[Avida-SVN] r1638 - in development/tests: . energy_asex_1000u energy_asex_1000u/config energy_asex_1000u/expected energy_asex_1000u/expected/data
beckma24 at myxo.css.msu.edu
beckma24 at myxo.css.msu.edu
Mon Jun 4 09:53:43 PDT 2007
Author: beckma24
Date: 2007-06-04 12:53:43 -0400 (Mon, 04 Jun 2007)
New Revision: 1638
Added:
development/tests/energy_asex_1000u/
development/tests/energy_asex_1000u/config/
development/tests/energy_asex_1000u/config/avida.cfg
development/tests/energy_asex_1000u/config/echo40.org
development/tests/energy_asex_1000u/config/environment-5tasks.cfg
development/tests/energy_asex_1000u/config/events-ConstResource.cfg
development/tests/energy_asex_1000u/config/instset-TEST.cfg
development/tests/energy_asex_1000u/expected/
development/tests/energy_asex_1000u/expected/data/
development/tests/energy_asex_1000u/expected/data/average.dat
development/tests/energy_asex_1000u/expected/data/count.dat
development/tests/energy_asex_1000u/expected/data/dominant.dat
development/tests/energy_asex_1000u/expected/data/instruction.dat
development/tests/energy_asex_1000u/expected/data/instruction_histogram.dat
development/tests/energy_asex_1000u/expected/data/resource.dat
development/tests/energy_asex_1000u/expected/data/stats.dat
development/tests/energy_asex_1000u/expected/data/tasks.dat
development/tests/energy_asex_1000u/expected/data/tasks_exe.dat
development/tests/energy_asex_1000u/expected/data/time.dat
development/tests/energy_asex_1000u/test_list
Log:
Consistency for energy model using asexual organisms.
Added: development/tests/energy_asex_1000u/config/avida.cfg
===================================================================
--- development/tests/energy_asex_1000u/config/avida.cfg (rev 0)
+++ development/tests/energy_asex_1000u/config/avida.cfg 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,233 @@
+#############################################################################
+# 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
+NUM_DEMES 0 # Number of independed groups in the population; 0=off
+RANDOM_SEED 7 # Random number seed (0 for based on time)
+HARDWARE_TYPE 0 # 0 = Original CPUs
+ # 1 = New SMT CPUs
+ # 2 = Transitional SMT
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET instset-TEST.cfg # File containing instruction set
+EVENT_FILE events-ConstResource.cfg # File containing list of events during run
+ANALYZE_FILE analyze.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment-5tasks.cfg # File that describes the environment
+START_CREATURE echo40.org # Organism to seed the soup
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 4 # 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?
+DEATH_METHOD 0 # 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 1 # 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
+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?
+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
+DONATE_SIZE 5.0 # Amount of merit donated with 'donate' command
+DONATE_MULT 10.0 # Multiple of merit given that the target receives.
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on edit distance for donate; -1=no max
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+
+### GENEOLOGY_GROUP ###
+# Geneology
+TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
+ # 0=no, 1=yes, 2=yes,w/sexual population
+THRESHOLD 3 # Number of organisms in a genotype needed for it
+ # to be considered viable.
+GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
+GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
+ # this many updates. (0 = off)
+SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
+SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
+SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
+TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
+
+### LOG_GROUP ###
+# Log Files
+LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
+LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
+LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
+LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
+
+### LINEAGE_GROUP ###
+# Lineage
+# NOTE: This should probably be called "Clade"
+# This one can slow down avida a lot. It is used to get an idea of how
+# often an advantageous mutation arises, and where it goes afterwards.
+# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
+# 0 = manual creation (on inject, use successive integers as lineage labels).
+# 1 = when a child's (potential) fitness is higher than that of its parent.
+# 2 = when a child's (potential) fitness is higher than max in population.
+# 3 = when a child's (potential) fitness is higher than max in dom. lineage
+# *and* the child is in the dominant lineage, or (2)
+# 4 = when a child's (potential) fitness is higher than max in dom. lineage
+# (and that of its own lineage)
+# 5 = same as child's (potential) fitness is higher than that of the
+# currently dominant organism, and also than that of any organism
+# currently in the same lineage.
