[Avida-SVN] r1610 - in development/tests: . bgs_dyn_mutrates_fit bgs_dyn_mutrates_fit/config bgs_dyn_mutrates_fit/expected bgs_dyn_mutrates_fit/expected/data
jclune at myxo.css.msu.edu
jclune at myxo.css.msu.edu
Fri May 25 05:04:55 PDT 2007
Author: jclune
Date: 2007-05-25 08:04:55 -0400 (Fri, 25 May 2007)
New Revision: 1610
Added:
development/tests/bgs_dyn_mutrates_fit/
development/tests/bgs_dyn_mutrates_fit/config/
development/tests/bgs_dyn_mutrates_fit/config/avida.cfg
development/tests/bgs_dyn_mutrates_fit/config/environment.77
development/tests/bgs_dyn_mutrates_fit/config/events-Test-ParentFitSelection.cfg
development/tests/bgs_dyn_mutrates_fit/config/inst_set.divide
development/tests/bgs_dyn_mutrates_fit/config/org.div1
development/tests/bgs_dyn_mutrates_fit/config/org.div10
development/tests/bgs_dyn_mutrates_fit/config/org.div100
development/tests/bgs_dyn_mutrates_fit/config/org.div3
development/tests/bgs_dyn_mutrates_fit/config/org.div32
development/tests/bgs_dyn_mutrates_fit/expected/
development/tests/bgs_dyn_mutrates_fit/expected/data/
development/tests/bgs_dyn_mutrates_fit/expected/data/average.dat
development/tests/bgs_dyn_mutrates_fit/expected/data/count.dat
development/tests/bgs_dyn_mutrates_fit/expected/data/creature.final
development/tests/bgs_dyn_mutrates_fit/expected/data/detail-100.pop
development/tests/bgs_dyn_mutrates_fit/expected/data/divide_mut.dat
development/tests/bgs_dyn_mutrates_fit/expected/data/dominant.dat
development/tests/bgs_dyn_mutrates_fit/expected/data/historic-100.pop
development/tests/bgs_dyn_mutrates_fit/expected/data/instruction.dat
development/tests/bgs_dyn_mutrates_fit/expected/data/resource.dat
development/tests/bgs_dyn_mutrates_fit/expected/data/stats.dat
development/tests/bgs_dyn_mutrates_fit/expected/data/tasks.dat
development/tests/bgs_dyn_mutrates_fit/expected/data/time.dat
development/tests/bgs_dyn_mutrates_fit/test_list
Log:
added bgs_dyn_mutrates_fit test
Added: development/tests/bgs_dyn_mutrates_fit/config/avida.cfg
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/avida.cfg (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/avida.cfg 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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_fit/config/environment.77
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/environment.77 (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/environment.77 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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_fit/config/events-Test-ParentFitSelection.cfg
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/events-Test-ParentFitSelection.cfg (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/events-Test-ParentFitSelection.cfg 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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 2
+
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Property changes on: development/tests/bgs_dyn_mutrates_fit/config/events-Test-ParentFitSelection.cfg
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_fit/config/inst_set.divide
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/inst_set.divide (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/inst_set.divide 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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_fit/config/inst_set.divide
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_fit/config/org.div1
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/org.div1 (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/org.div1 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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_fit/config/org.div1
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_fit/config/org.div10
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/org.div10 (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/org.div10 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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_fit/config/org.div10
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_fit/config/org.div100
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/org.div100 (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/org.div100 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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_fit/config/org.div100
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_fit/config/org.div3
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/org.div3 (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/org.div3 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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_fit/config/org.div3
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_fit/config/org.div32
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/config/org.div32 (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/config/org.div32 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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_fit/config/org.div32
___________________________________________________________________
Name: svn:executable
+ *
Added: development/tests/bgs_dyn_mutrates_fit/expected/data/average.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/average.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/average.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,120 @@
+# Avida Average Data
