[Avida-SVN] r1611 - in development/tests: . bgs_dyn_mutrates_births bgs_dyn_mutrates_births/config bgs_dyn_mutrates_births/expected bgs_dyn_mutrates_births/expected/data
jclune at myxo.css.msu.edu
jclune at myxo.css.msu.edu
Fri May 25 05:17:37 PDT 2007
Author: jclune
Date: 2007-05-25 08:17:37 -0400 (Fri, 25 May 2007)
New Revision: 1611
Added:
development/tests/bgs_dyn_mutrates_births/
development/tests/bgs_dyn_mutrates_births/config/
development/tests/bgs_dyn_mutrates_births/config/avida.cfg
development/tests/bgs_dyn_mutrates_births/config/environment.77
development/tests/bgs_dyn_mutrates_births/config/events-Test-NumBirthsSelection.cfg
development/tests/bgs_dyn_mutrates_births/config/inst_set.divide
development/tests/bgs_dyn_mutrates_births/config/org.div1
development/tests/bgs_dyn_mutrates_births/config/org.div10
development/tests/bgs_dyn_mutrates_births/config/org.div100
development/tests/bgs_dyn_mutrates_births/config/org.div3
development/tests/bgs_dyn_mutrates_births/config/org.div32
development/tests/bgs_dyn_mutrates_births/expected/
development/tests/bgs_dyn_mutrates_births/expected/data/
development/tests/bgs_dyn_mutrates_births/expected/data/average.dat
development/tests/bgs_dyn_mutrates_births/expected/data/count.dat
development/tests/bgs_dyn_mutrates_births/expected/data/creature.final
development/tests/bgs_dyn_mutrates_births/expected/data/detail-100.pop
development/tests/bgs_dyn_mutrates_births/expected/data/divide_mut.dat
development/tests/bgs_dyn_mutrates_births/expected/data/dominant.dat
development/tests/bgs_dyn_mutrates_births/expected/data/historic-100.pop
development/tests/bgs_dyn_mutrates_births/expected/data/instruction.dat
development/tests/bgs_dyn_mutrates_births/expected/data/resource.dat
development/tests/bgs_dyn_mutrates_births/expected/data/stats.dat
development/tests/bgs_dyn_mutrates_births/expected/data/tasks.dat
development/tests/bgs_dyn_mutrates_births/expected/data/time.dat
development/tests/bgs_dyn_mutrates_births/test_list
Log:
added bgs_dyn_mutrates_births test
Added: development/tests/bgs_dyn_mutrates_births/config/avida.cfg
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/avida.cfg (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/avida.cfg 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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_births/config/environment.77
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/environment.77 (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/environment.77 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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_births/config/events-Test-NumBirthsSelection.cfg
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/events-Test-NumBirthsSelection.cfg (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/events-Test-NumBirthsSelection.cfg 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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 1
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Property changes on: development/tests/bgs_dyn_mutrates_births/config/events-Test-NumBirthsSelection.cfg
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_births/config/inst_set.divide
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/inst_set.divide (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/inst_set.divide 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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_births/config/inst_set.divide
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_births/config/org.div1
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/org.div1 (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/org.div1 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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_births/config/org.div1
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_births/config/org.div10
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/org.div10 (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/org.div10 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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_births/config/org.div10
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_births/config/org.div100
