[Avida-SVN] r3143 - in branches/interrupt/tests: . energy_asex_1000u/config interruptModel_quorumSensing interruptModel_quorumSensing/config interruptModel_quorumSensing/expected interruptModel_quorumSensing/expected/data
beckma24 at myxo.css.msu.edu
beckma24 at myxo.css.msu.edu
Fri Feb 6 07:39:24 PST 2009
Author: beckma24
Date: 2009-02-06 10:39:23 -0500 (Fri, 06 Feb 2009)
New Revision: 3143
Added:
branches/interrupt/tests/interruptModel_quorumSensing/
branches/interrupt/tests/interruptModel_quorumSensing/config/
branches/interrupt/tests/interruptModel_quorumSensing/config/analyze.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/avida.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/default-classic.org
branches/interrupt/tests/interruptModel_quorumSensing/config/environment.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/events.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/instset-LabelRotate.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/instset-LabelRotate_even.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/instset-NextNeighborRotate.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/instset-NextNeighborRotate_even.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/instset-SingleStepRotate.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/instset-SingleStepRotate_even.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/instset-allRotate.cfg
branches/interrupt/tests/interruptModel_quorumSensing/config/instset-allRotate_even.cfg
branches/interrupt/tests/interruptModel_quorumSensing/expected/
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/average.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/count.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_average.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_compete.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_interrupt.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_repl.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_totalAvgEnergy.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/dominant.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/germline.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/instruction.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/instruction_histogram.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/message.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/stats.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/tasks.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/tasks_exe.dat
branches/interrupt/tests/interruptModel_quorumSensing/expected/data/time.dat
branches/interrupt/tests/interruptModel_quorumSensing/test_list
Modified:
branches/interrupt/tests/energy_asex_1000u/config/avida.cfg
branches/interrupt/tests/energy_asex_1000u/config/environment-5tasks.cfg
branches/interrupt/tests/energy_asex_1000u/config/instset-TEST.cfg
Log:
Commenting sleep paper config files in test. Added quorum sensing test.
Modified: branches/interrupt/tests/energy_asex_1000u/config/avida.cfg
===================================================================
--- branches/interrupt/tests/energy_asex_1000u/config/avida.cfg 2009-02-06 14:09:14 UTC (rev 3142)
+++ branches/interrupt/tests/energy_asex_1000u/config/avida.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -1,3 +1,10 @@
+########
+## Config file for:
+## B. E. Beckmann, P. K. McKinley, and C. Ofria. Evolution of an adaptive sleep response in digital organisms.
+## In Advances in Artificial Life - Proceedings of 9th European Conference on Artificial Life,
+## volume 4648 of Lecture Notes in Computer Science, pages 233–242. Springer, 2007.
+#
+#
#############################################################################
# This file includes all the basic run-time defines for Avida.
# For more information, see doc/config.html
Modified: branches/interrupt/tests/energy_asex_1000u/config/environment-5tasks.cfg
===================================================================
--- branches/interrupt/tests/energy_asex_1000u/config/environment-5tasks.cfg 2009-02-06 14:09:14 UTC (rev 3142)
+++ branches/interrupt/tests/energy_asex_1000u/config/environment-5tasks.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -12,8 +12,23 @@
#
##############################################################################
+## Configuration used in:
+## B. E. Beckmann, P. K. McKinley, and C. Ofria. Evolution of an adaptive sleep response in digital organisms.
+## In Advances in Artificial Life - Proceedings of 9th European Conference on Artificial Life,
+## volume 4648 of Lecture Notes in Computer Science, pages 233–242. Springer, 2007.
+##
+##
+
+# sun_light resource with intial value of ON. Resource is binary in above paper.
RESOURCE sun_light:initial=1.0
+
+# Available reactions.
+# Note 2 things:
+# 1. sun_light is required for every reaction. However, when sun_light is ON it is a non-depletable/infinite resource.
+# 2. The value of the simpler tasks are less, however the simpler tasks can be performed more.
+# Basically, the organsisms can feed on many different things when the resource is ON and nothing when its OFF.
+
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
@@ -23,10 +38,3 @@
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
Modified: branches/interrupt/tests/energy_asex_1000u/config/instset-TEST.cfg
===================================================================
--- branches/interrupt/tests/energy_asex_1000u/config/instset-TEST.cfg 2009-02-06 14:09:14 UTC (rev 3142)
+++ branches/interrupt/tests/energy_asex_1000u/config/instset-TEST.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -36,29 +36,3 @@
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: branches/interrupt/tests/interruptModel_quorumSensing/config/analyze.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/analyze.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/analyze.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,14 @@
+#############################################################################
+# This file is used to setup avida when it is in analysis-only mode (by
+# running "avida -a". It allows variety of methods to load organisms
+# (specifying the type of each) and analyze them once loaded.
+#
+# See the documentation in doc/analyze_mode.html for usage, or the file
+# doc/analyze_samples.html for guidelines on writing programs.
+#
+#############################################################################
+
+load ./data/detail-50000.pop
+find_genotype num_cpus
+trace
+print
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/avida.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/avida.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/avida.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,544 @@
+##########
+## Not yet published.
+##
+##
+#
+# Overall population is decreased in this file because its a test.