+# Fri May 25 08:07:14 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 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+52 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+53 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+54 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+55 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+56 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+57 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+58 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+59 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+60 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0 0 0.535556 3.11889 0.0041362 -1 0
+61 96.5778 388.859 0.248458 0 100 100 96.5778 4.05405 0.00333333 0.00333333 0.535556 3.12556 -0.00622895 -1 0
+62 96.6022 388.86 0.248522 0 100 100 96.6022 3.91304 0.0644444 0.05 0.551111 3.25111 -0.0151599 -1 0
+63 96.6178 388.313 0.24884 0 100 100 96.6178 3.20285 0.345556 0.227778 0.64 3.82556 0.0206265 -1 0
+64 96.6267 388.28 0.248883 0 100 100 96.6267 2.9316 0.211111 0.126667 0.686667 4.07222 0.0893373 -1 0
+65 96.59 388.239 0.248814 0 100 100 96.59 2.85714 0.0322222 0.0211111 0.698889 4.10889 0.0982627 -1 0
+66 96.5356 388.168 0.248709 0 100 100 96.5356 2.85714 0.00222222 0 0.703333 4.11111 0.09739 -1 0
+67 96.5356 388.168 0.248709 0 100 100 96.5356 2.85714 0 0 0.703333 4.11111 0.09739 -1 0
+68 96.5367 388.384 0.248618 0 100 100 96.5367 2.85714 0.00111111 0 0.703333 4.11111 0.102445 -1 0
+69 96.5367 388.384 0.248618 0 100 100 96.5367 2.85714 0 0 0.703333 4.11111 0.102445 -1 0
+70 96.5367 388.384 0.248618 0 100 100 96.5367 2.85714 0 0 0.703333 4.11111 0.102445 -1 0
+71 96.5389 388.85 0.248428 0 100 100 96.5389 2.85714 0.00111111 0.00111111 0.705556 4.11333 0.100191 -1 0
+72 96.5389 388.85 0.248428 0 100 100 96.5389 2.85714 0 0 0.705556 4.11333 0.100191 -1 0
+73 96.5167 388.827 0.248384 0 100 100 96.5167 2.86624 0.00111111 0.00111111 0.706667 4.11556 0.10334 -1 0
+74 96.5167 388.826 0.248385 0 100 100 96.5167 2.83912 0.0144444 0.00888889 0.71 4.14444 0.0928137 -1 0
+75 96.4589 388.486 0.248407 0 100 100 96.4589 2.76074 0.135556 0.0988889 0.754444 4.39333 0.13911 -1 0
+76 96.5533 388.538 0.24863 0 100 100 96.5533 2.69461 0.256667 0.182222 0.801111 4.80778 0.0827026 -1 0
+77 96.5856 388.587 0.248683 0 100 100 96.5856 2.66272 0.174444 0.116667 0.808889 5.02556 0.130538 -1 0
+78 96.5278 388.513 0.248578 0 100 100 96.5278 2.62391 0.0433333 0.0266667 0.83 5.07556 0.0994184 -1 0
+79 96.4744 388.456 0.248473 0 100 100 96.4744 2.6393 0.0166667 0.00888889 0.834444 5.09889 0.0777322 -1 0
+80 96.4667 388.667 0.248344 0 100 100 96.4667 2.6393 0.00222222 0.00111111 0.837778 5.10111 0.0775871 -1 0
+81 96.4667 388.667 0.248344 0 100 100 96.4667 2.6393 0 0 0.837778 5.10111 0.0775871 -1 0
+82 96.4689 389.107 0.248161 0 100 100 96.4689 2.6393 0.00111111 0 0.838889 5.10222 0.0758624 -1 0
+83 96.4711 389.57 0.247971 0 100 100 96.4711 2.6393 0.00111111 0 0.838889 5.10333 0.0784458 -1 0
+84 96.4733 390.012 0.247785 0 100 100 96.4733 2.63158 0.00111111 0 0.841111 5.10444 0.0817126 -1 0
+85 96.4733 390.012 0.247785 0 100 100 96.4733 2.63158 0 0 0.841111 5.10444 0.0817126 -1 0
+86 96.4733 390.009 0.247787 0 100 100 96.4733 2.63158 0.00555556 0.00444444 0.843333 5.11444 0.0623958 -1 0
+87 96.5 390.248 0.247749 0 100 100 96.5 2.62391 0.0511111 0.0388889 0.852222 5.21889 0.0481827 -1 0
+88 96.5378 390.116 0.24792 0 100 100 96.5378 2.54958 0.162222 0.1 0.906667 5.51 0.0316155 -1 0
+89 96.4756 389.586 0.248005 0 100 100 96.4756 2.54237 0.187778 0.133333 0.92 5.80333 0.0742234 -1 0
+90 96.4956 389.122 0.248253 0 100 100 96.4956 2.5 0.136667 0.0911111 0.917778 5.98667 -0.0292171 -1 0
+91 96.4633 389.316 0.248097 0 100 100 96.4633 2.49307 0.0666667 0.0411111 0.935556 6.06 -0.00110517 -1 0
+92 96.4144 389.478 0.247892 0 100 100 96.4144 2.48619 0.0188889 0.0122222 0.946667 6.08222 0.00411356 -1 0
+93 96.4044 389.467 0.247873 0 100 100 96.4044 2.49307 0.00444444 0.00333333 0.946667 6.08778 0.00372124 -1 0
+94 96.4078 389.469 0.247881 0 100 100 96.4078 2.48619 0.00111111 0 0.95 6.08889 0.00270797 -1 0
+95 96.3856 389.443 0.247837 0 100 100 96.3856 2.48619 0.00111111 0 0.953333 6.08889 0.00215264 -1 0
+96 96.3856 389.443 0.247837 0 100 100 96.3856 2.48619 0 0 0.953333 6.08889 0.00215264 -1 0
+97 96.3856 389.443 0.247837 0 100 100 96.3856 2.48619 0 0 0.953333 6.08889 0.00215264 -1 0
+98 96.3856 389.442 0.247838 0 100 100 96.3856 2.48619 0.00444444 0.00333333 0.953333 6.09778 -0.00145323 -1 0
+99 96.3856 389.44 0.247839 0 100 100 96.3856 2.47253 0.0155556 0.00888889 0.96 6.12556 0.0364026 -1 0
+100 96.3256 389.332 0.247751 0 100 100 96.3256 2.45232 0.0855556 0.0588889 0.993333 6.3 -0.0316091 -1 0
Added: development/tests/bgs_dyn_mutrates_fit/expected/data/count.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/count.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/count.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,30 @@
+# Avida count data
+# Fri May 25 08:07:14 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 900 222 22 0 0 0 0 0 0 261 900 900 0 0
+70 27000 900 315 38 0 0 0 0 0 0 399 464 900 0 0
+80 27000 900 341 45 0 0 0 2 2 1 505 486 900 0 0
+90 27000 900 360 49 0 0 0 123 123 82 544 478 900 0 0
+100 27000 900 367 51 0 0 0 77 77 53 549 480 900 0 0
Added: development/tests/bgs_dyn_mutrates_fit/expected/data/creature.final
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/creature.final (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/creature.final 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,202 @@