+# 6 = when a child's (potential) fitness is higher than any organism
+# currently in the same lineage.
+# 7 = when a child's (potential) fitness is higher than that of any
+# organism in its line of descent
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
+
+### 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
+
+### ENERGY_GROUP ###
+# Energy Settings
+ENERGY_ENABLED 1 # Enable Energy Model. 0/1 (off/on)
+ENERGY_GIVEN_ON_INJECT 100000 # Energy given to organism upon injection.
+ENERGY_GIVEN_AT_BIRTH 0.0 # Energy given to offspring upon birth.
+FRAC_PARENT_ENERGY_GIVEN_AT_BIRTH 0.5 # Fraction of energy given to offspring.
+FRAC_ENERGY_DECAY_AT_BIRTH 0.05 # Fraction of energy lost due to decay during reproduction.
+NUM_INST_EXC_BEFORE_0_ENERGY 1000000 # Number of instructions executed before energy is exhausted.
+ENERGY_CAP -1 # Maximun amount of energy that can be stored in an organism. -1 means the cap is set to Max Int
+ENERGY_VERBOSE 0 # Print energy and merit values. 0/1 (off/on)
Added: development/tests/energy_asex_1000u/config/echo40.org
===================================================================
--- development/tests/energy_asex_1000u/config/echo40.org (rev 0)
+++ development/tests/energy_asex_1000u/config/echo40.org 2007-06-04 16:53:43 UTC (rev 1638)
@@ -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 #
+IO
+nop-C #
+IO # 1
+nop-C #
+IO # 2
+nop-C #
+IO # 3
+nop-C #
+IO # 4
+nop-C #
+IO # 5
+nop-C #
+IO # 6
+nop-C #
+IO # 7
+nop-C #
+IO # 8
+nop-C #
+IO # 9
+nop-C #
+IO # 10
+nop-C #
+IO # 11
+nop-C #
+IO # 12
+nop-C #
+IO # 13
+nop-C #
+IO # 14
+nop-C #
+IO # 15
+nop-C #
+IO # 16
+nop-C #
+IO # 17
+nop-C #
+IO # 18
+nop-C #
+IO # 19
+nop-C #
+IO # 20
+nop-C #
+IO # 21
+nop-C #
+IO # 22
+nop-C #
+IO # 23
+nop-C #
+IO # 24
+nop-C #
+IO # 25
+nop-C #
+IO # 26
+nop-C #
+IO # 27
+nop-C #
+IO # 28
+nop-C #
+IO # 29
+nop-C #
+IO # 30
+nop-C #
+IO # 31
+nop-C #
+IO # 32
+nop-C #
+IO # 33
+nop-C #
+IO # 34
+nop-C #
+IO # 35
+nop-C #
+IO # 36
+nop-C #
+IO # 37
+nop-C #
+IO # 38
+nop-C #
+IO # 39
+nop-C #
+IO # 40
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+h-search # Mark the beginning of the copy loop
+h-copy # Do the copy
+if-label # If we're done copying....