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/org.div100 (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/org.div100 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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_births/config/org.div100
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_births/config/org.div3
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/org.div3 (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/org.div3 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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_births/config/org.div3
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_births/config/org.div32
===================================================================
--- development/tests/bgs_dyn_mutrates_births/config/org.div32 (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/config/org.div32 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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_births/config/org.div32
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_births/expected/data/average.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/average.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/average.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,120 @@
+# Avida Average Data
+# Fri May 25 08:19:43 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 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+52 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+53 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+54 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+55 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+56 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+57 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+58 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+59 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+60 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0 0 0.514444 3.08889 -0.124997 -1 0
+61 96.5622 389.514 0.248095 0 100 100 96.5622 4.14747 0.00111111 0.00111111 0.514444 3.09111 -0.1281 -1 0
+62 96.5789 389.518 0.248138 0 100 100 96.5789 4 0.0711111 0.0566667 0.523333 3.23333 -0.135682 -1 0
+63 96.5278 388.562 0.248483 0 100 100 96.5278 3.10345 0.335556 0.21 0.617778 3.77111 -0.171432 -1 0
+64 96.51 388.5 0.248477 0 100 100 96.51 2.82132 0.216667 0.133333 0.677778 4.03667 -0.182452 -1 0
+65 96.4944 388.482 0.24845 0 100 100 96.4944 2.77778 0.0311111 0.0177778 0.69 4.07333 -0.191393 -1 0
+66 96.4956 388.591 0.248396 0 100 100 96.4956 2.77778 0.00111111 0 0.691111 4.07444 -0.186922 -1 0
+67 96.4956 388.591 0.248396 0 100 100 96.4956 2.77778 0 0 0.691111 4.07444 -0.186922 -1 0
+68 96.4956 388.591 0.248396 0 100 100 96.4956 2.77778 0 0 0.691111 4.07444 -0.186922 -1 0
+69 96.4967 388.807 0.248306 0 100 100 96.4967 2.77778 0.00111111 0.00111111 0.692222 4.07444 -0.181528 -1 0
+70 96.4967 388.807 0.248306 0 100 100 96.4967 2.77778 0 0 0.692222 4.07444 -0.181528 -1 0
+71 96.4967 388.807 0.248306 0 100 100 96.4967 2.77778 0 0 0.692222 4.07444 -0.181528 -1 0
+72 96.4967 388.807 0.248306 0 100 100 96.4967 2.77778 0 0 0.692222 4.07444 -0.181528 -1 0
+73 96.4967 388.807 0.248306 0 100 100 96.4967 2.77778 0.00111111 0.00111111 0.692222 4.07667 -0.186867 -1 0
+74 96.4589 388.76 0.248235 0 100 100 96.4589 2.78638 0.0155556 0.0144444 0.695556 4.10444 -0.186285 -1 0
+75 96.45 388.692 0.248255 0 100 100 96.45 2.7027 0.124444 0.0866667 0.726667 4.33667 -0.105272 -1 0
+76 96.4467 388.394 0.248393 0 100 100 96.4467 2.63158 0.273333 0.187778 0.782222 4.76556 -0.130347 -1 0
+77 96.4267 388.234 0.248428 0 100 100 96.4267 2.59366 0.155556 0.103333 0.814444 4.95889 -0.208572 -1 0
+78 96.3867 388.177 0.24836 0 100 100 96.3867 2.5788 0.0566667 0.0366667 0.841111 5.02778 -0.219239 -1 0
+79 96.3667 388.371 0.248209 0 100 100 96.3667 2.57143 0.00888889 0.00444444 0.844444 5.03778 -0.21624 -1 0
+80 96.3667 388.371 0.248209 0 100 100 96.3667 2.57143 0 0 0.844444 5.03778 -0.21624 -1 0
+81 96.3689 388.594 0.248106 0 100 100 96.3689 2.5641 0.00111111 0 0.845556 5.03889 -0.212448 -1 0
+82 96.37 388.703 0.248053 0 100 100 96.37 2.5641 0.00111111 0 0.846667 5.04 -0.215408 -1 0
+83 96.37 388.703 0.248053 0 100 100 96.37 2.5641 0 0 0.846667 5.04 -0.215408 -1 0
+84 96.3444 389.558 0.247646 0 100 100 96.3444 2.5641 0.00222222 0.00222222 0.846667 5.04556 -0.204252 -1 0