+# In above paper WORLD_Y == 2000 and NUM_DEMES == 400
+#
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.9.0 # 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 # 0 = No output at all
+ # 1 = Normal output
+ # 2 = Verbose output, detailing progress
+ # 3 = High level of details, as available
+ # 4 = Print Debug Information, as applicable
+
+### ARCH_GROUP ###
+# Architecture Variables
+WORLD_X 5 # Width of the Avida world
+WORLD_Y 100 # Height of the Avida world
+WORLD_Z 1 # Depth of the Avida world
+WORLD_GEOMETRY 2 # 1 = Bounded Grid
+ # 2 = Torus
+ # 3 = Clique
+ # 4 = Hexagonal grid
+ # 5 = Lattice
+RANDOM_SEED 7 # 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
+SPECULATIVE 0 # Enable speculative execution
+TRACE_EXECUTION 0 # Trace the execution of all organisms in the population (default=off,SLOW!)
+BCAST_HOPS 1 # Number of hops to broadcast an alarm
+ALARM_SELF 0 # Does sending an alarm move sender IP to alarm label?
+ # 0=no
+ # 1=yes
+IO_EXPIRE 1 # Is the expiration functionality of '-expire' I/O instructions enabled?
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET - # File containing instruction set
+INST_SET_FORMAT 0 # Instruction set file format.
+ # 0 = Default
+ # 1 = New Style
+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 20 # Number of independent groups in the
+ # population (default=1).
+DEMES_USE_GERMLINE 1 # Whether demes use a distinct germline (default=0).
+DEMES_PREVENT_STERILE 1 # Whether to prevent sterile demes from
+ # replicating (default=0 or no).
+DEMES_RESET_RESOURCES 0 # Reset resources in demes on replication.
+ # 0 = reset both demes
+ # 1 = reset target deme
+ # 2 = deme resources remain unchanged
+DEMES_REPLICATE_SIZE 1 # Number of identical organisms to create or copy from the
+ # source deme to the target deme (default=1).
+LOG_DEMES_REPLICATE 0 # Log deme replications. 0/1 (off/on)
+DEMES_REPLICATE_LOG_START 0 # Update at which to start logging deme replications
+DEMES_PROB_ORG_TRANSFER 0.0 # Probablity of an organism being transferred from the
+ # source deme to the target deme (default=0.0).
+DEMES_ORGANISM_SELECTION 0 # How organisms are selected for transfer from
+ # source to target during deme replication.
+ # 0=random with replacement (default).
+ # 1=sequential.
+DEMES_ORGANISM_PLACEMENT 2 # How organisms are placed during deme replication.
+ # 0=cell-array middle (default).
+ # 1=deme center.
+ # 2=random placement.
+ # 3=sequential.
+DEMES_ORGANISM_FACING 2 # How organisms are facing during deme replication.
+ # 0=unchanged (default).
+ # 1=northwest.
+ # 2=random.
+DEMES_MAX_AGE 500 # The maximum age of a deme (in updates) to be
+ # used for age-based replication (default=500).
+DEMES_MAX_BIRTHS 100 # The maximum number of births that can occur
+ # within a deme; used with birth-count
+ # replication (default=100).
+DEMES_MIM_EVENTS_KILLED_RATIO 0.7 # Minimum ratio of events killed required for event period to be a success.
+DEMES_MIM_SUCCESSFUL_EVENT_PERIODS 1 # Minimum number of consecutive event periods that must be a success.
+GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
+ # germline replication (default=0.0075).
+GERMLINE_INS_MUT 0.05 # Prob. of an insertion mutation occuring
+ # during germline replication (default=0.05).
+GERMLINE_DEL_MUT 0.05 # Prob. of a deletion mutation occuring
+ # during germline replication (default=0.05).
+DEMES_REPLICATE_CPU_CYCLES 0.0 # Replicate a deme immediately after it has used
+ # this number of cpu cycles, normalized
+ # by number of orgs in deme (0 = OFF).
+DEMES_REPLICATE_TIME 0.0 # Replicate a deme immediately after it has used
+ # this number of cpu cycles, normalized
+ # by number of orgs in deme and organism merit (0 = OFF).
+DEMES_REPLICATE_BIRTHS 0 # Replicate a deme immediately after it has
+ # produced this many offspring (0 = OFF).
+DEMES_REPLICATE_ORGS 0 # Replicate a deme immediately once it reaches a
+ # certain number of organisms (0 = OFF).
+DEMES_REPLICATION_ONLY_RESETS 0 # Kin selection mode. Deme replication really:
+ # 1=resets deme resources
+ # 2=rests deme resources and re-injects organisms
+DEMES_MIGRATION_RATE 0.0 # Probability of an offspring being born in a different deme.
+DEMES_MIGRATION_METHOD 0 # How do we choose what demes an org may land in when it migrates?
+ # 0=all other demes
+ # 1=eight adjacent neighbors
+ # 2=two adjacent demes in list
+ # 3=proportional based on the number of points
+DEMES_NUM_X 0 # Simulated number of demes in X dimension. Only used for migration.
+DEMES_SEED_METHOD 0 # Deme seeding method.
+ # 0=maintain old consistency
+ # 1=new method using genotypes
+DEMES_DIVIDE_METHOD 0 # Deme divide method. Only works with DEMES_SEED_METHOD 1
+ # 0=replace and target demes
+ # 1= replace target deme, reset source deme to founders
+ # 2=replace target deme, leave source deme unchanged
+DEMES_DEFAULT_GERMLINE_PROPENSITY 0.0 # Default germline propensity of organisms in deme.