+# Fri May 25 08:07:18 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_fit/expected/data/detail-100.pop
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/detail-100.pop (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/detail-100.pop 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,384 @@
+#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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+1268 393 3 1 1 100 0 0 0 91 -1 3 rycazccccccccccccccccccccccccccccccccccccBecccbccccczcccccccccccccccccccccccccBCcccccccccccyxCcaszab
+1269 1077 1 1 1 100 0 0 0 91 -1 3 rycazcccccccccyuccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccqccccccccccyxCcatzab
+1270 535 2 1 1 100 0 0 0 91 -1 3 jycazcccccccccccccccccBcccccccncccccccCciccccccccccccccccccccccvsccccccccccccccccccccjcccccyxCcaszab
+1271 882 1 1 1 100 0 0 0 92 -1 2 rycazcccccccccccccccccccccccccccccccccccccccclccccccccccccccccccccccccccccccccccccrccccccccyxCcavzab
+1272 639 3 1 1 100 0 0 0 92 -1 3 rycazccccccccCcchccccccccccccccccccccccccccccccsccccccccccxcccrcccccccccccccccccccccccchcccyxCxaszab
+1273 571 2 1 1 100 0 0 0 92 -1 3 rycaCccccccfcccccccccccccccccccdccccyccccccccccccccccpccccczcccccccccccccccccccccccccccccccyxCcaszab
+1274 686 3 1 1 100 0 0 0 92 -1 4 rycazcccccccccccccccccccCccccccccccccccccccccccccccccccccccccgckcccccccccccccfcccccccocccccyxCcatzab
+811 426 1 1 2 100 97 387 0.250646 63 -1 2 rycazcccccccaccccccccccccccccccccccccccccccccccccccccccfcccccccccccjcccccccccccccccccccccccyxCcaszab
+1275 592 2 1 1 100 0 0 0 92 -1 2 rycazcDccccccccccccccccccccccccccjcccccccccccccccccwcccccccccccccccccccccccccccccccccccccckyxCcaszab
+1276 895 5 1 1 100 0 0 0 92 -1 3 rycazccccccvgCcccckccccccccchcccccccirccccccccBcccccccccccccccrfcccccccAcccccccccccvcccceccyxCcaszab
+1277 1078 2 1 1 100 0 0 0 93 -1 4 rycazcrcfcccccccccccccccccccccccccccccccccccccchcccczcccccccccccccccccccccccccBCccccccccclcyxCcaszab
+1278 1084 3 1 1 100 0 0 0 94 -1 4 rycazcccccccccccccccccccCccccccccsncccccccccccccccccccccccccccckccccccccccccccccccccccccccAyxCcatzaw
+1279 610 1 1 1 100 0 0 0 95 -1 4 rycazcccccccccccccccccczmccccccccCcccccccccccccccccczcccccccccccccccccccccccccBCcccccccccccyxCcaszab
+1280 908 4 1 1 100 0 0 0 98 -1 3 rycaiccccccccccccccccccccccccccccncccccccccctckccccccccccccccccccfccccccccccfccccccccccccccyxCcaszab
+882 4 1 1 3 100 97 389 0.249357 64 -1 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccrccccccccyxCcavzab
+1281 256 2 1 1 100 0 0 0 99 -1 3 rycazcccciccccccccccccccccccccclccccccccccccccccccccccwcccccccccccccccccccccccccczcccccccncyxCcatzab
+1282 1 3 1 1 100 0 0 0 99 -1 1 rycazccccccccccccccccccccccccccccccccccccmcccccccccccccccccccccccccccccccccccccccDcccccccccyxCzaszab
+1283 1093 1 1 1 100 0 0 0 99 -1 3 rycazccccccccccccccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccrccccccccccccyxCcatzac
+1285 2 1 1 1 100 0 0 0 99 -1 1 ryqazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+1286 4 1 1 1 100 0 0 0 99 -1 1 rycazccccccccccccccccccccccccccchccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcavzab
+479 2 1 1 4 100 97 388 0.25 37 -1 1 rycazccccccccccccccccccccccccccccccccccccccccecccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+975 628 1 1 2 100 0 0 0 76 -1 2 rycazccccDcccccccccccccccccccccccccccccccccccccccccccccccccccctccccccccccccccccccccccccccccyxCcauzab
+36 3 1 1 6 100 97 389 0.249357 13 -1 1 rycazccccccchccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+1287 19 2 1 1 100 0 0 0 100 -1 2 rycazcmcccccccccccccccccccccaccccccccccccccccccccccccccicccccccccccccccjcccccccccccccccccccyxCcaszab
+695 2 1 1 3 100 0 0 0 50 -1 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccAcccccccccccccccccccyxCcatzab
+1288 789 2 1 1 100 0 0 0 100 -1 4 rycazcccccccccdcccwccccccccvcccccqcCcvxccccccccccccccccctccccccccccmccccccccccccgccccccccccyxCcaszab
+1289 5 2 1 1 100 0 0 0 100 -1 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccctcccccccccciccccccccyxCcawzab
+1290 491 1 1 1 100 0 0 0 100 -1 3 rycazcyccccccccccccccccqzccccccccccccccccccccccccpccccCccwcccccccccccccccccccccccccccccccccyxCcatzab
+520 1 1 1 3 100 97 388 0.25 38 -1 1 rycazcccccccccccccclcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+1291 339 2 1 1 100 0 0 0 100 -1 2 rycazccccccccccccccccccccccccccmcccccpcccvcccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+1292 964 5 1 1 100 0 0 0 100 -1 3 rycazzDccccccccccccccccccccccccccicccccccccccccccccwtcccccccccccccccccccccccchccclcccccccccyvCcaszab
+1293 525 5 1 1 100 0 0 0 100 -1 3 ryiazccccccccccccscccccccccccccccccccgccncccccccccccccjejccccccccccccccccccccccccccccccccccyxCcaszab
+1294 3 1 1 1 100 0 0 0 100 -1 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccczcccyxCcauzab
+863 221 2 1 2 100 97 388 0.25 64 -1 2 rycazccchcccccccccccccccccccccwcccccccccccccccccccccccccccccccczcccccccccccccccccccccccccccyxCcatzab
+1295 1146 1 1 1 100 0 0 0 100 -1 5 rycazcccccceccCccccccccccccecccccccczccccccccccccccccccccccccccccccccccccccceccccroccccBcccyxCcatzab
+1296 916 1 1 1 100 0 0 0 100 -1 3 rycazcccpcccccccccccccccccccccccccccccpcccccccccccccccccccccccccccccccccccccchccccccncccccmyxCcatzab
+1297 660 2 1 1 100 0 0 0 100 -1 3 rycazccccccccmccccccccccrccccccccccccccccccccccccccctccccccccccccccccccccvcccccccccdcccccccyxCcatzab
+1298 1114 2 1 1 100 0 0 0 100 -1 4 rycazccccccccccccsccccccccccccdccjcccrccccccccccccckccccccccccccccccccccccCcccccccccfccccgcyxCcaszab