+85 96.3444 389.558 0.247646 0 100 100 96.3444 2.5641 0.00111111 0.00111111 0.846667 5.04778 -0.200428 -1 0
+86 96.3222 389.532 0.247604 0 100 100 96.3222 2.54958 0.00555556 0.00222222 0.852222 5.06 -0.205365 -1 0
+87 96.3233 389.517 0.247617 0 100 100 96.3233 2.52809 0.06 0.0422222 0.863333 5.17333 -0.212688 -1 0
+88 96.3467 389.506 0.247679 0 100 100 96.3467 2.47934 0.154444 0.102222 0.9 5.44 -0.172901 -1 0
+89 96.2689 389.043 0.247703 0 100 100 96.2689 2.44565 0.207778 0.15 0.936667 5.73667 -0.289955 -1 0
+90 96.2356 388.978 0.247656 0 100 100 96.2356 2.43243 0.127778 0.0777778 0.971111 5.92667 -0.33694 -1 0
+91 96.2511 388.973 0.247702 0 100 100 96.2511 2.39362 0.0611111 0.04 0.997778 6.00667 -0.332863 -1 0
+92 96.24 388.964 0.247679 0 100 100 96.24 2.4 0.0111111 0.00666667 1.00444 6.01778 -0.326407 -1 0
+93 96.2089 388.93 0.247619 0 100 100 96.2089 2.39362 0.00555556 0.00111111 1.01222 6.02778 -0.312826 -1 0
+94 96.2089 388.93 0.247619 0 100 100 96.2089 2.39362 0 0 1.01222 6.02778 -0.312826 -1 0
+95 96.2089 388.93 0.247619 0 100 100 96.2089 2.39362 0 0 1.01222 6.02778 -0.312826 -1 0
+96 96.2011 389.247 0.247441 0 100 100 96.2011 2.39362 0.00222222 0 1.01333 6.03 -0.313439 -1 0
+97 96.2033 389.683 0.247257 0 100 100 96.2033 2.39362 0.00222222 0.00111111 1.01667 6.03333 -0.322922 -1 0
+98 96.1878 389.88 0.247121 0 100 100 96.1878 2.39362 0.00333333 0.00222222 1.02111 6.04111 -0.320195 -1 0
+99 96.1578 389.976 0.246999 0 100 100 96.1578 2.38727 0.0222222 0.0144444 1.02222 6.08444 -0.319428 -1 0
+100 96.1656 389.647 0.247187 0 100 100 96.1656 2.36842 0.09 0.0622222 1.03778 6.25444 -0.259943 -1 0
Added: development/tests/bgs_dyn_mutrates_births/expected/data/count.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/count.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/count.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,30 @@
+# Avida count data
+# Fri May 25 08:19:43 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 900 217 18 0 0 0 0 0 0 262 900 900 0 0
+70 27000 900 324 35 0 0 0 0 0 0 410 480 900 0 0
+80 27000 900 350 48 0 0 0 0 0 0 495 475 900 0 0
+90 27000 900 370 57 0 0 0 115 115 70 535 489 900 0 0
+100 27000 900 380 58 0 0 0 81 81 56 538 498 900 0 0
Added: development/tests/bgs_dyn_mutrates_births/expected/data/creature.final
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/creature.final (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/creature.final 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,202 @@
+# Fri May 25 08:19:47 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_births/expected/data/detail-100.pop
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/detail-100.pop (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/detail-100.pop 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,397 @@
+#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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+1280 361 1 1 1 100 0 0 0 92 -1 3 rycazcccfcccccccccmccccccccccccccccccccccccccfccpcccccccccccchcccccccccccccccccccccccccccccyxCcaszab
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+649 411 1 1 5 100 97 387 0.250646 41 -1 2 rycazccccccccccccicccccccccccccccccccccccqcccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+1295 3 1 1 1 100 0 0 0 99 -1 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyccccccccccccccccccccccccyxCcauzab
+1296 1118 2 1 1 100 0 0 0 99 -1 2 rycagccccccccccccccccccccczccccccccccxcccccccccccccccccccccccccccccccccccccccccfcccccccccccyxCcaszac
+772 580 1 1 3 100 97 387 0.250646 63 -1 2 rycazccccccccccccccccccccccccccccfccccccccccccccccnccccccccccccccccccccccccccccccccccccccccyxCcatzab
+687 5 1 1 8 100 97 388 0.25 50 -1 1 rycazcccccccccccccccccccccccccccccccccccqccccccccccccccccccccccccccccccccccccccccccccccccccyxCcawzab
+858 562 1 1 2 100 97 387 0.250646 64 -1 2 rycazcvcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccfcccqccccccyxCcatzab
+1297 932 1 1 1 100 0 0 0 99 -1 2 rycazccccrcccccccccccccccccpcccccccccccccccaccccccccccccccccccccccccccccCccccccccccccccccccyxCcatzab
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+1299 692 2 1 1 100 0 0 0 100 -1 3 hycazccccccccccccscccccccccccccccccccccccccccccccccccccccqcccccccccccccccjvccccccccccccccccyxCcaszab