+nop-C #
+nop-A #
+h-divide # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Added: development/tests/energy_asex_1000u/config/environment-5tasks.cfg
===================================================================
--- development/tests/energy_asex_1000u/config/environment-5tasks.cfg (rev 0)
+++ development/tests/energy_asex_1000u/config/environment-5tasks.cfg 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,32 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This file is currently setup to reward 9 tasks, all of which use the
+# "infinite" resource, which is undepletable.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+RESOURCE sun_light:initial=1.0
+
+REACTION ECHO echo process:resource=sun_light:value=1000.0:type=energy:frac=1.0:product=sun_light:conversion=1.0 requisite:max_count=35
+
+REACTION NAND nand process:resource=sun_light:value=1500.0:type=energy:frac=1.0:product=sun_light:conversion=1.0 requisite:max_count=20
+
+REACTION NOT not process:resource=sun_light:value=1500.0:type=energy:frac=1.0:product=sun_light:conversion=1.0 requisite:max_count=20
+
+REACTION AND and process:resource=sun_light:value=2000.0:type=energy:frac=1.0:product=sun_light:conversion=1.0 requisite:max_count=13
+
+REACTION ORN orn process:resource=sun_light:value=2000.0:type=energy:frac=1.0:product=sun_light:conversion=1.0 requisite:max_count=13
+
+
+#REACTION OR or process:value=3.0:type=pow requisite:max_count=1
+#REACTION ANDN andn process:value=3.0:type=pow requisite:max_count=1
+#REACTION NOR nor process:value=4.0:type=pow requisite:max_count=1
+#REACTION XOR xor process:value=4.0:type=pow requisite:max_count=1
+#REACTION EQU equ process:value=5.0:type=pow requisite:max_count=1
Added: development/tests/energy_asex_1000u/config/events-ConstResource.cfg
===================================================================
--- development/tests/energy_asex_1000u/config/events-ConstResource.cfg (rev 0)
+++ development/tests/energy_asex_1000u/config/events-ConstResource.cfg 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,47 @@
+##############################################################################
+#
+# This is the setup file for the events system. From here, you can
+# configure any actions that you want to have happen during the course of
+# an experiment, including setting the times for data collection.
+#
+# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
+#
+# This file is currently setup to record key information every 100 updates.
+#
+# For information on how to use this file, see: doc/events.html
+# For other sample event configurations, see: support/config/
+#
+##############################################################################
+
+
+# Print all of the standard data files...
+u 0:100:end PrintAverageData # Save info about they average genotypes
+u 0:100:end PrintDominantData # Save info about most abundant genotypes
+u 0:100:end PrintStatsData # Collect satistics about entire pop.
+u 0:100:end PrintCountData # Count organisms, genotypes, species, etc.
+u 0:100:end PrintTasksData # Save organisms counts for each task.
+u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
+u 0:4:end PrintResourceData # Track resource abundance.
+
+# A few data files not printed by default
+# u 0:100 PrintDominantGenotype # Save the most abundant genotypes
+# u 100:100:end PrintErrorData # Std. Error on averages.
+# u 100:100:end PrintVarianceData # Variance on averages.
+# u 100:100:end PrintTotalsData # Total counts over entire run.
+u 100:100:end PrintTasksExeData # Num. times tasks have been executed.
+# u 100:100:end PrintTasksQualData # Task quality information
+
+# Setup the exit time and full population data collection.
+
+u 0:100:end PrintInstructionAbundanceHistogram
+u 0:100:end PrintInstructionData
+#u 128000:128000:end PrintSleepLog
+u end PrintSleepLog
+u 16:16:end PrintSleepCount
+
+#u 128000:128000:end SavePopulation # Save current state of population.
+#u 128000:128000:end SaveHistoricPopulation # Save ancestors of current population.
+#u end SavePopulation # Save current state of population.
+#u end SaveHistoricPopulation # Save ancestors of current population.
+
+u 1000 exit
\ No newline at end of file
Added: development/tests/energy_asex_1000u/config/instset-TEST.cfg
===================================================================
--- development/tests/energy_asex_1000u/config/instset-TEST.cfg (rev 0)
+++ development/tests/energy_asex_1000u/config/instset-TEST.cfg 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,64 @@
+nop-A 1 1 0 100 # a
+nop-B 1 1 0 100 # b
+nop-C 1 1 0 100 # c
+if-n-equ 1 1 0 100 # d
+if-less 1 1 0 100 # e
+pop 1 1 0 100 # f
+push 1 1 0 100 # g
+swap-stk 1 1 0 100 # h
+swap 1 1 0 100 # i
+shift-r 1 1 0 100 # j
+shift-l 1 1 0 100 # k
+inc 1 1 0 100 # l
+dec 1 1 0 100 # m
+add 1 1 0 100 # n
+sub 1 1 0 100 # o
+nand 1 1 0 100 # p
+IO 1 1 0 100 # q Puts current contents of register and gets new.