+ # For use with DEMES_DIVIDE_METHOD 2.
+DEMES_FOUNDER_GERMLINE_PROPENSITY -1.0 # Default germline propensity of founder organisms in deme.
+ # For use with DEMES_DIVIDE_METHOD 2.
+ # <0 = OFF
+DEMES_PREFER_EMPTY 1 # Give empty demes preference as targets of deme replication?
+DEMES_PROTECTION_POINTS 0 # The number of points a deme receives for each suicide.
+POINT_DECAY_PERCENT 0 # The percentage of points decayed each time cActionDecayPoints is called.
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 6 # 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 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)
+ # 3 = Divide resets mother stats, but not state.
+ # 4 = 3 + child inherits mother registers and stack values.
+EPIGENETIC_METHOD 0 # Inheritance of state information other than genome
+ # 0 = none
+ # 1 = offspring inherits registers and stacks of first thread
+ # 1 = parent maintains registers and stacks of first thread
+ #
+ # 1 = offspring and parent keep state information
+INJECT_METHOD 0 # 0 = Leaves the parasite thread state untouched.
+ # 1 = Resets the calling thread state on inject
+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).
+RESET_INPUTS_ON_DIVIDE 0 # Reset environment inputs of parent upon successful divide.
+REPRO_METHOD 1 # Replace existing organism: 1=yes
+
+### 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 0.0 # Code fraction which must be executed before divide.
+MIN_GENOME_SIZE 0 # Minimum number of instructions allowed in a genome. 0 = OFF
+MAX_GENOME_SIZE 0 # Maximum number of instructions allowed in a genome. 0 = OFF
+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 0.0 # Required bonus to divide.
+IMPLICIT_REPRO_BONUS 0 # Call Inst_Repro to divide upon achieving this bonus. 0 = OFF
+IMPLICIT_REPRO_CPU_CYCLES 0 # Call Inst_Repro after this many cpu cycles. 0 = OFF
+IMPLICIT_REPRO_TIME 0 # Call Inst_Repro after this time used. 0 = OFF
+IMPLICIT_REPRO_END 0 # Call Inst_Repro after executing the last instruction in the genome.
+IMPLICIT_REPRO_ENERGY 0.0 # Call Inst_Repro if organism accumulates this amount of energy.
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0 # Mutation rate (per copy)
+COPY_INS_PROB 0.0 # Insertion rate (per copy)
+COPY_DEL_PROB 0.0 # Deletion rate (per copy)
+COPY_UNIFORM_PROB 0.0 # Uniform mutation probability (per copy)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+COPY_SLIP_PROB 0.0 # Slip rate (per copy)
+DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
+DIV_INS_PROB 0.0 # Insertion rate (per site, applied on divide)
+DIV_DEL_PROB 0.0 # Deletion rate (per site, applied on divide)
+DIV_UNIFORM_PROB 0.0 # Uniform mutation probability (per site, applied on divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+DIV_SLIP_PROB 0.0 # Slip rate
+DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
+DIVIDE_INS_PROB 0.0 # Insertion rate (per divide)
+DIVIDE_DEL_PROB 0.0 # Deletion rate (per divide)
+DIVIDE_UNIFORM_PROB 0.0 # Uniform mutation probability (per divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
+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)
+SLIP_FILL_MODE 0 # Fill insertions from slip mutations with 0=duplication, 1=nop-X, 2=random, 3=scrambled
+SLIP_COPY_MODE 0 # How to handle 'on-copy' slip mutations:
+ # 0 = actual read head slip
+ # 1 = instant large mutation (obeys slip mode)
+PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+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.
+MIGRATION_RATE 0.0 # Uniform probability of offspring migrating to a new deme.
+
+### 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 1 # 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 50 # 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.
+ # 3 = DemeProbabalistic, each deme gets the same number of CPU cycles, which are awarded probabalistically within each deme.
+ # 4 = ProbDemeProbabalistic, each deme gets CPU cycles proportional to its living population size, which are awarded probabalistically within each deme.
+ # 5 = CONSTANT BURST: all organisms get default, in SLICING_BURST_SIZE chunks
+SLICING_BURST_SIZE 1 # Sets the scheduler burst size, when supported.
+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 this default bonus
+ # rather than the accumulated bonus of the parent? 0 = off
+MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
+ # (-1 = none, 0 = First in INST_SET.)
+MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
+ # per instruction (-1 = penalty, 0 = no effect.)
+FITNESS_METHOD 0 # 0 = default, >=1 = experimental
+FITNESS_COEFF_1 1.0 # 1st FITNESS_METHOD parameter
+FITNESS_COEFF_2 1.0 # 2nd FITNESS_METHOD parameter
+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.
+NO_CPU_CYCLE_TIME 0 # Don't count each CPU cycle as part of gestation time
+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.
+PRECALC_PHENOTYPE 0 # 0 = Disabled
+ # 1 = Assign precalculated merit at birth (unlimited resources only)
+ # 2 = Assign precalculated gestation time
+ # 3 = Assign precalculated merit AND gestation time.
+ # Fitness will be evaluated for organism based on these settings.
