0 14 10 10 2 8 9 0 2 47 4 0 44 7 900 0 195 255 30 420 90000 1800 89951 0 5 89951 16
+63 0 17 75830 5 10 11 9 7 11 15 2 6 45 12 3 49 10 900 0 193 257 30 420 90000 1800 89954 0 8 89947 19
+64 0 15 75745 10 9 11 13 10 11 15 5 8 57 16 4 53 10 900 0 195 255 30 420 90000 1800 89955 0 10 89950 25
+65 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+66 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+67 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+68 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+69 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+70 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+71 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+72 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+73 0 15 75755 9 8 11 13 9 12 15 5 7 55 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 9 89948 27
+74 0 15 75751 9 8 11 14 9 10 15 5 7 57 15 4 52 10 900 0 195 255 30 420 90000 1800 89953 0 10 89948 27
+75 0 16 75711 7 9 12 13 13 12 14 4 11 57 15 4 52 11 900 0 197 253 30 420 90000 1800 89941 0 13 89937 30
+76 4 16 75583 14 8 11 13 11 15 15 7 10 66 17 8 54 12 900 0 196 254 30 420 90000 1800 89949 0 11 89945 28
+77 5 20 75522 14 9 15 17 10 18 19 8 8 70 15 10 52 15 900 0 196 254 30 420 90000 1800 89946 0 12 89947 31
+78 4 19 75537 15 8 14 17 8 19 18 8 8 66 15 9 54 15 900 0 197 253 30 420 90000 1800 89949 0 11 89950 32
+79 4 19 75543 15 8 14 17 8 19 19 8 7 66 15 9 52 15 900 0 197 253 30 420 90000 1800 89951 0 11 89952 32
+80 4 19 75543 15 8 14 17 8 19 19 8 7 66 15 9 52 15 900 0 197 253 30 420 90000 1800 89951 0 11 89952 32
+81 204 19 75542 15 9 14 17 8 19 19 8 7 66 15 9 52 15 900 0 197 253 30 420 90000 1800 89951 0 11 89952 32
+82 402 21 75540 213 9 14 17 8 19 19 8 7 66 15 9 52 15 900 0 197 253 30 420 90000 1800 89950 0 11 89753 31
+83 402 21 75540 213 9 14 17 8 19 19 8 7 66 15 9 52 15 900 0 197 253 30 420 90000 1800 89950 0 11 89753 31
+84 402 21 75540 213 9 14 17 8 19 19 8 7 66 15 9 52 15 900 0 197 253 30 420 90000 1800 89950 0 11 89753 31
+85 402 21 75540 213 9 14 17 8 19 19 8 7 66 15 9 52 15 900 0 197 253 30 420 90000 1800 89950 0 11 89753 31
+86 402 21 75532 213 9 14 17 8 19 19 8 7 69 15 9 52 15 900 0 197 253 30 420 90000 1800 89951 0 11 89754 31
+87 402 19 75524 213 10 15 17 9 19 17 8 9 66 15 9 55 17 900 0 198 252 30 420 90000 1800 89952 0 11 89755 31
+88 403 19 75395 214 15 15 17 13 28 18 12 9 60 17 8 59 16 900 0 198 252 30 420 90000 1802 89943 0 11 89748 30
+89 304 23 75335 122 15 16 19 13 25 16 16 11 67 24 11 59 20 900 0 196 254 30 420 90000 1803 89948 0 13 89852 30
+90 305 26 75271 125 15 15 20 15 29 18 20 10 70 26 10 61 23 900 0 196 254 30 420 90000 1803 89949 0 16 89855 32
+91 305 27 75284 122 13 14 22 15 27 18 24 10 68 29 10 57 23 900 0 197 253 30 420 90000 1803 89952 0 17 89857 30
+92 305 26 75272 122 13 13 22 15 28 18 24 10 67 29 9 58 26 900 0 198 252 30 420 90000 1803 89952 0 18 89858 31
+93 305 26 75273 122 13 13 21 15 27 20 26 10 67 29 9 58 26 900 0 198 252 30 420 90000 1803 89952 0 18 89858 31