+h-alloc 1 1 0 100 # r Allocate as much memory as organism can use.
+h-divide 1 1 0 100 # s Cuts off everything between the read and write heads
+h-copy 1 1 0 100 # t Combine h-read and h-write
+h-search 1 1 0 100 # u Search for matching template, set flow head & return info
+ # # if no template, move flow-head here, set size&offset=0.
+mov-head 1 1 0 100 # v Move ?IP? head to flow control.
+jmp-head 1 1 0 100 # w Move ?IP? head by fixed amount in CX. Set old pos in CX.
+get-head 1 1 0 100 # x Get position of specified head in CX.
+if-label 1 1 0 100 # y
+set-flow 1 1 0 100 # z Move flow-head to address in ?CX?
+
+sense-m100 1 1 0 100
+
+if-equ-0 1 1 0 100
+
+time 1 1 0 100
+
+sleep1 1 10 0 1
+sleep2 1 20 0 1
+sleep3 1 40 0 1
+sleep4 1 80 0 1
+
+
+#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.
\ No newline at end of file
Added: development/tests/energy_asex_1000u/expected/data/average.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/average.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/average.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,30 @@
+# Avida Average Data
+# Mon Jun 4 12:58:21 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 97.000000 348.000000 0.000000 0.000000 100.000000 100.000000 97.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+100 97 348 0 0 100 100 97 1 0 0 0 0 0 0 0
+200 97 348 0 0 100 100 97 1 0 0 0 0 0 0 0
+300 97 348 0 0 100 100 97 1 0 0 0 0 0 0 0
+400 4.80909 348 0.278736 0 100 100 97 2 0 0 0 1 0.411824 0 0
+500 4.80909 348 0.278736 0 100 100 97 2 0 0 0 1 0.411824 0 0.198809
+600 4.80909 348 0.278736 0 100 100 97 2 0 0 0 1 0.411824 0 0.00480909
+700 4.69857 348 0.278736 0 100 100 97 2 0.25 0 0.25 2 0.812366 0 0.00759659
+800 4.69857 348 0.278736 0 100 100 97 2 0 0 0.25 2 0.812366 0 0.00994587
+900 4.69857 348 0.278736 0 100 100 97 2 0 0 0.25 2 0.812366 0 0.00513678
+1000 4.33189 348.4 0.278416 0 100 100 97 2.5 0 0 0.4 2.4 0.956967 0 0.00686954
Added: development/tests/energy_asex_1000u/expected/data/count.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/count.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/count.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,30 @@
+# Avida count data
+# Mon Jun 4 12:58:21 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 1 1 1 1 0 0 0 1 0 1 1 1 1 0 0
+100 1 1 1 1 0 0 0 0 0 0 1 1 1 0 0
+200 1 1 1 1 0 0 0 0 0 0 1 1 1 0 0
+300 1 1 1 1 0 0 0 0 0 0 1 1 1 0 0
+400 2 2 1 1 0 0 0 0 0 0 2 1 2 0 0
+500 2 2 1 1 0 0 0 0 0 0 2 1 2 0 0
+600 2 2 1 1 0 0 0 0 0 0 2 1 2 0 0
+700 3 4 2 1 0 0 0 1 0 0 3 2 4 0 0
+800 4 4 2 1 0 0 0 0 0 0 3 2 4 0 0
+900 4 4 2 1 0 0 0 0 0 0 3 2 4 0 0
+1000 5 5 2 1 0 0 0 0 0 0 4 2 5 0 0
Added: development/tests/energy_asex_1000u/expected/data/dominant.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/dominant.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/dominant.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,30 @@
+# Avida Dominant Data
+# Mon Jun 4 12:58:21 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
+100 0 0 0 0 100 0 0 1 0 0 0 0 0 1 100-aaaaa
+200 0 0 0 0 100 0 0 1 0 0 0 0 0 1 100-aaaaa
+300 0 0 0 0 100 0 0 1 0 0 0 0 0 1 100-aaaaa
+400 4.80909 348 0.278736 0.00287356 100 100 97 2 0 0 0 0 0.278736 1 100-aaaaa
+500 4.80909 348 0.278736 0.00287356 100 100 97 2 0 0 0 0 0.278736 1 100-aaaaa
+600 4.80909 348 0.278736 0.00287356 100 100 97 2 0 0 0 0 0.278736 1 100-aaaaa
+700 4.73541 348 0.278736 0.00287356 100 100 97 3 1 0 0 0 0.278736 1 100-aaaaa
+800 4.73541 348 0.278736 0.00287356 100 100 97 3 0 0 0 0 0.278736 1 100-aaaaa