+FASTFORWARD_UPDATES 0 # Fast-forward if the average generation has not changed in this many updates. (0 = off)
+FASTFORWARD_NUM_ORGS 0 # Fast-forward if population is equal to this
+
+### 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
+
+### ORGANISM_MESSAGING_GROUP ###
+# Organism Message-Based Communication
+MESSAGE_TYPE 0 # Messaging Style. 0=Receiver Facing, 1=Broadcast
+MESSAGE_BCAST_RADIUS 1 # Broadcast message radius (cells)
+ORGANISMS_REMEMBER_MESSAGES 0 # Does an organism remember all messages it has sent or received? 0=false, 1=true (default)
+MESSAGE_QUEUE_SIZE 20 # Maximum number of unretrieved messages an organism can store (-1 for no limit is the default)
+MESSAGE_QUEUE_BEHAVIOR_WHEN_FULL 0 # 0 = Drop incoming message (default), 1 = Drop oldest unretrieved message
+
+### 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
+
+### HOARD_RESOURCE_GROUP ###
+# Resource Hoarding Parameters
+USE_RESOURCE_BINS 0 # Enable resource bin use. This serves as a guard on most resource hoarding code.
+ABSORB_RESOURCE_FRACTION .0025 # Fraction of available environmental resource an organism absorbs.
+MULTI_ABSORB_TYPE 0 # What to do if a collect instruction is called on a range of resources.
+ # 0 = absorb a random resource in the range
+ # 1 = absorb the first resource in the range
+ # 2 = absorb the last resource in the range
+ # 3 = absorb ABSORB_RESOURCE_FRACTION / (# of resources in range) of each resource in the range
+MAX_TOTAL_STORED -1 # Maximum total amount of all resources an organism can store.
+ # <0 = no maximum
+USE_STORED_FRACTION 1.0 # The fraction of stored resource to use.
+ENV_FRACTION_THRESHOLD 1.0 # The fraction of available environmental resource to compare available stored resource to when deciding whether to use stored resource.
+RETURN_STORED_ON_DEATH 1 # Return an organism's stored resources to the world when it dies?
+
+### ANALYZE_GROUP ###
+# Analysis Settings
+MAX_CONCURRENCY -1 # Maximum number of analyze threads, -1 == use all available.
+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 100000000.0 # Energy given to organism upon injection.
+ENERGY_GIVEN_AT_BIRTH 0.0 # Energy given to offspring upon birth.
+FRAC_PARENT_ENERGY_GIVEN_TO_ORG_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring organism.
+FRAC_PARENT_ENERGY_GIVEN_TO_DEME_AT_BIRTH 0.0 # Fraction of parent's energy given to offspring deme.
+FRAC_ENERGY_DECAY_AT_ORG_BIRTH 0.0 # Fraction of energy lost due to decay during organism reproduction.
+FRAC_ENERGY_DECAY_AT_DEME_BIRTH 1.0 # Fraction of energy lost due to decay during deme reproduction.
+NUM_CYCLES_EXC_BEFORE_0_ENERGY 10000 # Number of instructions executed before energy is exhausted.
+ENERGY_CAP -1.0 # Maximum amount of energy that can be stored in an organism. -1 means the cap is set to Max Double
+APPLY_ENERGY_METHOD 0 # When should rewarded energy be applied to current energy?
+ # 0 = on divide
+ # 1 = on completion of task
+ # 2 = on sleep
+FRAC_ENERGY_TRANSFER 0.0 # Fraction of replaced organism's energy take by new resident
+LOG_SLEEP_TIMES 0 # Log sleep start and end times. 0/1 (off/on)
+ # WARNING: may use lots of memory.
+FRAC_ENERGY_RELINQUISH 1.0 # Fraction of organisms energy to relinquish
+ENERGY_PASSED_ON_DEME_REPLICATION_METHOD 0 # Who get energy passed from a parent deme
+ # 0 = Energy divided among organisms injected to offspring deme
+ # 1 = Energy divided among cells in offspring deme
+INHERIT_EXE_RATE 0 # Inherit energy rate from parent? 0=no 1=yes
+ATTACK_DECAY_RATE 0.0 # Percent of cell's energy decayed by attack
+ENERGY_THRESH_LOW .33 # Threshold percent below which energy level is considered low. Requires ENERGY_CAP.
+ENERGY_THRESH_HIGH .75 # Threshold percent above which energy level is considered high. Requires ENERGY_CAP.
+
+### ENERGY_SHARING_GROUP ###
+# Energy Sharing Settings
+ENERGY_SHARING_METHOD 0 # Method for sharing energy. 0=receiver must actively receive/request, 1=energy pushed on receiver
+ENERGY_SHARING_PCT 0.0 # Percent of energy to share
+ENERGY_SHARING_INCREMENT 0.01 # Amount to change percent energy shared
+ENERGY_SHARING_LOSS 0.0 # Percent of shared energy lost in transfer
+
+### INTERRUPT_GROUP ###
+# Interrupt Settings
+INTERRUPT_ENABLED 1 # Enable Interrupt Model. 0/1 (off/on)
+
+### 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
+
+### GX_GROUP ###
+# Gene Expression CPU Settings
+MAX_PROGRAMIDS 16 # Maximum number of programids an organism can create.
+MAX_PROGRAMID_AGE 2000 # Max number of CPU cycles a programid executes before it is removed.