+1299 1149 2 1 1 100 0 0 0 100 -1 4 rycazcccfccccccctcccccycchcccccccccccccccccccccuccccccxicccccccccccccrcjcccccccccccccccccccyxCcaszab
+1300 3 1 1 1 100 0 0 0 100 -1 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCuauzab
+1301 687 1 1 1 100 0 0 0 100 -1 2 rycazccccccccccccccccccccccpccccccccccccqccccccccccccccccccccccccccccccccccccccccccccccccccyxCcawzab
+1302 295 3 1 1 100 0 0 0 100 -1 3 rycazcccccccccccccccccccccccccccrcccccccccccccccccccccccccccpccccccccccccccccccpcccccccrctcyxCcatzab
+1303 2 1 1 1 100 0 0 0 100 -1 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccccyxCcatzab
+1305 770 4 1 1 100 0 0 0 100 -1 3 rycazcccccccccscccrcccccccccccacccccccccccccccAcccceczcccccccccccccccccccccccccccxccBcccctcyxCcaszab
+7 2 2 1 7 100 97 388 0.25 12 -1 1 rycazcccccccccccsccccccccccccccccccccccccccccccccDcccccccccccccccccccccccccccccccccccccccccyxCcatzab
+1306 928 1 1 1 100 0 0 0 100 -1 5 rycazccccccccccuccccccccccccccccrcccccccccccccccbccccccaaccccccccccccccccccccccccccccccccccyxCcauzab
+839 179 2 1 3 100 97 387 0.250646 64 -1 2 rycazccccccccccccccuccccccccccccccccccmccccccccccccccccccccccccccccccccccccccccncccccccccccyxCcatzab
+1307 1120 1 1 1 100 0 0 0 100 -1 4 rycazbcccccccccygcccccccccccccluccccccCcicccccccccccccccccccccclscccccccccAccccccccccjcccccyxCcaszab
+1308 1147 2 1 1 100 0 0 0 100 -1 5 rycazcccccccccoccsccccccocccccceavccccccmccccccccccccccccqccccccccccccccccvccccccccccccccccyxCcaszab
+1309 742 7 1 1 100 0 0 0 100 -1 3 rycfzcccccccvuccaccccccccscccccccccscccccccccnlcccccccgccccccjccccqcccccccocyccccccccccccccyxCcaszab
+1310 1119 6 1 1 100 0 0 0 100 -1 5 rycpzcccccccvtcpccccccccccccccccccclcvsccccccqcccccbccccccCccczcccccccccccccucccccccccccvccyxCcaszab
Added: development/tests/bgs_dyn_mutrates_fit/expected/data/divide_mut.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/divide_mut.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/divide_mut.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,105 @@
+# Avida divide mutation rate data
+# Fri May 25 08:07:15 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 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.2572 3.0078 1.7343 -2.22552 15.229
+52 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.27071 3.01531 1.73647 -2.17524 15.2207
+53 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.2837 3.0222 1.73845 -2.12628 15.2117
+54 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.29622 3.02852 1.74026 -2.07865 15.2021
+55 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.30828 3.03431 1.74193 -2.03232 15.192
+56 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.31991 3.03961 1.74345 -1.98726 15.1815
+57 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.33112 3.04448 1.74484 -1.94344 15.1706
+58 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.34196 3.04893 1.74612 -1.90082 15.1596
+59 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.35242 3.05302 1.74729 -1.85939 15.1483
+60 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.36254 3.05675 1.74836 -1.8191 15.1369
+61 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.37232 3.06017 1.74934 -1.77993 15.1254
+62 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.38179 3.0633 1.75023 -1.74183 15.1139
+63 0.00848736 0.00012654 0.011249 1.74608e-06 4.51094e-08 -5.39095 3.06616 1.75105 -1.70479 15.1023
+64 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.39985 3.06876 1.75179 -1.66857 15.0907
+65 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.40848 3.07113 1.75246 -1.63334 15.079
+66 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.41684 3.07328 1.75308 -1.59906 15.0674
+67 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.42496 3.07524 1.75364 -1.56571 15.0559
+68 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.43283 3.07701 1.75414 -1.53325 15.0445
+69 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.44048 3.07861 1.7546 -1.50166 15.0332
+70 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.44791 3.08006 1.75501 -1.4709 15.022
+71 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.45513 3.08136 1.75538 -1.44095 15.0109
+72 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.46214 3.08252 1.75571 -1.41179 14.9999
+73 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.46897 3.08356 1.75601 -1.38337 14.989
+74 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.47561 3.08448 1.75627 -1.35569 14.9783
+75 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.48209 3.08527 1.7565 -1.32856 14.9676
+76 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.48839 3.08598 1.7567 -1.30227 14.9572
+77 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.49452 3.0866 1.75687 -1.27663 14.9468
+78 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.50049 3.08712 1.75702 -1.25164 14.9367
+79 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.50631 3.08756 1.75715 -1.22726 14.9266
+80 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.51198 3.08793 1.75725 -1.20347 14.9167
+81 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.51752 3.08823 1.75734 -1.18027 14.9069
+82 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.52292 3.08846 1.7574 -1.15762 14.8973
+83 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.52819 3.08862 1.75745 -1.13551 14.8878
+84 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.53333 3.08873 1.75748 -1.11392 14.8784
+85 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.53835 3.08879 1.7575 -1.09284 14.8692
+86 0.00847958 0.000126571 0.0112504 1.74885e-06 4.5165e-08 -5.54326 3.0888 1.7575 -1.07225 14.8601