+900 4.73541 348 0.278736 0.00287356 100 100 97 3 0 0 0 0 0.278736 1 100-aaaaa
+1000 4.73541 348 0.278736 0.00287356 100 100 97 3 0 0 0 0 0.278736 1 100-aaaaa
Added: development/tests/energy_asex_1000u/expected/data/instruction.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/instruction.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/instruction.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,48 @@
+# Avida instruction execution data
+# Mon Jun 4 12:58:21 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-divide
+# 21: h-copy
+# 22: h-search
+# 23: mov-head
+# 24: jmp-head
+# 25: get-head
+# 26: if-label
+# 27: set-flow
+# 28: sense-m100
+# 29: if-equ-0
+# 30: time
+# 31: sleep1
+# 32: sleep2
+# 33: sleep3
+# 34: sleep4
+
+0 0 0 0 0 0 0 0 0 0 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
+200 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+300 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+400 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 82 2 2 200 4 200 0 0 200 0 0 0 0 0 0 0 0
+500 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 82 2 2 200 4 200 0 0 200 0 0 0 0 0 0 0 0
+600 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 82 2 2 200 4 200 0 0 200 0 0 0 0 0 0 0 0
+700 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 164 4 4 400 8 400 0 0 400 0 0 0 0 0 0 0 0
+800 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 164 4 4 400 8 400 0 0 400 0 0 0 0 0 0 0 0
+900 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 164 4 4 400 8 400 0 0 400 0 0 0 0 0 0 0 0
+1000 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 203 5 5 500 10 500 0 0 500 0 2 0 0 0 0 0 0
Added: development/tests/energy_asex_1000u/expected/data/instruction_histogram.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/instruction_histogram.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/instruction_histogram.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,46 @@
+# 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-divide
+# 21: h-copy
+# 22: h-search
+# 23: mov-head
+# 24: jmp-head
+# 25: get-head
+# 26: if-label
+# 27: set-flow
+# 28: sense-m100
+# 29: if-equ-0
+# 30: time
+# 31: sleep1
+# 32: sleep2
+# 33: sleep3
+# 34: sleep4
+
+0 203 1 47 0 0 0 0 0 0 0 0 0 0 0 0 0 41 1 1 1 2 2 0 0 1 0 0 0 0 0 0 0 0
+100 186 1 55 0 0 0 0 0 0 0 0 0 0 0 0 0 47 2 1 1 3 3 0 0 1 0 0 0 0 0 0 0 0
+200 153 1 71 0 0 0 0 0 0 0 0 0 0 0 0 0 64 2 1 1 3 3 0 0 1 0 0 0 0 0 0 0 0
+300 119 1 88 0 0 0 0 0 0 0 0 0 0 0 0 0 81 2 1 1 3 3 0 0 1 0 0 0 0 0 0 0 0
+400 403 2 95 0 0 0 0 0 0 0 0 0 0 0 0 0 82 3 2 2 5 4 0 0 2 0 0 0 0 0 0 0 0
+500 338 2 127 0 0 0 0 0 0 0 0 0 0 0 0 0 111 4 2 2 6 6 0 0 2 0 0 0 0 0 0 0 0
+600 270 2 160 0 0 0 0 0 0 0 0 0 0 0 0 0 145 4 2 2 6 6 0 0 2 0 1 0 0 0 0 0 0
+700 412 4 188 0 0 0 0 0 0 0 0 0 0 0 0 0 163 4 4 4 8 8 0 0 4 0 1 0 0 0 0 0 0
+800 739 4 222 0 0 0 0 0 0 0 0 0 0 0 0 0 190 8 4 5 11 12 0 0 4 0 1 0 0 0 0 0 0
+900 605 4 287 0 0 0 0 0 0 0 0 0 0 0 0 0 257 8 4 5 11 12 0 0 4 0 2 0 0 0 0 1 0
+1000 778 5 351 0 0 0 0 0 0 0 0 0 0 0 0 0 311 8 5 7 13 13 0 0 6 0 2 0 0 0 0 1 0
Added: development/tests/energy_asex_1000u/expected/data/resource.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/resource.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/resource.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,258 @@
+# Avida resource data
+# Mon Jun 4 12:58:21 2007
+# First column gives the current update, all further columns give the quantity
+# of the particular resource at that update.