+IMPLICIT_GENE_EXPRESSION 0 # Create executable programids from the genome without explicit allocation and copying?
+IMPLICIT_BG_PROMOTER_RATE 0.0 # Relative rate of non-promoter sites creating programids.
+IMPLICIT_TURNOVER_RATE 0.0 # Number of programids recycled per CPU cycle. 0 = OFF
+IMPLICIT_MAX_PROGRAMID_LENGTH 0 # Creation of an executable programid terminates after this many instructions. 0 = disabled
+
+### PROMOTER_GROUP ###
+# Promoters
+PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
+ # Certain instructions must also be included.
+PROMOTER_INST_MAX 0 # Maximum number of instructions to execute before terminating. 0 = off
+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_TO_REGISTER 0 # Place a promoter's base bit code in register BX when starting execution from it?
+TERMINATION_RESETS 0 # Does termination reset the thread's state?
+NO_ACTIVE_PROMOTER_EFFECT 0 # What happens when there are no active promoters?
+ # 0 = Start execution at the beginning of the genome.
+ # 1 = Kill the organism.
+ # 2 = Stop the organism from executing any further instructions.
+PROMOTER_CODE_SIZE 24 # Size of a promoter code in bits. (Maximum value is 32)
+PROMOTER_EXE_LENGTH 3 # Length of promoter windows used to determine execution.
+PROMOTER_EXE_THRESHOLD 2 # Minimum number of bits that must be set in a promoter window to allow execution.
+INST_CODE_LENGTH 3 # Instruction binary code length (number of bits)
+INST_CODE_DEFAULT_TYPE 0 # Default value of instruction binary code value.
+ # 0 = All zeros
+ # 1 = Based off the instruction number
+CONSTITUTIVE_REGULATION 0 # Sense a new regulation value before each CPU cycle?
+
+### COLORS_GROUP ###
+# Output colors for when data files are printed in HTML mode.
+# There are two sets of these; the first are for lineages,
+# and the second are for mutation tests.
+COLOR_DIFF CCCCFF # Color to flag stat that has changed since parent.
+COLOR_SAME FFFFFF # Color to flag stat that has NOT changed since parent.
+COLOR_NEG2 FF0000 # Color to flag stat that is significantly worse than parent.
+COLOR_NEG1 FFCCCC # Color to flag stat that is minorly worse than parent.
+COLOR_POS1 CCFFCC # Color to flag stat that is minorly better than parent.
+COLOR_POS2 00FF00 # Color to flag stat that is significantly better than parent.
+COLOR_MUT_POS 00FF00 # Color to flag stat that has changed since parent.
+COLOR_MUT_NEUT FFFFFF # Color to flag stat that has changed since parent.
+COLOR_MUT_NEG FFFF00 # Color to flag stat that has changed since parent.
+COLOR_MUT_LETHAL FF0000 # Color to flag stat that has changed since parent.
+
+### BIOMIMETIC_GROUP ###
+# Biomimetic Features Settings
+BIOMIMETIC_REFRACTORY_PERIOD 0.0 # Number of updates affected by refractory period
+BIOMIMETIC_MOVEMENT_STEP 1 # Number of cells to move Avidian on move instruction
+BIOMIMETIC_MOVEMENT_LOG 0 # Log detailed movement information (WARNING: large data file)
+BIOMIMETIC_MOVEMENT_FACTOR 1.0 # Scale merit bonus due to movement (m<1.0 applies a cost)
+BIOMIMETIC_EVAL_ON_MOVEMENT 0 # Force task evaluation on each movement step
+BIOMIMETIC_K 0 # Carrying capacity in number of organisms
+
+### PHEROMONE_GROUP ###
+# Pheromone Settings
+PHEROMONE_ENABLED 0 # Enable pheromone usage. 0/1 (off/on)
+PHEROMONE_AMOUNT 1.0 # Amount of pheromone to add per drop
+PHEROMONE_DROP_MODE 0 # Where to drop pheromone
+ # 0 = Half amount at src, half at dest
+ # 1 = All at source
+ # 2 = All at dest
+EXPLOIT_EXPLORE_PROB 0.00 # Probability of random exploration
+ # instead of pheromone trail following
+LOG_PHEROMONE 0 # Log pheromone drops. 0/1 (off/on)
+PHEROMONE_LOG_START 0 # Update at which to start logging pheromone drops
+EXPLOIT_LOG_START 0 # Update at which to start logging exploit moves
+EXPLORE_LOG_START 0 # Update at which to start logging explore moves
+MOVETARGET_LOG_START 0 # Update at which to start logging movetarget moves
+LOG_INJECT 0 # Log injection of organisms. 0/1 (off/on)
+INJECT_LOG_START 0 # Update at which to start logging injection of
+ # organisms
+
+### SYNCHRONIZATION_GROUP ###
+# Synchronization settings
+SYNC_FITNESS_WINDOW 100 # Number of updates over which to calculate fitness (default=100).
+SYNC_FLASH_LOSSRATE 0.0 # P() to lose a flash send (0.0==off).
+SYNC_TEST_FLASH_ARRIVAL -1 # CPU cycle at which an organism will receive a flash (off=-1, default=-1, analyze mode only.)