+87 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.54807 3.08875 1.75748 -1.05201 14.851
+88 0.00846403 0.000126633 0.0112531 1.7544e-06 4.52765e-08 -5.55278 3.08864 1.75745 -1.03209 14.842
+89 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.55737 3.08851 1.75741 -1.01276 14.8332
+90 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.56187 3.08833 1.75737 -0.993856 14.8245
+91 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.56626 3.08813 1.75731 -0.975376 14.816
+92 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.57055 3.08789 1.75724 -0.957303 14.8076
+93 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.57476 3.08762 1.75716 -0.939627 14.7993
+94 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.57887 3.08732 1.75708 -0.922333 14.7911
+95 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.5829 3.08699 1.75698 -0.905412 14.783
+96 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.58684 3.08664 1.75688 -0.888851 14.7751
+97 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.59071 3.08627 1.75678 -0.872641 14.7672
+98 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.59449 3.08587 1.75666 -0.85677 14.7595
+99 0.00847181 0.000126602 0.0112518 1.75162e-06 4.52207e-08 -5.5982 3.08546 1.75655 -0.84123 14.7519
+100 0.00845625 0.000126663 0.0112545 1.75717e-06 4.53323e-08 -5.60186 3.085 1.75642 -0.825784 14.7442
Added: development/tests/bgs_dyn_mutrates_fit/expected/data/dominant.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/dominant.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/dominant.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,30 @@
+# Avida Dominant Data
+# Fri May 25 08:07:14 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 97 224 0 0 0 0 0.252604 5 100-aaaae
+70 97 389 0.249357 0.00257069 100 100 97 219 0 0 0 0 0.252604 5 100-aaaae
+80 97 389 0.249357 0.00257069 100 100 97 217 0 0 0 0 0.252604 5 100-aaaae
+90 97 389 0.249357 0.00257069 100 100 97 220 38 36 0 0 0.253927 5 100-aaaae
+100 97 389 0.249357 0.00257069 100 100 97 217 24 23 0 0 0.253927 5 100-aaaae
Added: development/tests/bgs_dyn_mutrates_fit/expected/data/historic-100.pop
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/historic-100.pop (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/historic-100.pop 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,117 @@
+#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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+900 563 2 0 1 100 96 384 0.25 65 100 3 rycazcccccccccdccccccccccccvcccccqcCcvcccccccccccccccccBtccccccccccmcccccccccccccccacccccccyxCcaszab
+967 607 6 0 1 100 0 0 0 76 100 3 rycazcccfccrcccccccccccccccckcccxccccccccccccccrcccccccilccccccccccccrcjccccccccbccccccccccyxCcaszab
+19 1 2 0 3 100 97 387 0.250646 12 100 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccicccccccccccccccjcccccccccccccccccccyxCcaszab
+570 295 1 0 4 100 97 387 0.250646 39 100 3 rycazcccccccccccccccccccccccccccrcccccdccccccccccccccccccccccccccccccccccccccccpcccccccccccyxCcatzab
+1093 372 1 0 1 100 0 0 0 87 99 2 rycazccccccccccccccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccrccccccccccccyxCcatzab
+625 2 1 0 2 100 97 388 0.25 40 99 1 rycazccccccccccccccccccccccccccccccccccccccccccccccicccccccccccccccccccccccccccccccccccccccyxCcatzab
+693 1 5 0 3 100 97 388 0.25 50 95 1 rycazccccgcccccccwccccBvcccccccccccccccccccccccccccccccccccccccccctccccccccccccccccccccccccyxCcaszab
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+602 396 2 0 3 100 97 386 0.251295 40 92 2 rycazccccccccccccwccccccccccccccccccccclcccrcccccccccccccccccccccccccccccccccclcjacccccccccyxCcaszab
+271 108 1 0 3 100 88 377 0.233422 25 91 2 rycazcccccccccccccccuccccrccccccccccccczccccDccccccccccccccccccccycccccccccccccccccccccccccyxCcaszab
+930 807 3 0 1 100 0 0 0 75 91 3 rycawccccccccccccccchcccccucwcccccccccccccccccccccchccccccccccccakcocccccccccccccccczccccccyxCcaszab
+258 2 1 0 6 100 97 389 0.249357 25 91 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchccccccccccccccccccccyxCcatzab
+1075 900 3 0 1 100 0 0 0 78 91 4 rycazcecccccccdccccccccccccvcccccqcCcvcccccccccccccccccBtccccccDcccmccccccccccccDccacccccccyxCcaszab
+1073 871 3 0 1 100 0 0 0 78 91 3 rycazccccccccccccccccccccccccgccpccicccccccccccdccccccccccccccccccccwccccccccccccccccccccccyxCcatzab
+1068 4 1 0 1 100 0 0 0 78 90 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccfcccccccccccyxCcavzab
+783 236 3 0 1 100 97 387 0.250646 63 90 2 rycazcccccccvccccccccccccccccccccccccccccccccccccccciccccaoccccccccccccccccccccccccvccccvccyxCcaszab
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+732 2 2 0 1 100 97 387 0.250646 63 90 1 rycazcccccccccccccccccccccccccccccccccpcccccccccccccccccccccccccccccccccccccccccccccnccccccyxCcatzab
+708 599 2 0 1 100 97 387 0.250646 62 90 2 rycazcccccccccccccccccccccccccccczccccccccccccccccccccccccccccccccccccccccccccccccczcccccccyxCcatzab
+965 762 2 0 1 100 0 0 0 76 90 3 rycazcccwccccccccccccccccccccccccpcccsccccccmccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+395 128 4 0 2 100 97 387 0.250646 27 90 2 rycazcmcccccccccccccccccccccccccccccccccccccccccccccccccvnuccccccccccccccccccccmcccccccccccyxCcaszab
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+1013 2 3 0 1 100 0 0 0 77 89 1 rycazcccxccccccccccccccccccccccccccccccccccccccccccccccccccrccccccccccCccccccccccccccccccccyxCcatzab
+426 1 2 0 6 100 97 387 0.250646 27 89 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccfcccccccccccjcccccccccccccccccccccccyxCcaszab