+441 2 1 1 7 100 97 389 0.249357 27 -1 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccrccccccccccccccccccccccccccccccccccccccyxCcatzab
+1300 19 1 1 1 100 0 0 0 100 -1 2 rycazccccccccccccccccccccccccccccccccwcccccccccccccccccicccccccccccccccjcccccccccccccccccccyxCcaszab
+1301 1122 2 1 1 100 0 0 0 100 -1 2 rycamcccmccccccccccccccccccccccccccccccccccccccccccccccccccccccwcccccccccccccccccccccccccccyxCcaszab
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+963 3 1 1 2 100 0 0 0 76 -1 1 rycazccccccccccccccccBcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
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+1081 3 1 1 2 100 0 0 0 78 -1 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccqcccyxCcauzab
+1310 888 1 1 1 100 0 0 0 100 -1 2 rycazccccccccccccccccccccccccccccccccccccccccccccgccccccccccccccccccccccccccccccccccccccuccyxCcauzab
+1311 4 1 1 1 100 0 0 0 100 -1 1 rycazccccccccccccccccccccccccccccccccccccccccccscccccccccccccccccccccccccccccccccccccccccccyxCcavzab
+1312 1124 1 1 1 100 0 0 0 100 -1 5 rycazcmceccccccccccccccccccccccccccccccccccccccccccccockvnucccccccccctBcccccBycmcccccccccccyxCcaszab
+647 3 1 1 5 100 97 388 0.25 41 -1 1 rycazcccccccccoccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+1313 773 3 1 1 100 0 0 0 100 -1 3 rycazccccccnccwocwccccccccccccccccccccrlcccccccccccccccccccccccccccccccccccccclcwacccccccccyxCcaszab
+1097 177 2 1 2 100 0 0 0 82 -1 2 rycazccccccccccccccccccccccccccccccccccCcccccccccccccccccccccckccccccccccccccccccccccccccccyxCcztzab
+1314 575 1 1 1 100 0 0 0 100 -1 2 rycazcccccccccccccccccccccccccccccccccccccccccclcccccccccccccycccccccccccccccccccccccccccccyxCcatzab
+1315 339 2 1 1 100 0 0 0 100 -1 2 rycazccccccccccccccccccccccccccmccccrcccccccccccccccccccccccccccccccccccccccccccrccccccccccyxCcaszab
+1316 172 1 1 1 100 0 0 0 100 -1 2 rycazcccccceccccjccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+1317 1121 3 1 1 100 0 0 0 100 -1 5 rycazcmcecccccccccccxcccccccccccccccccccccchcccccccccoccvnuccccccccvctBcccccccsmccccrccccccyxCcaszab
+1318 658 5 1 1 100 0 0 0 100 -1 4 rycazcmceccicccccccccccccccccccccccccccncccccccccccccoccvnucccccccyhctBccccccccmcccccccccccyxCcaszqb
+1319 3 1 1 1 100 0 0 0 100 -1 1 rycazccccccccccccccccccccccccccccccccccccccccBcccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+1320 1103 1 1 1 100 0 0 0 100 -1 2 rycazcccbccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzap
+1321 4 2 1 1 100 0 0 0 100 -1 1 rycazccccccccccccccccccvcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcavvab
+880 3 1 1 2 100 97 388 0.25 64 -1 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccccccyxCcauzab
+1322 284 1 1 1 100 0 0 0 100 -1 2 rycazcccccccccccccccccccrccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcCtzab
+1323 735 1 1 1 100 0 0 0 100 -1 3 rycazcccccccccccccccccccccccccccccccmbcccccccccccccccccccccccccccccccccvccccvccccccccccccccyxCcaszab
Added: development/tests/bgs_dyn_mutrates_births/expected/data/divide_mut.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/divide_mut.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/divide_mut.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,105 @@
+# Avida divide mutation rate data
+# Fri May 25 08:19:43 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 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.25725 3.00785 1.73432 -2.22517 15.2287
+52 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.27081 3.01542 1.7365 -2.17454 15.2202
+53 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.28385 3.02235 1.73849 -2.12526 15.211
+54 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.29641 3.02871 1.74032 -2.0773 15.2011
+55 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.30852 3.03454 1.74199 -2.03064 15.1908
+56 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.32019 3.03988 1.74352 -1.98527 15.1801
+57 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.33145 3.04477 1.74493 -1.94114 15.1691
+58 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.34232 3.04926 1.74621 -1.89823 15.1578
+59 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.35282 3.05337 1.74739 -1.8565 15.1464
+60 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.36298 3.05713 1.74846 -1.81593 15.1349