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/default-classic.org
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/default-classic.org (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/default-classic.org 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,50 @@
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X #
+nop-X
+repro
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/environment.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/environment.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/environment.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+##############################################################################
+#
+# 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/
+#
+##############################################################################
+
+#problem with multiple task counting
+#REACTION ECHO echo process:value=50.0:type=energy
+
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/events.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/events.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/events.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,53 @@
+##############################################################################
+#
+# 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/
+#
+##############################################################################
+
+i InjectDemes
+u 20:20:end CompeteDemes_EnergyConserve
+
+# 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 PrintTasksExeData
+u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
+#u 0:100:end PrintResourceData # Track resource abundance.
+
+u 0:100:end PrintInstructionData
+u 0:100:end PrintInstructionAbundanceHistogram
+u 99:100:end PrintMessageData
+u 99:100:end PrintDemeInterrupt
+
+u 0:20:end PrintDemeReplicationData
+u 0:20:end PrintGermlineData
+u 0:20:end PrintDemeCompetitionData
+u 0:20:end PrintDemesTotalAvgEnergy
+u 0:20:end PrintDemeAverageData
+u 19:20:end PrintDemeAverageData
+
+# 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 25000:25000:end SavePopulation # Save current state of population.
+#u 50000:50000 SaveHistoricPopulation # Save ancestors of current population.
+#u 100000 exit # exit
+u 100 exit
\ No newline at end of file
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/instset-LabelRotate.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/instset-LabelRotate.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/instset-LabelRotate.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+nop-A 1 1 0 1 # a
+nop-B 1 1 0 1 # b
+nop-C 1 1 0 1 # c
+nop-X 1 1 0 1
+repro 1 1 0 1
+
+send-msg 1 5 0 10
+MSG_received_handler_START 1 1 0 1
+interrupt_handler_END 1 1 0 1
+
+#rotate-left-one 1 2 0 4
+#rotate-right-one 1 2 0 4
+rotate-label 1 2 0 4
+#rotate-to-unoccupied-cell 1 2 0 4
+#rotate-to-occupied-cell 1 2 0 4
+#rotate-to-next-unoccupied-cell 1 2 0 4
+#rotate-to-next-occupied-cell 1 2 0 4
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/instset-LabelRotate_even.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/instset-LabelRotate_even.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/instset-LabelRotate_even.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+nop-A 1 1 0 1 # a
+nop-B 1 1 0 1 # b
+nop-C 1 1 0 1 # c
+nop-X 1 1 0 1
+repro 1 1 0 1
+
+send-msg 1 1 0 1
+MSG_received_handler_START 1 1 0 1
+interrupt_handler_END 1 1 0 1
+
+#rotate-left-one 1 1 0 1
+#rotate-right-one 1 1 0 1
+rotate-label 1 1 0 1
+#rotate-to-unoccupied-cell 1 1 0 1
+#rotate-to-occupied-cell 1 1 0 1
+#rotate-to-next-unoccupied-cell 1 1 0 1
+#rotate-to-next-occupied-cell 1 1 0 1
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/instset-NextNeighborRotate.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/instset-NextNeighborRotate.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/instset-NextNeighborRotate.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+nop-A 1 1 0 1 # a
+nop-B 1 1 0 1 # b
+nop-C 1 1 0 1 # c
+nop-X 1 1 0 1
+repro 1 1 0 1
+
+send-msg 1 5 0 10
+MSG_received_handler_START 1 1 0 1
+interrupt_handler_END 1 1 0 1
+
+#rotate-left-one 1 2 0 4
+#rotate-right-one 1 2 0 4
+#rotate-label 1 2 0 4
+#rotate-to-unoccupied-cell 1 2 0 4
+#rotate-to-occupied-cell 1 2 0 4
+rotate-to-next-unoccupied-cell 1 2 0 4
+rotate-to-next-occupied-cell 1 2 0 4
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/instset-NextNeighborRotate_even.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/instset-NextNeighborRotate_even.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/instset-NextNeighborRotate_even.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+nop-A 1 1 0 1 # a
+nop-B 1 1 0 1 # b
+nop-C 1 1 0 1 # c
+nop-X 1 1 0 1
+repro 1 1 0 1
+
+send-msg 1 1 0 1
+MSG_received_handler_START 1 1 0 1
+interrupt_handler_END 1 1 0 1
+
+#rotate-left-one 1 1 0 1
+#rotate-right-one 1 1 0 1
+#rotate-label 1 1 0 1
+#rotate-to-unoccupied-cell 1 1 0 1
+#rotate-to-occupied-cell 1 1 0 1
+rotate-to-next-unoccupied-cell 1 1 0 1
+rotate-to-next-occupied-cell 1 1 0 1
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/instset-SingleStepRotate.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/instset-SingleStepRotate.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/instset-SingleStepRotate.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+nop-A 1 1 0 1 # a
+nop-B 1 1 0 1 # b
+nop-C 1 1 0 1 # c
+nop-X 1 1 0 1
+repro 1 1 0 1
+
+send-msg 1 5 0 10