+94 305 25 75274 122 13 13 21 15 27 20 26 210 67 29 9 58 26 900 2 197 251 30 420 90000 1803 89952 0 18 89658 31
+95 305 25 75274 122 13 13 21 15 27 20 26 210 67 29 9 58 26 900 2 197 251 30 420 90000 1803 89952 0 18 89658 31
+96 505 25 75271 122 13 15 21 15 27 20 26 210 67 29 9 58 26 900 2 197 251 30 420 90000 1803 89952 200 18 89458 31
+97 505 25 75271 122 13 15 21 15 27 20 26 210 67 29 9 58 26 900 2 197 251 30 420 90000 1803 89952 200 18 89458 31
+98 677 24 75263 122 13 15 21 15 27 20 26 210 67 29 37 59 27 900 2 197 251 30 420 90000 1803 89953 200 18 89459 31
+99 677 24 75254 124 13 16 23 15 27 20 28 210 67 28 37 59 27 900 2 197 251 30 420 90000 1803 89953 200 18 89459 30
+100 774 24 75280 222 14 15 23 15 26 20 26 213 64 26 35 60 26 900 2 197 251 30 420 90000 1802 89948 200 16 89350 29
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/resource.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/resource.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/resource.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,17 @@
+# Avida resource data
+# Fri May 25 07:54:14 2007
+# First column gives the current update, all further columns give the quantity
+# of the particular resource at that update.
+# 1: Update
+
+0
+10
+20
+30
+40
+50
+60
+70
+80
+90
+100
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/stats.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/stats.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/stats.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,26 @@
+# Generic Statistics Data
+# Fri May 25 07:54:14 2007
+# 1: update
+# 2: average inferiority (energy)
+# 3: ave probability of any mutations in genome
+# 4: probability of any mutations in dom genome
+# 5: log(average fidelity)
+# 6: log(dominant fidelity)
+# 7: change in number of genotypes
+# 8: genotypic entropy
+# 9: species entropy
+# 10: depth of most reacent coalescence
+# 11: Total number of resamplings this generation
+# 12: Total number of organisms that failed to resample this generation
+
+0 0.000000 0.000000 0.000000 -0.000000 -0.000000 1 0.000000 0.000000 0 0 0
+10 0 0 0 -0 -0 0 1.60944 0 0 0 0
+20 0 0 0 -0 -0 0 2.7433 0 0 0 0
+30 0.00125112 0 0 -0 -0 1 3.39078 0 0 0 0
+40 0.00366773 0 0 -0 -0 12 3.71987 0 0 0 0
+50 0.00577676 0 0 -0 -0 5 3.8154 0 0 0 0
+60 -0.000846372 0 0 -0 -0 0 2.63764 0 0 0 0
+70 -0.00110777 0 0 -0 -0 0 3.02157 0 0 0 0
+80 -0.000796719 0 0 -0 -0 0 3.39461 0 0 0 0
+90 0.000589893 0 0 -0 -0 2 3.51759 0 0 0 0
+100 0.00339982 0 0 -0 -0 6 3.60505 0 0 0 0
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/tasks.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/tasks.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/tasks.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,94 @@
+# Avida tasks data
+# Fri May 25 07:54:14 2007
+# First column gives the current update, next columns give the number
+# of organisms that have the particular task as a component of their merit
+# 1: Update
+# 2: Not
+# 3: Nand
+# 4: And
+# 5: OrNot