+959 580 1 0 1 100 0 0 0 76 89 2 rycazcclcccccccccccccccccccccccccfcccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+943 258 1 0 1 100 0 0 0 75 89 2 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchcccczcccccccccccccccyxCcatzab
+917 772 2 0 1 100 0 0 0 75 89 2 rycazcccccccccccccceccpccccsBcccccccccccCbcccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+701 655 1 0 2 100 87 378 0.230159 62 89 3 rycazcccccccvccccccccccccccccccccccccvcccccccccccccbccccccCcccccccccccccccccccccccccccccvccyxCcaszab
+810 1 2 0 2 100 97 385 0.251948 63 89 1 rycazcccciccccccccccccccccccccccccccccccccccccccccccccccxccccccccccccccccccccccccccccccccccyxCcaszab
+377 1 1 0 3 100 97 389 0.249357 26 88 1 rycazccccccccccccscccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
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+979 878 3 0 1 100 0 0 0 76 88 4 rycazcccccccccccccccccccccccccccccceccccccccccceccccccniccqcccccccccccmjcccctccccccccccccsByxCcaszab
+948 509 1 0 1 100 0 0 0 76 88 3 rycazcccccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccccccjccccccccccgxccccccyxCcatzab
+787 638 3 0 1 100 0 0 0 63 88 2 rycazccccccccccccccccccrcccccccccccccbcccccccccccczcccccccccccccccccccccccccvccccccccccccccyxCcpszab
+849 607 1 0 1 100 0 0 0 64 88 3 rycazcccfccccccccccccccccccccccccccccccccccccccccccccccicczccccccccccrcjcccccccccccccccccccyxCcaszab
+682 1 3 0 2 100 88 378 0.232804 50 88 1 rycazccccccccccccccccccccycccccccccccccccccccccccccccccgcccvcccccccccccccccccccccccccccccccyxCcaszab
+599 2 1 0 2 100 97 388 0.25 39 88 1 rycazccccccccccccccccccccccccccccocccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+580 2 1 0 2 100 97 388 0.25 39 88 1 rycazccccccccccccccccccccccccccccfcccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+630 1 2 0 3 100 97 388 0.25 40 88 1 rycazcccccccccccccccccccccccccccccccccccccccccccclcccccccccccccccccccccccccccccwcccccccccccyxCcaszab
+563 381 4 0 3 100 96 384 0.25 39 87 2 rycazcccccccccdccccccccccccvcccccqcCcvcccccccccccccccccctccccccccccmcccccccccccccccccccccccyxCcaszab
+898 520 4 0 1 100 0 0 0 65 87 2 rycazcccccccccccccclccccccsccccccccqccccccccccccccccbcccccccfccccccccccccccccccccccccccccccyxCcaszab
+762 200 1 0 1 100 0 0 0 63 83 2 rycazcccwccccccccccccccccccccccccpcccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+338 1 1 0 3 100 97 389 0.249357 26 79 1 rycazccccccccccccccccccccccccccccccccchccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+161 1 2 0 3 100 87 378 0.230159 14 78 1 rycazccccccccCccccccccccccccccccccccccccccccccccccccccccccccccrccccccccccccccccccccccccccccyxCcaszab
+590 340 1 0 4 100 97 387 0.250646 39 78 2 rycazccccccccccccccccccccccccccccccccccccccccccccccckccccccccccccccccccccfcccccccccccccccccyxCcatzab
+348 1 2 0 2 100 97 387 0.250646 26 78 1 rycazccccccccccccccccccccccccccgcccccccccccccccccccccccccBcccccccccccccccccccccccccccccccccyxCcaszab
+887 1 5 0 1 100 0 0 0 64 77 1 rycazcccccccdccccccccccccccccccccccccccccccccccdcccccccpcccBcccccccCcccccccccccccccccccccccyxCcaszab
+878 380 3 0 1 100 0 0 0 64 77 3 rycazcccccccccccccccccccccccccccccceccccccccccccccccccniccccccccccccccmjcccctcccccccccccccByxCcaszab
+691 2 1 0 4 100 97 388 0.25 50 77 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccccccccccccccccccyxCcatzab
+677 3 1 0 3 100 97 388 0.25 49 77 1 rycazcccccccccccccccnccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+358 2 1 0 3 100 97 388 0.25 26 76 1 rycazccccccccccccccccccccccccccccqcccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+301 2 1 0 4 100 97 389 0.249357 26 76 1 rycazccccccccccccccccccccccccccwcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+509 312 1 0 2 100 97 384 0.252604 38 76 2 rycazcccccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccccccjcccccccccccxccccccyxCcatzab
+688 2 1 0 2 100 97 388 0.25 50 76 1 rycazccccccccccccccccccccccccccccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+586 3 1 0 2 100 97 388 0.25 39 76 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccgcccccccccccccccccccccccccyxCcauzab
+807 231 2 0 1 100 0 0 0 63 76 2 rycazccccccccccccccchcccccccccccccccccccccccccccccchccccccccccccakcocccccccccccccccczccccccyxCcaszab
+769 245 1 0 1 100 0 0 0 63 76 2 rycazcccccccccccccccccccccccccccccccccmcccccccccccccccccccccccccccwccccccccccccccccccccccccyxCcauzab
+269 1 2 0 2 100 87 378 0.230159 25 76 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccCccccccccccdcccccccccccccccccccccyxCcaszab
+179 2 1 0 3 100 97 388 0.25 14 76 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccncccccccccccyxCcatzab
+704 543 2 0 1 100 0 0 0 62 75 3 rycazcccccccccccrocccccccccccccccccccccccccdcccccccccccccccccccccdccccccccccCccccccccccccccyxCcatzab
+94 2 2 0 3 100 97 388 0.25 13 75 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccwcccccccccccccccccccccccccczcccccccccyxCcatzab
+722 1 1 0 1 100 0 0 0 63 75 1 rycazccccccccccccccccccccccccccccccccccccccccckccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+210 2 1 0 3 100 97 389 0.249357 14 75 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccctcccyxCcatzab
+221 2 1 0 5 100 97 389 0.249357 14 75 1 rycazccchccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+581 1 2 0 3 100 0 0 0 39 66 1 rycazcccccccaccccccccccccccccccccccceccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+435 1 2 0 2 100 97 388 0.25 27 64 1 rycazccccccccccccccccccccsccccccccccccccccccccccccccccccccccccccccccccccccoccccccccccccccccyxCcaszab