+MSG_received_handler_START 1 1 0 1
+interrupt_handler_END 1 1 0 1
+
+rotate-left-one 1 2 0 4
+rotate-right-one 1 2 0 4
+#rotate-label 1 2 0 4
+#rotate-to-unoccupied-cell 1 2 0 4
+#rotate-to-occupied-cell 1 2 0 4
+#rotate-to-next-unoccupied-cell 1 2 0 4
+#rotate-to-next-occupied-cell 1 2 0 4
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/instset-SingleStepRotate_even.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/instset-SingleStepRotate_even.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/instset-SingleStepRotate_even.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+nop-A 1 1 0 1 # a
+nop-B 1 1 0 1 # b
+nop-C 1 1 0 1 # c
+nop-X 1 1 0 1
+repro 1 1 0 1
+
+send-msg 1 1 0 1
+MSG_received_handler_START 1 1 0 1
+interrupt_handler_END 1 1 0 1
+
+rotate-left-one 1 1 0 1
+rotate-right-one 1 1 0 1
+#rotate-label 1 1 0 1
+#rotate-to-unoccupied-cell 1 1 0 1
+#rotate-to-occupied-cell 1 1 0 1
+#rotate-to-next-unoccupied-cell 1 1 0 1
+#rotate-to-next-occupied-cell 1 1 0 1
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/instset-allRotate.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/instset-allRotate.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/instset-allRotate.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+nop-A 1 1 0 1 # a
+nop-B 1 1 0 1 # b
+nop-C 1 1 0 1 # c
+nop-X 1 1 0 1
+repro 1 1 0 1
+
+send-msg 1 5 0 10
+MSG_received_handler_START 1 1 0 1
+interrupt_handler_END 1 1 0 1
+
+rotate-left-one 1 2 0 4
+rotate-right-one 1 2 0 4
+rotate-label 1 2 0 4
+#rotate-to-unoccupied-cell 1 2 0 4
+#rotate-to-occupied-cell 1 2 0 4
+rotate-to-next-unoccupied-cell 1 2 0 4
+rotate-to-next-occupied-cell 1 2 0 4
Added: branches/interrupt/tests/interruptModel_quorumSensing/config/instset-allRotate_even.cfg
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/config/instset-allRotate_even.cfg (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/config/instset-allRotate_even.cfg 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+nop-A 1 1 0 1 # a
+nop-B 1 1 0 1 # b
+nop-C 1 1 0 1 # c
+nop-X 1 1 0 1
+repro 1 1 0 1
+
+send-msg 1 1 0 1
+MSG_received_handler_START 1 1 0 1
+interrupt_handler_END 1 1 0 1
+
+rotate-left-one 1 1 0 1
+rotate-right-one 1 1 0 1
+rotate-label 1 1 0 1
+#rotate-to-unoccupied-cell 1 1 0 1
+#rotate-to-occupied-cell 1 1 0 1
+rotate-to-next-unoccupied-cell 1 1 0 1
+rotate-to-next-occupied-cell 1 1 0 1
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/average.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/average.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/average.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,21 @@
+# Avida Average Data
+# Fri Feb 6 10:36:45 2009
+# 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 643387.096774 50.000000 0.709677 0.000000 50.000000 50.000000 50.000000 31.000000 1.000000 1.000000 0.000000 0.709677 0.218400 0.000000 0.000000
+100 0 47.45 1 0 50.15 50.15 47.45 38.4615 0.682 0.682 0 20 0.662448 -1 0
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/count.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/count.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/count.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,21 @@
+# Avida count data
+# Fri Feb 6 10:36:45 2009
+# 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 1000 31 1 1 0 0 0 31 0 31 31 20 31 0 0
+100 13868 500 13 3 0 0 0 341 821 341 500 257 500 0 0
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_average.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_average.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_average.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,28 @@
+# Avida Average Deme Data
+# Fri Feb 6 10:36:45 2009
+# 1: Update
+# 2: Count
+# 3: Age
+# 4: Births
+# 5: Organisms
+# 6: Generation
+# 7: Births (at last replication)
+# 8: Organisms (at last replication)
+# 9: Merit
+# 10: Gestation Time
+# 11: Time Used (normalized by org fitness)
+# 12: Generations between current and last founders
+# 13: Events killed
+# 14: Attempts to kill event
+
+0 20 0.000000 0.550000 1.550000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+19 20 19 274.5 25 0 0 0 1 0 0 0 0 0
+20 20 20 292 25 0 0 0 1 0 0 0 0 0
+39 20 18 276 25 1.95 41.8713 10.735 1 5915.4 inf 0 0 0
+40 20 19 291.95 25 1.95 43 11.0244 1 5915.4 inf 0 0 0
+59 19 18 268.842 25 3.84211 53.0976 14.2111 1 5196.32 inf 0 0 0
+60 19 19 291.947 25 3.84211 53.4768 14.3212 1 5196.32 inf 0 0 0
+79 20 18 291.85 25 5.4 65.1599 15.716 1 4719.9 inf 0 0 0
+80 20 19 291.85 25 5.4 65.6219 15.7711 1 4719.9 inf 0 0 0
+99 20 18 277.6 25 7.15 66.9175 16.8471 1 4926 inf 0 0 0
+100 20 19 293.55 25 7.15 66.9721 16.8924 1 4926 inf 0 0 0
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_compete.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_compete.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_compete.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,11 @@
+# Avida compete demes data
+# Fri Feb 6 10:36:45 2009
+# 1: Update [update]
+# 2: Avg. deme fitness [avgfit]
+
+0 0.000000
+20 1.00002
+40 1.00002
+60 1.00002
+80 1.00002
+100 1.00002
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_interrupt.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_interrupt.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_interrupt.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,7 @@
+# Interrupt model stats averaged over all demes
+# Assumes each organism only contains a single thread!