+# 1: Update
+# 2: sun_light
+
+0 1.000000
+4 1
+8 1
+12 1
+16 1
+20 1
+24 1
+28 1
+32 1
+36 1
+40 1
+44 1
+48 1
+52 1
+56 1
+60 1
+64 1
+68 1
+72 1
+76 1
+80 1
+84 1
+88 1
+92 1
+96 1
+100 1
+104 1
+108 1
+112 1
+116 1
+120 1
+124 1
+128 1
+132 1
+136 1
+140 1
+144 1
+148 1
+152 1
+156 1
+160 1
+164 1
+168 1
+172 1
+176 1
+180 1
+184 1
+188 1
+192 1
+196 1
+200 1
+204 1
+208 1
+212 1
+216 1
+220 1
+224 1
+228 1
+232 1
+236 1
+240 1
+244 1
+248 1
+252 1
+256 1
+260 1
+264 1
+268 1
+272 1
+276 1
+280 1
+284 1
+288 1
+292 1
+296 1
+300 1
+304 1
+308 1
+312 1
+316 1
+320 1
+324 1
+328 1
+332 1
+336 1
+340 1
+344 1
+348 1
+352 1
+356 1
+360 1
+364 1
+368 1
+372 1
+376 1
+380 1
+384 1
+388 1
+392 1
+396 1
+400 1
+404 1
+408 1
+412 1
+416 1
+420 1
+424 1
+428 1
+432 1
+436 1
+440 1
+444 1
+448 1
+452 1
+456 1
+460 1
+464 1
+468 1
+472 1
+476 1
+480 1
+484 1
+488 1
+492 1
+496 1
+500 1
+504 1
+508 1
+512 1
+516 1
+520 1
+524 1
+528 1
+532 1
+536 1
+540 1
+544 1
+548 1
+552 1
+556 1
+560 1
+564 1
+568 1
+572 1
+576 1
+580 1
+584 1
+588 1
+592 1
+596 1
+600 1
+604 1
+608 1
+612 1
+616 1
+620 1
+624 1
+628 1
+632 1
+636 1
+640 1
+644 1
+648 1
+652 1
+656 1
+660 1
+664 1
+668 1
+672 1
+676 1
+680 1
+684 1
+688 1
+692 1
+696 1
+700 1
+704 1
+708 1
+712 1
+716 1
+720 1
+724 1
+728 1
+732 1
+736 1
+740 1
+744 1
+748 1
+752 1
+756 1
+760 1
+764 1
+768 1
+772 1
+776 1
+780 1
+784 1
+788 1
+792 1
+796 1
+800 1
+804 1
+808 1
+812 1
+816 1
+820 1
+824 1
+828 1
+832 1
+836 1
+840 1
+844 1
+848 1
+852 1
+856 1
+860 1
+864 1
+868 1
+872 1
+876 1
+880 1
+884 1
+888 1
+892 1
+896 1
+900 1
+904 1
+908 1
+912 1
+916 1
+920 1
+924 1
+928 1
+932 1
+936 1
+940 1
+944 1
+948 1
+952 1
+956 1
+960 1
+964 1
+968 1
+972 1
+976 1
+980 1
+984 1
+988 1
+992 1
+996 1
+1000 1
Added: development/tests/energy_asex_1000u/expected/data/stats.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/stats.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/stats.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,26 @@
+# Generic Statistics Data
+# Mon Jun 4 12:58:21 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 0.565047 0.565047 0.832517 0.832517 1 0.000000 0.000000 0 0 0
+100 0 0.565047 0.565047 0.832517 0.832517 0 0 0 0 0 0
+200 0 0.565047 0.565047 0.832517 0.832517 0 0 0 0 0 0
+300 0 0.565047 0.565047 0.832517 0.832517 0 0 0 0 0 0
+400 0 0.565047 0.565047 0.832517 0.832517 0 0 0 0 0 0
+500 0 0.565047 0.565047 0.832517 0.832517 0 0 0 0 0 0
+600 0 0.565047 0.565047 0.832517 0.832517 0 0 0 0 0 0
+700 0 0.565047 0.565047 0.832517 0.832517 1 0.562335 0 0 0 0
+800 0 0.565047 0.565047 0.832517 0.832517 0 0.562335 0 0 0 0
+900 0 0.565047 0.565047 0.832517 0.832517 0 0.562335 0 0 0 0
