[Avida-SVN] r2336 - in development: . source/main support/config
covertar at myxo.css.msu.edu
covertar at myxo.css.msu.edu
Sun Feb 17 13:45:36 PST 2008
Author: covertar
Date: 2008-02-17 16:45:36 -0500 (Sun, 17 Feb 2008)
New Revision: 2336
Modified:
development/build_avida
development/source/main/cPopulation.cc
development/support/config/avida.cfg
Log:
Restored config files to defaults and added comments.
Modified: development/build_avida
===================================================================
--- development/build_avida 2008-02-17 21:23:33 UTC (rev 2335)
+++ development/build_avida 2008-02-17 21:45:36 UTC (rev 2336)
@@ -3,6 +3,6 @@
mkdir -p cbuild
cd cbuild
cmake "$@" ../
-make -j9
+make
make install
Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc 2008-02-17 21:23:33 UTC (rev 2335)
+++ development/source/main/cPopulation.cc 2008-02-17 21:45:36 UTC (rev 2336)
@@ -2125,7 +2125,7 @@
int deme_id = parent_cell.GetDemeID();
//@AWC -- decide wether the child will migrate to another deme
- if((m_world->GetConfig().MIGRATION_RATE.Get() > 0.0)
+ if((m_world->GetConfig().MIGRATION_RATE.Get() > 0.0) //@AWC -- Pedantic test to maintain consistancy.
&& m_world->GetRandom().P(m_world->GetConfig().MIGRATION_RATE.Get())){
//get another -unadjusted- deme id
Modified: development/support/config/avida.cfg
===================================================================
--- development/support/config/avida.cfg 2008-02-17 21:23:33 UTC (rev 2335)
+++ development/support/config/avida.cfg 2008-02-17 21:45:36 UTC (rev 2336)
@@ -3,7 +3,7 @@
# For more information, see doc/config.html
#############################################################################
-VERSION_ID 2.7.0 # Do not change this value.
+VERSION_ID 2.9.0 # Do not change this value.
### GENERAL_GROUP ###
# General Settings
@@ -12,7 +12,11 @@
# 2 = Interactive
VIEW_MODE 1 # Initial viewer screen
CLONE_FILE - # Clone file to load
-VERBOSITY 1 # Control output verbosity
+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
@@ -32,6 +36,9 @@
# 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
@@ -46,45 +53,51 @@
# germline replication.
GERMLINE_REPLACES_SOURCE 0 # Whether the source germline is updated
# on replication; 0=no.
-GERMLINE_RANDOM_PLACEMENT 0 # Whether the seed for a germline is placed
- # randomly within the deme; 0=no.
+GERMLINE_RANDOM_PLACEMENT 0 # Defines how the seed for a germline is placed
+ # within the deme;
+ # 0 = organisms is placed in center of deme, no orientation
+ # 1 = organisms is placed in center of deme and oriented
+ # 2 = organism is randomly placed in deme, no orientation
MAX_DEME_AGE 500 # The maximum age of a deme (in updates) to be
# used for age-based replication (default=500).
### REPRODUCTION_GROUP ###
# Birth and Death
-BIRTH_METHOD 0 # Which organism should be replaced on birth?
- # 0 = Random organism in neighborhood
- # 1 = Oldest in neighborhood
- # 2 = Largest Age/Merit in neighborhood
- # 3 = None (use only empty cells in neighborhood)
- # 4 = Random from population (Mass Action)
- # 5 = Oldest in entire population
- # 6 = Random within deme
- # 7 = Organism faced by parent
- # 8 = Next grid cell (id+1)
- # 9 = Largest energy used in entire population
- # 10 = Largest energy used in neighborhood
-PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
-ALLOW_PARENT 1 # Allow births to replace the parent organism?
-DEATH_METHOD 2 # 0 = Never die of old age.
- # 1 = Die when inst executed = AGE_LIMIT (+deviation)
- # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
-AGE_LIMIT 20 # Modifies DEATH_METHOD
-AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
-ALLOC_METHOD 0 # (Orignal CPU Only)
- # 0 = Allocated space is set to default instruction.
- # 1 = Set to section of dead genome (Necrophilia)
- # 2 = Allocated space is set to random instruction.
-DIVIDE_METHOD 1 # 0 = Divide leaves state of mother untouched.
- # 1 = Divide resets state of mother
- # (after the divide, we have 2 children)
- # 2 = Divide resets state of current thread only
- # (does not touch possible parasite threads)
-GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
- # increased on divide.
- # 1 = Both the generation of the mother and child are
- # increased on divide (good with DIVIDE_METHOD 1).