+61 0.00847729 0.000126601 0.0112517 1.74943e-06 4.51837e-08 -5.37279 3.06057 1.74945 -1.77648 15.1233
+62 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.38225 3.06368 1.75034 -1.73843 15.1118
+63 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.39143 3.06652 1.75115 -1.70123 15.1002
+64 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.40033 3.0691 1.75189 -1.66506 15.0886
+65 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.40895 3.07146 1.75256 -1.62987 15.077
+66 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.4173 3.0736 1.75317 -1.59563 15.0655
+67 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.42541 3.07554 1.75372 -1.56232 15.054
+68 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.43328 3.07731 1.75423 -1.52991 15.0427
+69 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.44092 3.0789 1.75468 -1.49835 15.0314
+70 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.44834 3.08033 1.75509 -1.46764 15.0203
+71 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.45555 3.08162 1.75545 -1.43773 15.0092
+72 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.46257 3.08277 1.75578 -1.4086 14.9983
+73 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.46939 3.0838 1.75608 -1.38022 14.9875
+74 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.47602 3.08471 1.75633 -1.35258 14.9768
+75 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.4825 3.0855 1.75656 -1.32548 14.9662
+76 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.48878 3.0862 1.75676 -1.29922 14.9558
+77 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.49491 3.08681 1.75693 -1.27362 14.9455
+78 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.50088 3.08732 1.75708 -1.24866 14.9353
+79 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.50669 3.08776 1.7572 -1.22432 14.9253
+80 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.51236 3.08812 1.75731 -1.20057 14.9155
+81 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.51789 3.08841 1.75739 -1.17739 14.9057
+82 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.52329 3.08863 1.75745 -1.15478 14.8961
+83 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.52855 3.0888 1.7575 -1.1327 14.8867
+84 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.53369 3.0889 1.75753 -1.11114 14.8773
+85 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.53871 3.08895 1.75754 -1.09009 14.8681
+86 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.54361 3.08895 1.75754 -1.06953 14.859
+87 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.5484 3.08891 1.75753 -1.04945 14.8501
+88 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.55306 3.08883 1.75751 -1.02995 14.8413
+89 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.55762 3.08871 1.75747 -1.01089 14.8327
+90 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.56208 3.08855 1.75743 -0.992263 14.8242
+91 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.56646 3.08835 1.75737 -0.973923 14.8157
+92 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.57074 3.08812 1.7573 -0.955987 14.8074
+93 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.57493 3.08785 1.75723 -0.938444 14.7991
+94 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.57902 3.08756 1.75715 -0.921282 14.791
+95 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.58304 3.08724 1.75705 -0.904488 14.783
+96 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.58696 3.0869 1.75696 -0.888052 14.7751
+97 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.59081 3.08653 1.75685 -0.871964 14.7673
+98 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.59458 3.08614 1.75674 -0.856213 14.7597
+99 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.59827 3.08574 1.75663 -0.840789 14.7521
+100 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.60189 3.08531 1.75651 -0.825683 14.7446
Added: development/tests/bgs_dyn_mutrates_births/expected/data/dominant.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/dominant.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/dominant.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,30 @@
+# Avida Dominant Data
+# Fri May 25 08:19:43 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 97 224 0 0 0 0 0.252604 5 100-aaaae
+70 97 389 0.249357 0.00257069 100 100 97 225 0 0 0 0 0.252604 5 100-aaaae