+# Fri Feb 6 10:36:58 2009
+# 1: Update
+# 2: Organisms interrupted per deme
+
+99 0.600000
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_repl.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_repl.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_repl.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,15 @@
+# Avida deme replication data
+# Fri Feb 6 10:36:45 2009
+# 1: Update [update]
+# 2: Number of deme replications [numrepl]
+# 3: Mean deme gestation time [gesttime]
+# 4: Mean number of births within replicated demes [numbirths]
+# 5: Mean heritable merit of replicated demes [merit]
+# 6: Mean generation of replicated demes [generation]
+
+0 0 0.000000 0.000000 0.000000 0.000000
+20 16 15.75 218.875 1 0.4375
+40 16 16.25 237.312 1 2.25
+60 15 14.6667 214.733 1 4
+80 16 15 218.812 1 5.625
+100 15 17.3333 253.867 1 7.06667
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_totalAvgEnergy.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_totalAvgEnergy.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/deme_totalAvgEnergy.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,11 @@
+# Average energy for demes in the population
+# Fri Feb 6 10:36:45 2009
+# 1: update
+# 2: Total Average Energy
+
+0 99509045.000000
+20 1e+08
+40 1e+08
+60 1e+08
+80 1e+08
+100 1e+08
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/dominant.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/dominant.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/dominant.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,21 @@
+# Avida Dominant Data
+# Fri Feb 6 10:36:45 2009
+# 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 497500.000000 50.000000 1.000000 0.020000 50 50.000000 50.000000 31 11 11 0 0 1.000000 1 050-aaaaa
+100 10178.4 50 1 0.02 50 50 50 75 53 53 0 0 1 33 050-aaaaq
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/germline.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/germline.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/germline.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,11 @@
+# Avida germline data
+# Fri Feb 6 10:36:45 2009
+# 1: Update [update]
+# 2: Mean germline generation of replicated germlines [replgen]
+
+0 0.000000
+20 1.5
+40 2.4375
+60 3.06667
+80 3.875
+100 4.4
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/instruction.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/instruction.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/instruction.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,16 @@
+# Avida instruction execution data
+# Fri Feb 6 10:36:45 2009
+# 1: Update
+# 2: nop-A
+# 3: nop-B
+# 4: nop-C
+# 5: nop-X
+# 6: repro
+# 7: send-msg
+# 8: MSG_received_handler_START
+# 9: interrupt_handler_END
+# 10: rotate-left-one
+# 11: rotate-right-one
+
+0 0 0 0 1078 22 0 0 0 0 0
+100 275 175 25 22475 500 50 0 25 0 200
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/instruction_histogram.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/instruction_histogram.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/instruction_histogram.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,14 @@
+# 1: Update
+# 2: nop-A
+# 3: nop-B
+# 4: nop-C
+# 5: nop-X
+# 6: repro
+# 7: send-msg
+# 8: MSG_received_handler_START
+# 9: interrupt_handler_END
+# 10: rotate-left-one
+# 11: rotate-right-one
+
+0 0 0 0 1519 31 0 0 0 0 0
+100 15 6 3 947 21 2 0 1 2 8
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/message.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/message.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/message.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,9 @@
+# Number of organsism to organisms messages
+
+# 1: update
+# 2: Totlal messages sent
+# 3: Sent successfully
+# 4: Dropped
+# 5: Failed
+
+99 687 658 0 29
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/stats.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/stats.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/stats.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,17 @@
+# Generic Statistics Data
+# Fri Feb 6 10:36:45 2009
+# 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 0.342945 0.000000 0.000000 -0.000000 -0.000000 1 0.000000 0.000000 0 0 0
+100 0 0 0 -0 -0 0 2.43204 0 0 0 0
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/tasks.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/tasks.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/tasks.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,8 @@
+# Avida tasks data
+# Fri Feb 6 10:36:45 2009
+# 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
+
+0
+100
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/tasks_exe.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/tasks_exe.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/tasks_exe.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,8 @@
+# Avida tasks execution data
+# Fri Feb 6 10:36:45 2009
+# First column gives the current update, all further columns give the number
+# of times the particular task has been executed this update.
+# 1: Update
+
+0
+100
Added: branches/interrupt/tests/interruptModel_quorumSensing/expected/data/time.dat
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/expected/data/time.dat (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/expected/data/time.dat 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,9 @@
+# Avida time data
+# Fri Feb 6 10:36:45 2009
+# 1: update
+# 2: avida time
+# 3: average generation
+# 4: num_executed?
+
+0 0.000000 0.709677 1000
+100 5.50895 20 13868
Added: branches/interrupt/tests/interruptModel_quorumSensing/test_list
===================================================================
--- branches/interrupt/tests/interruptModel_quorumSensing/test_list (rev 0)
+++ branches/interrupt/tests/interruptModel_quorumSensing/test_list 2009-02-06 15:39:23 UTC (rev 3143)
@@ -0,0 +1,37 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+; Command line arguments to pass to the application
+args = -set FRAC_ENERGY_DECAY_AT_ORG_BIRTH 0.0 -set INST_SET instset-SingleStepRotate_even.cfg
+
+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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