+BIRTH_METHOD 0 # Which organism should be replaced on birth?
+ # 0 = Random organism in neighborhood
+ # 1 = Oldest in neighborhood
+ # 2 = Largest Age/Merit in neighborhood
+ # 3 = None (use only empty cells in neighborhood)
+ # 4 = Random from population (Mass Action)
+ # 5 = Oldest in entire population
+ # 6 = Random within deme
+ # 7 = Organism faced by parent
+ # 8 = Next grid cell (id+1)
+ # 9 = Largest energy used in entire population
+ # 10 = Largest energy used in neighborhood
+PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
+ALLOW_PARENT 1 # Allow births to replace the parent organism?
+DEATH_METHOD 2 # 0 = Never die of old age.
+ # 1 = Die when inst executed = AGE_LIMIT (+deviation)
+ # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
+AGE_LIMIT 20 # Modifies DEATH_METHOD
+AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
+ALLOC_METHOD 0 # (Orignal CPU Only)
+ # 0 = Allocated space is set to default instruction.
+ # 1 = Set to section of dead genome (Necrophilia)
+ # 2 = Allocated space is set to random instruction.
+DIVIDE_METHOD 1 # 0 = Divide leaves state of mother untouched.
+ # 1 = Divide resets state of mother
+ # (after the divide, we have 2 children)
+ # 2 = Divide resets state of current thread only
+ # (does not touch possible parasite threads)
+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.
### RECOMBINATION_GROUP ###
# Sexual Recombination and Modularity
@@ -101,25 +114,34 @@
### 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.
+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 0.0 # 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.
### MUTATION_GROUP ###
# Mutations
POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
+COPY_SLIP_PROB 0.0 # Slip 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)
+UNIFORM_MUT_PROB 0.0 # Uniform mutation probability (per site, applied on divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
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)
+DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
+SLIP_FILL_MODE 0 # Fill insertions from slip mutations with 0=duplication, 1=nop-X, 2=random, 3=scrambled
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)
@@ -129,6 +151,7 @@
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 # Probability of new orgs being born in a different deme -- only works with BIRTH_METHOD 6
### REVERSION_GROUP ###
# Mutation Reversion
@@ -143,8 +166,10 @@
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.
+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
@@ -161,39 +186,44 @@
# 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
DEFAULT_BONUS 1.0 # Initial bonus before any tasks
-MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by the default bonus
- # rather than the accumulated bonus of the parent?
-MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts (-1=none, 0= 1st in INST_SET.)
-MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned per INST (-1=penalty, 0= no effect.)
-FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP (0= off, 1=on)
-FITNESS_VALLEY_START 0 # if FITNESS_VALLEY =1, orgs with num_key_instructions from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP get fitness 1 (lowest)
-FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY =1, orgs with num_key_instructions from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP get fitness 1 (lowest)
+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 1.0 # A 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
+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.
-### PROMOTER_GROUP ###
-# Promoters
-PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
- # Certain instructions must also be included.
-PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating after each cpu cycle.
-PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after each instruction.
-PROMOTER_BG_STRENGTH 0 # Probability of positions that are not promoter
- # instructions initiating execution (promoters are 1).
-REGULATION_STRENGTH 1 # Strength added or subtracted to a promoter by regulation.
-REGULATION_DECAY_FRAC 0.1 # Fraction of regulation that decays away.
- # Max regulation = 2^(REGULATION_STRENGTH/REGULATION_DECAY_FRAC)
-
### GENEOLOGY_GROUP ###
# Geneology
TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
@@ -254,11 +284,80 @@
### 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
+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 0 # Enable Energy Model. 0/1 (off/on)
+ENERGY_GIVEN_ON_INJECT 0 # Energy given to organism upon injection.
+ENERGY_GIVEN_AT_BIRTH 0 # Energy given to offspring upon birth.
+FRAC_PARENT_ENERGY_GIVEN_AT_BIRTH 0.5 # Fraction of perent's energy given to offspring.
+FRAC_ENERGY_DECAY_AT_BIRTH 0.0 # Fraction of energy lost due to decay during reproduction.
+NUM_INST_EXC_BEFORE_0_ENERGY 0 # Number of instructions executed before energy is exhausted.
+ENERGY_CAP -1 # Maximum amount of energy that can be stored in an organism. -1 means the cap is set to Max Int
+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.
+
### 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 0 # Number of cells to move Avidian on move instruction
+BIOMIMETIC_K 0 # Carrying capacity in number of organisms
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