+80 97 389 0.249357 0.00257069 100 100 97 225 0 0 0 0 0.253927 5 100-aaaae
+90 97 389 0.249357 0.00257069 100 100 97 221 26 25 0 0 0.253927 5 100-aaaae
+100 97 389 0.249357 0.00257069 100 100 97 219 31 30 0 0 0.253927 5 100-aaaae
Added: development/tests/bgs_dyn_mutrates_births/expected/data/historic-100.pop
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/historic-100.pop (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/historic-100.pop 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,113 @@
+#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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+475 3 1 0 6 100 97 388 0.25 37 99 1 rycazcccccccccccccDccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
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+749 607 4 0 1 100 88 372 0.236559 63 99 3 rycazcccfccccccccccccccccccccycccccccccchccccccccccecccicccccccccccccrcjcxcccccccccccccccccyxCcaszab
+699 2 1 0 5 100 97 388 0.25 50 93 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccnccccccccccccccccccccccccccccccccccccccyxCcatzab
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+814 699 1 0 2 100 97 387 0.250646 63 92 2 rycazcccccccccccccccccccccccccccccccccccccccccccccccnccccccccccccccccccccqcccccccccccccccccyxCcatzab
+380 19 2 0 3 100 97 387 0.250646 26 91 2 rycazcccccccccccccccccccccccccccccccccccccccccccccccccnicccccccccccccccjccccccccccccccccccByxCcaszab
+739 377 3 0 1 100 97 387 0.250646 63 91 2 rycazcccDccccccdcsccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccvccccccyxCcaszab
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+200 2 1 0 4 100 97 388 0.25 14 91 1 rycazccccccccccccccccccccccccccccpcccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
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+449 192 1 0 3 100 97 384 0.252604 28 90 2 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccctcccccccccccccccctcxcccccfcdcyxCcaszab
+602 396 2 0 3 100 97 386 0.251295 40 90 2 rycazccccccccccccwccccccccccccccccccccclcccrcccccccccccccccccccccccccccccccccclcjacccccccccyxCcaszab
+604 98 3 0 2 100 97 386 0.251295 40 90 2 rycazcccccccccccccucccccchccccccccccccccccccccccccxccccccccccccccccccccccccccccccccccccccclyxCcaszab
+503 1 3 0 4 100 97 386 0.251295 38 90 1 rycazcccccccccccccccccccccccccccccccccccccccccfcccccczcccccccccccccccccjcccccccccccccccccccyxCcaszab
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+432 1 3 0 3 100 97 386 0.251295 27 90 1 rycazcccccccccscccccccccccccccaccccccccccccccccccccccccccccccccccccccccccccccccccxcccccccccyxCcaszab
+490 2 1 0 5 100 88 379 0.23219 38 90 1 rycazcccccccccyccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+338 1 1 0 2 100 97 389 0.249357 26 90 1 rycazccccccccccccccccccccccccccccccccchccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
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+947 784 1 0 1 100 0 0 0 75 89 2 rycazccccccccccccscccccccccccccccccccccccccccccnccccccccsccccccccccccccccccccccccccccccccccyxCcatzab
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+769 449 1 0 1 100 97 383 0.253264 63 88 3 rycazcccccccccccccccccccccccccccccccccccccccccclcccccccccccccctcccccccccccccccctcxcccccfcdcyxCcaszab
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+98 1 1 0 2 100 97 389 0.249357 13 88 1 rycazcccccccccccccccccccchcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
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+301 2 1 0 2 100 97 389 0.249357 26 77 1 rycazccccccccccccccccccccccccccwcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
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+660 444 1 0 2 100 97 388 0.25 41 77 2 rycazcccccccccccccccccccrccccccccccccccccccccccccccctccccccccccccccccccccccccccccccdcccccccyxCcatzab
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+765 509 1 0 1 100 0 0 0 63 76 3 rycazcccccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccccccjccccccccccmxccccccyxCcatzab
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+382 2 2 0 1 100 0 0 0 26 39 1 rycazccccccccccccocccccccccccccccccccccccccccccccccccccccccccccccdcccccccccccccccccccccccccyxCcatzab
+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