+1000 0.00114679 0.565047 0.565047 0.832517 0.832517 0 0.673012 0 0 0 0
Added: development/tests/energy_asex_1000u/expected/data/tasks.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/tasks.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/tasks.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,22 @@
+# Avida tasks data
+# Mon Jun 4 12:58:21 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: Echo
+# 3: Nand
+# 4: Not
+# 5: And
+# 6: OrNot
+
+0 0 0 0 0 0
+100 0 0 0 0 0
+200 0 0 0 0 0
+300 0 0 0 0 0
+400 2 0 0 0 0
+500 2 0 0 0 0
+600 2 0 0 0 0
+700 4 0 0 0 0
+800 4 0 0 0 0
+900 4 0 0 0 0
+1000 5 0 0 0 0
Added: development/tests/energy_asex_1000u/expected/data/tasks_exe.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/tasks_exe.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/tasks_exe.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,21 @@
+# Avida tasks execution data
+# Mon Jun 4 12:58:21 2007
+# First column gives the current update, all further columns give the number
+# of times the particular task has been executed this update.
+# 1: Update
+# 2: Echo
+# 3: Nand
+# 4: Not
+# 5: And
+# 6: OrNot
+
+100 0 0 0 0 0
+200 0 0 0 0 0
+300 0 0 0 0 0
+400 70 0 0 0 0
+500 70 0 0 0 0
+600 70 0 0 0 0
+700 140 0 0 0 0
+800 140 0 0 0 0
+900 140 0 0 0 0
+1000 175 0 0 0 0
Added: development/tests/energy_asex_1000u/expected/data/time.dat
===================================================================
--- development/tests/energy_asex_1000u/expected/data/time.dat (rev 0)
+++ development/tests/energy_asex_1000u/expected/data/time.dat 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,18 @@
+# Avida time data
+# Mon Jun 4 12:58:21 2007
+# 1: update
+# 2: avida time
+# 3: average generation
+# 4: num_executed?
+
+0 0.000000 0.000000 1
+100 1.03093 0 1
+200 2.06186 0 1
+300 3.09278 0 1
+400 14.5981 1 2
+500 35.3921 1 2
+600 56.186 1 2
+700 77.3547 2 3
+800 98.6377 2 4
+900 119.921 2 4
+1000 141.384 2.4 5
Added: development/tests/energy_asex_1000u/test_list
===================================================================
--- development/tests/energy_asex_1000u/test_list (rev 0)
+++ development/tests/energy_asex_1000u/test_list 2007-06-04 16:53:43 UTC (rev 1638)
@@ -0,0 +1,37 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+; Command line arguments to pass to the application
+args =
+
+app = %(default_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 = Ben Beckmann ; Who created the test
+email = beckma24 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.
+;
+; builddir
+; cpus
+; default_app
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
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