+647 3 1 0 3 100 0 0 0 41 64 1 rycazcccccccccoccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcauzab
+692 377 2 0 3 100 97 388 0.25 50 64 2 rycazccccccccccccscccccccccccccccccccccccccccccccccccccccqccccccccccccccccvccccccccccccccccyxCcaszab
+638 1 2 0 2 100 0 0 0 40 64 1 rycazccccccccccccccccccccccccccccccccbccccccccccccccccccccccccccccccccccccccvccccccccccccccyxCcaszab
+97 2 1 0 4 100 97 388 0.25 13 63 1 rycazccccccccccccccccccccccccccccccczccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+449 192 1 0 2 100 97 384 0.252604 28 63 2 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccctcccccccccccccccctcxcccccfcdcyxCcaszab
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+661 210 2 0 2 100 0 0 0 41 63 2 rycazcccccccccccccccccccccvccccccccccccccccccrccccccccccccccccccccccccccccccccccccccccctcccyxCcatzab
+409 1 1 0 3 100 97 389 0.249357 27 63 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccrccccccccccccccccccccccccccccccccccccccyxCcaszab
+493 3 1 0 3 100 0 0 0 38 63 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccwcccccccccccccccccccccccccyxCcauzab
+345 97 1 0 2 100 0 0 0 26 63 2 rycazccccccccccccccccccccccccccccccczccccccccccccccccccccccccccccccccccccccceccccccccccccccyxCcatzab
+543 382 1 0 2 100 0 0 0 39 63 2 rycazcccccccccccrocccccccccccccccccccccccccccccccccccccccccccccccdcccccccccccccccccccccccccyxCcatzab
+200 2 1 0 3 100 97 388 0.25 14 63 1 rycazccccccccccccccccccccccccccccpcccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+148 1 2 0 2 100 87 378 0.230159 14 62 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccBCcccccccccccyxCcaszab
+381 1 3 0 1 100 0 0 0 26 50 1 rycazcccccccccdccccccccccccvcccccccccccccccccccccccccccccccccccccccmcccccccccccccccccccccccyxCcaszab
+340 2 1 0 1 100 0 0 0 26 50 1 rycazccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccfcccccccccccccccccyxCcatzab
+444 2 2 0 1 100 0 0 0 27 50 1 rycazcccccccccccccccccccrccccccccccccccccccccccccccccccccccccccccccccccccccccccccccdcccccccyxCcatzab
+64 2 1 0 2 100 97 388 0.25 13 41 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccckcccccccccccccccccccccccccccyxCcatzab
+376 1 2 0 1 100 0 0 0 26 41 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccxccccccccccccccccccccccccocccyxCcaszab
+158 1 3 0 1 100 97 387 0.250646 14 40 1 rycazccccccccccDccccccccccccccccccccccccccccccccccccucccccccccccccccccccccnccccccccccccccccyxCcaszab
+433 1 3 0 1 100 0 0 0 27 40 1 rycaCccccccccccccccccccccccccccccccccccccccccccccccccpccccczcccccccccccccccccccccccccccccccyxCcaszab
+312 2 2 0 1 100 0 0 0 26 40 1 rycazcccccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccxccccccyxCcatzab
+382 2 2 0 1 100 0 0 0 26 39 1 rycazccccccccccccocccccccccccccccccccccccccccccccccccccccccccccccdcccccccccccccccccccccccccyxCcatzab
+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
+192 1 4 0 1 100 0 0 0 14 38 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccctcxcccccfcdcyxCcaszab
+128 1 1 0 1 100 0 0 0 13 38 1 rycazcmccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyxCcaszab
+89 2 1 0 1 100 0 0 0 13 37 1 rycazcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccqccccccccccccccccccccccccyxCcatzab
+68 2 1 0 1 100 0 0 0 13 28 1 rycazccccccccccccccccccccccccccccccccccccqcccccccccccccccccccccccccccccccccccccccccccccccccyxCcatzab
+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_fit/expected/data/instruction.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/instruction.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/instruction.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,115 @@
+# Avida instruction execution data
+# Fri May 25 08:07:15 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
+
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+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
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+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
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+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
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+60 201 13 75322 15 7 21 6 35 16 29 112 22 25 28 18 26 11 900 180 148 182 150 240 90000 1823 90008 1 17 89907 12
+61 201 13 75322 15 7 21 6 35 16 29 112 22 25 28 18 26 11 900 180 148 182 150 240 90000 1823 90008 1 17 89907 12
+62 201 17 75302 16 7 21 8 34 15 33 114 22 22 30 22 24 12 900 180 148 182 150 240 90000 1821 90006 1 18 89906 16
+63 109 16 75061 21 8 24 16 46 24 45 114 28 27 24 34 30 31 900 180 148 182 150 240 90000 1825 90008 1 20 89902 21
+64 113 18 74992 21 12 30 15 42 30 50 114 28 31 25 32 32 28 900 180 147 183 150 240 90000 1821 90010 1 28 89903 17
+65 113 18 74945 22 12 28 15 40 31 49 114 29 33 25 30 33 30 900 180 147 183 150 240 90000 1822 90009 1 28 89909 17
+66 112 18 74877 22 11 29 15 40 31 49 114 29 33 25 31 33 30 900 180 147 183 150 240 90000 1823 90006 1 28 89910 17
+67 112 18 74877 22 11 29 15 40 31 49 114 29 33 25 31 33 30 900 180 147 183 150 240 90000 1823 90006 1 28 89910 17
+68 211 18 74878 22 11 28 15 40 31 49 213 29 33 25 31 33 30 900 180 147 183 150 240 90000 1823 90005 1 28 89810 17
+69 211 18 74878 22 11 28 15 40 31 49 213 29 33 25 31 33 30 900 180 147 183 150 240 90000 1823 90005 1 28 89810 17
+70 211 18 74878 22 11 28 15 40 31 49 213 29 33 25 31 33 30 900 180 147 183 150 240 90000 1823 90005 1 28 89810 17
+71 411 18 74875 22 11 28 15 40 31 49 213 29 33 25 31 33 30 900 180 147 183 150 240 90000 1823 90006 1 28 89810 17