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+128 1 1 0 1 100 0 0 0 13 38 1 rycazcmccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+138 1 1 0 1 100 0 0 0 13 38 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccecccccccccccccccccccccccccccccccccyxCcaszab
+89 2 1 0 1 100 0 0 0 13 37 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccqccccccccccccccccccccccccyxCcatzab
+56 1 5 0 1 100 0 0 0 13 28 1 rycazccccccdcccccchcccccjcccccocccccccpccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+157 1 2 0 1 100 0 0 0 14 27 1 rycazcccccccccccccmccccccccccccccccccccccccccfcccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+108 1 4 0 1 100 0 0 0 13 27 1 rycazcccccccccccccccuccccrccccccccccccczcccccccccccccccccccccccccycccccccccccccccccccccccccyxCcaszab
Added: development/tests/bgs_dyn_mutrates_births/expected/data/instruction.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/instruction.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/instruction.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,115 @@
+# Avida instruction execution data
+# Fri May 25 08:19:44 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
+
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+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
+51 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+52 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+53 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+54 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+55 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+56 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+57 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+58 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+59 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+60 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+61 300 18 75366 13 6 21 6 25 16 20 206 17 19 30 18 24 8 900 180 147 182 151 240 90000 1823 89998 0 19 89805 12
+62 300 23 75355 13 5 21 8 25 16 22 208 17 18 28 18 24 10 900 180 148 182 150 240 90000 1823 89997 0 20 89803 16
+63 112 24 75072 19 11 23 15 28 23 38 115 22 20 27 28 25 13 900 180 147 183 150 240 90000 1833 89993 0 27 89892 21
+64 119 26 74941 18 12 31 19 22 29 44 120 23 17 33 24 31 19 900 180 147 183 150 240 90000 1831 89991 0 35 89898 22
+65 118 26 74918 17 12 31 19 19 31 43 120 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89992 0 36 89903 23
+66 118 26 74918 17 12 31 19 19 31 43 120 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89992 0 36 89903 23
+67 118 26 74918 17 12 31 19 19 31 43 120 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89992 0 36 89903 23
+68 118 26 74918 17 12 31 19 19 31 43 120 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89992 0 36 89903 23
+69 217 26 74917 17 12 31 19 19 31 43 219 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89991 0 36 89803 23
+70 217 26 74917 17 12 31 19 19 31 43 219 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89991 0 36 89803 23
+71 217 26 74917 17 12 31 19 19 31 43 219 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89991 0 36 89803 23
+72 217 26 74917 17 12 31 19 19 31 43 219 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89991 0 36 89803 23
+73 217 26 74917 17 12 31 19 19 31 43 219 21 19 32 22 32 21 900 180 147 183 150 240 90000 1831 89991 0 36 89803 23
+74 217 26 74860 17 13 31 20 20 30 43 219 20 21 34 23 32 21 900 180 147 183 150 240 90000 1833 89992 0 38 89806 23
+75 214 31 74765 23 16 39 19 22 31 44 222 24 23 35 26 33 24 900 180 146 184 150 240 90000 1839 89987 0 34 89795 24
+76 119 27 74630 36 23 42 20 25 32 52 132 26 29 35 26 32 21 900 180 147 183 150 240 90000 1842 89982 0 37 89884 34
+77 119 36 74567 39 22 48 20 26 39 51 131 23 28 31 26 33 25 900 180 147 183 150 240 90000 1843 89973 0 36 89882 37
+78 128 36 74465 35 26 53 20 25 43 50 132 25 33 33 23 33 28 900 180 147 183 150 240 90000 1845 89975 0 38 89889 32
+79 128 36 74432 34 28 53 20 25 43 50 131 25 33 33 23 33 30 900 180 147 183 150 240 90000 1845 89980 0 40 89892 32
+80 128 36 74432 34 28 53 20 25 43 50 131 25 33 33 23 33 30 900 180 147 183 150 240 90000 1845 89980 0 40 89892 32
+81 128 36 74434 34 28 53 20 27 43 50 131 25 33 33 23 33 30 900 180 147 183 150 240 90000 1845 89979 0 40 89892 32
+82 128 35 74435 34 28 53 20 27 43 50 131 25 33 33 23 33 30 900 180 147 183 150 240 90000 1845 89979 0 40 89892 32