+# 6: Or
+# 7: AndNot
+# 8: Nor
+# 9: Xor
+# 10: Equals
+# 11: Logic 3AA (A+B+C == 0)
+# 12: Logic 3AB (A+B+C == 1)
+# 13: Logic 3AC (A+B+C <= 1)
+# 14: Logic 3AD (A+B+C == 2)
+# 15: Logic 3AE (A+B+C == 0,2)
+# 16: Logic 3AF (A+B+C == 1,2)
+# 17: Logic 3AG (A+B+C <= 2)
+# 18: Logic 3AH (A+B+C == 3)
+# 19: Logic 3AI (A+B+C == 0,3)
+# 20: Logic 3AJ (A+B+C == 1,3) XOR
+# 21: Logic 3AK (A+B+C != 2)
+# 22: Logic 3AL (A+B+C >= 2)
+# 23: Logic 3AM (A+B+C != 1)
+# 24: Logic 3AN (A+B+C != 0)
+# 25: Logic 3AO (A & ~B & ~C) [3]
+# 26: Logic 3AP (A^B & ~C) [3]
+# 27: Logic 3AQ (A==B & ~C) [3]
+# 28: Logic 3AR (A & B & ~C) [3]
+# 29: Logic 3AS
+# 30: Logic 3AT
+# 31: Logic 3AU
+# 32: Logic 3AV
+# 33: Logic 3AW
+# 34: Logic 3AX
+# 35: Logic 3AY
+# 36: Logic 3AZ
+# 37: Logic 3BA
+# 38: Logic 3BB
+# 39: Logic 3BC
+# 40: Logic 3BD
+# 41: Logic 3BE
+# 42: Logic 3BF
+# 43: Logic 3BG
+# 44: Logic 3BH
+# 45: Logic 3BI
+# 46: Logic 3BJ
+# 47: Logic 3BK
+# 48: Logic 3BL
+# 49: Logic 3BM
+# 50: Logic 3BN
+# 51: Logic 3BO
+# 52: Logic 3BP
+# 53: Logic 3BQ
+# 54: Logic 3BR
+# 55: Logic 3BS
+# 56: Logic 3BT
+# 57: Logic 3BU
+# 58: Logic 3BV
+# 59: Logic 3BW
+# 60: Logic 3BX
+# 61: Logic 3BY
+# 62: Logic 3BZ
+# 63: Logic 3CA
+# 64: Logic 3CB
+# 65: Logic 3CC
+# 66: Logic 3CD
+# 67: Logic 3CE
+# 68: Logic 3CF
+# 69: Logic 3CG
+# 70: Logic 3CH
+# 71: Logic 3CI
+# 72: Logic 3CJ
+# 73: Logic 3CK
+# 74: Logic 3CL
+# 75: Logic 3CM
+# 76: Logic 3CN
+# 77: Logic 3CO
+# 78: Logic 3CP
+
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Added: development/tests/bgs_dyn_mutrates_rank/expected/data/time.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/expected/data/time.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/expected/data/time.dat 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,18 @@
+# Avida time data
+# Fri May 25 07:54:14 2007
+# 1: update
+# 2: avida time
+# 3: average generation
+# 4: num_executed?
+
+0 0.000000 0.000000 30
+10 0.0927835 0 26880
+20 0.195876 1 26940
+30 0.299042 1.96667 27000
+40 0.402327 2.85222 27000
+50 0.505788 3.10111 27000
+60 0.608934 3.27889 27000
+70 0.712045 4.27667 27000
+80 0.815183 5.27 27000
+90 0.918374 6.16778 27000
+100 1.02162 6.44778 27000
Added: development/tests/bgs_dyn_mutrates_rank/test_list
===================================================================
--- development/tests/bgs_dyn_mutrates_rank/test_list (rev 0)
+++ development/tests/bgs_dyn_mutrates_rank/test_list 2007-05-25 11:51:30 UTC (rev 1609)
@@ -0,0 +1,37 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+args = -s 1 -set BIRTH_METHOD 6 -set NUM_DEMES 30 -set EVENT_FILE events-Test-RankSelection.cfg -set INST_SET inst_set.divide -set ENVIRONMENT_FILE environment.77 -set WORLD_X 15 -set WORLD_Y 60 -set CHILD_SIZE_RANGE 1.0 -set COPY_MUT_PROB 0.0 -set DIVIDE_INS_PROB 0.0 -set DIVIDE_DEL_PROB 0.0 -set DIV_MUT_PROB 0.03 -set START_CREATURE org.div1
+
+ ; 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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