+72 411 18 74875 22 11 28 15 40 31 49 213 29 33 25 31 33 30 900 180 147 183 150 240 90000 1823 90006 1 28 89810 17
+73 411 19 74850 22 11 28 15 39 31 49 213 29 33 25 30 33 30 900 180 147 183 150 240 90000 1823 90006 1 28 89812 17
+74 411 19 74848 22 11 28 16 39 31 49 215 29 32 26 30 33 30 900 180 147 183 150 240 90000 1823 90006 1 27 89812 16
+75 318 19 74690 27 15 28 18 44 33 48 118 30 36 32 29 35 34 900 180 146 184 150 240 90000 1824 90003 1 34 89911 16
+76 325 17 74683 32 20 34 20 41 37 49 116 31 36 29 33 31 40 900 180 147 183 150 240 90000 1819 90007 1 34 89905 23
+77 327 21 74708 38 20 32 25 37 38 42 110 33 39 27 28 32 39 900 180 147 183 150 240 90000 1817 90012 1 39 89908 21
+78 329 23 74616 42 20 34 24 38 37 46 111 29 40 26 28 36 38 900 180 147 183 150 240 90000 1822 90016 1 40 89911 23
+79 328 25 74554 42 20 34 24 37 37 43 112 30 39 26 28 35 40 900 180 147 183 150 240 90000 1824 90015 1 41 89914 23
+80 328 26 74539 42 20 34 23 37 37 43 112 30 39 26 28 37 40 900 180 147 183 150 240 90000 1825 90017 1 40 89914 23
+81 328 26 74539 42 20 34 23 37 37 43 112 30 39 26 28 37 40 900 180 147 183 150 240 90000 1825 90017 1 40 89914 23
+82 508 26 74535 42 20 34 43 37 37 43 112 30 39 26 28 37 40 900 180 147 183 150 240 90000 1825 90019 1 40 89914 23
+83 708 28 74532 42 20 34 43 37 37 43 112 30 39 26 28 36 40 900 180 147 183 150 240 90000 1825 90019 1 42 89914 23
+84 908 28 74529 42 20 33 43 37 36 43 112 32 39 26 28 36 40 900 180 147 183 150 240 90000 1825 90019 201 42 89714 23
+85 908 28 74529 42 20 33 43 37 36 43 112 32 39 26 28 36 40 900 180 147 183 150 240 90000 1825 90019 201 42 89714 23
+86 908 27 74522 42 20 33 43 37 36 43 113 32 39 28 28 36 40 900 180 147 183 150 240 90000 1825 90019 201 42 89714 23
+87 1009 27 74536 43 22 32 44 41 37 44 215 31 40 26 29 35 38 900 180 146 184 150 240 90000 1822 90017 201 42 89613 21
+88 1017 29 74463 45 27 36 49 43 32 45 221 37 44 30 28 44 38 900 180 145 185 150 240 90000 1817 90014 201 42 89611 23
+89 824 26 74330 48 31 38 38 45 38 47 126 41 40 28 37 44 42 900 180 146 184 150 240 90000 1822 90016 202 44 89717 24
+90 621 23 74324 50 33 41 45 47 43 48 125 42 38 29 42 43 47 900 180 146 184 150 240 90000 1821 90010 202 41 89716 26
+91 717 26 74277 48 34 43 45 48 41 50 126 43 38 28 43 47 49 900 180 146 184 150 240 90000 1826 90008 202 37 89716 29
+92 716 26 74214 48 35 42 45 48 42 48 126 41 38 28 43 48 49 900 180 146 184 150 240 90000 1827 90008 202 40 89719 30
+93 716 27 74202 48 35 42 45 48 42 48 127 41 38 28 43 48 48 900 180 146 184 150 240 90000 1827 90008 202 40 89720 30
+94 716 27 74203 48 35 42 45 48 42 48 128 41 38 28 43 48 48 900 180 146 184 150 240 90000 1826 90008 202 40 89721 30
+95 716 27 74180 48 35 42 44 48 42 48 128 41 39 28 43 48 48 900 180 146 184 150 240 90000 1826 90009 202 40 89723 30
+96 716 27 74180 48 35 42 44 48 42 48 128 41 39 28 43 48 48 900 180 146 184 150 240 90000 1826 90009 202 40 89723 30
+97 716 27 74180 48 35 42 44 48 42 48 128 41 39 28 43 48 48 900 180 146 184 150 240 90000 1826 90009 202 40 89723 30
+98 716 27 74179 48 35 42 44 48 41 48 129 41 39 29 43 48 48 900 180 146 184 150 240 90000 1826 90009 202 40 89723 30
+99 716 27 74170 48 35 42 44 48 40 47 129 41 40 30 44 48 48 900 180 146 184 150 240 90000 1826 90010 202 40 89723 30
+100 719 28 74033 48 39 40 47 47 40 48 128 44 45 31 43 51 50 900 180 144 186 150 240 90000 1830 90008 204 40 89725 28
Added: development/tests/bgs_dyn_mutrates_fit/expected/data/resource.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/resource.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/resource.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,17 @@
+# Avida resource data
+# Fri May 25 08:07:14 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_fit/expected/data/stats.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/stats.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/stats.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,26 @@
+# Generic Statistics Data
+# Fri May 25 08:07:14 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 0.00361181 0 0 -0 -0 0 3.57641 0 0 0 0
+70 0.00296782 0 0 -0 -0 0 3.92006 0 0 0 0
+80 0.0040709 0 0 -0 -0 0 4.06934 0 0 0 0
+90 0.00443965 0 0 -0 -0 6 4.09949 0 0 0 0
+100 0.0064624 0 0 -0 -0 3 4.15066 0 0 0 0
Added: development/tests/bgs_dyn_mutrates_fit/expected/data/tasks.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/tasks.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/tasks.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,94 @@
+# Avida tasks data
+# Fri May 25 08:07:14 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_fit/expected/data/time.dat
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/expected/data/time.dat (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/expected/data/time.dat 2007-05-25 12:04:55 UTC (rev 1610)
@@ -0,0 +1,18 @@
+# Avida time data
+# Fri May 25 08:07:14 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 0.609324 3.11889 27000
+70 0.712872 4.11111 27000
+80 0.816473 5.10111 27000
+90 0.92012 5.98667 27000
+100 1.02384 6.3 27000
Added: development/tests/bgs_dyn_mutrates_fit/test_list
===================================================================
--- development/tests/bgs_dyn_mutrates_fit/test_list (rev 0)
+++ development/tests/bgs_dyn_mutrates_fit/test_list 2007-05-25 12:04:55 UTC (rev 1610)
@@ -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-ParentFitSelection.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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