+83 128 35 74435 34 28 53 20 27 43 50 131 25 33 33 23 33 30 900 180 147 183 150 240 90000 1845 89979 0 40 89892 32
+84 306 37 74405 56 28 52 219 27 43 250 131 25 33 33 23 33 30 900 180 147 183 150 240 90000 1848 89979 0 39 89692 32
+85 306 37 74405 56 28 52 219 27 43 250 131 25 33 33 23 33 30 900 180 147 183 150 240 90000 1848 89979 0 39 89692 32
+86 306 37 74373 56 28 51 219 27 43 250 131 25 33 34 23 35 30 900 180 147 183 150 240 90000 1848 89978 0 39 89694 32
+87 305 38 74330 56 23 54 218 29 44 253 135 27 34 37 26 38 30 900 180 147 183 150 240 90000 1849 89978 0 39 89695 38
+88 408 37 74301 58 25 56 122 31 48 156 232 30 35 37 26 37 29 900 180 148 182 150 240 90000 1843 89976 0 41 89693 35
+89 317 44 74156 48 22 61 124 31 49 164 231 35 35 38 24 39 36 900 180 148 182 150 240 90000 1844 89974 2 43 89692 36
+90 324 46 74008 45 22 59 133 34 46 167 236 36 34 44 25 37 40 900 180 148 182 150 240 90000 1860 89977 2 53 89695 39
+91 329 49 73966 46 25 60 131 36 44 166 237 37 40 44 28 39 43 900 180 147 183 150 240 90000 1859 89978 1 53 89698 40
+92 335 52 73938 45 25 61 131 36 44 164 236 37 41 43 28 41 42 900 180 147 183 150 240 90000 1859 89979 1 56 89700 40
+93 336 52 73903 45 25 60 131 36 45 163 236 37 40 43 28 41 42 900 180 147 183 150 240 90000 1861 89981 1 56 89701 41
+94 336 52 73903 45 25 60 131 36 45 163 236 37 40 43 28 41 42 900 180 147 183 150 240 90000 1861 89981 1 56 89701 41
+95 336 52 73903 45 25 60 131 36 45 163 236 37 40 43 28 41 42 900 180 147 183 150 240 90000 1861 89981 1 56 89701 41
+96 493 52 73916 44 26 60 131 35 48 163 235 36 40 42 28 40 43 900 180 147 183 150 240 90000 1863 89986 5 56 89702 42
+97 693 52 73903 44 26 61 131 35 49 162 235 36 40 42 28 40 43 900 180 147 183 150 240 90000 1863 89988 205 56 89502 44
+98 693 52 73869 44 26 61 131 36 49 164 237 36 40 44 27 40 43 900 180 147 183 150 240 90000 1863 89988 207 56 89505 44
+99 692 52 73849 43 25 62 131 35 46 162 238 34 39 45 28 42 41 900 180 147 183 150 240 90000 1865 89992 207 57 89510 45
+100 693 55 73814 42 25 61 130 35 44 163 238 39 42 49 31 44 39 900 180 147 183 150 240 90000 1867 89992 207 58 89509 43
Added: development/tests/bgs_dyn_mutrates_births/expected/data/resource.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/resource.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/resource.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,17 @@
+# Avida resource data
+# Fri May 25 08:19:43 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_births/expected/data/stats.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/stats.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/stats.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,26 @@
+# Generic Statistics Data
+# Fri May 25 08:19:43 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 0.00507554 0 0 -0 -0 0 3.53885 0 0 0 0
+70 0.00422479 0 0 -0 -0 0 3.9849 0 0 0 0
+80 0.00461506 0 0 -0 -0 0 4.18052 0 0 0 0
+90 0.0068471 0 0 -0 -0 2 4.30835 0 0 0 0
+100 0.00874213 0 0 -0 -0 3 4.37071 0 0 0 0
Added: development/tests/bgs_dyn_mutrates_births/expected/data/tasks.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/tasks.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/tasks.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,94 @@
+# Avida tasks data
+# Fri May 25 08:19:43 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_births/expected/data/time.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_births/expected/data/time.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/expected/data/time.dat 2007-05-25 12:17:37 UTC (rev 1611)
@@ -0,0 +1,18 @@
+# Avida time data
+# Fri May 25 08:19:43 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 0.609339 3.08889 27000
+70 0.712943 4.07444 27000
+80 0.816621 5.03778 27000
+90 0.920418 5.92667 27000
+100 1.02436 6.25444 27000
Added: development/tests/bgs_dyn_mutrates_births/test_list
===================================================================
--- development/tests/bgs_dyn_mutrates_births/test_list (rev 0)
+++ development/tests/bgs_dyn_mutrates_births/test_list 2007-05-25 12:17:37 UTC (rev 1611)
@@ -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-NumBirthsSelection.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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