[Avida-SVN] r1911 - development/support/config
barrick at myxo.css.msu.edu
barrick at myxo.css.msu.edu
Wed Aug 8 20:15:26 PDT 2007
Author: barrick
Date: 2007-08-08 23:15:26 -0400 (Wed, 08 Aug 2007)
New Revision: 1911
Modified:
development/support/config/avida.cfg
Log:
Modified: development/support/config/avida.cfg
===================================================================
--- development/support/config/avida.cfg 2007-08-09 03:14:09 UTC (rev 1910)
+++ development/support/config/avida.cfg 2007-08-09 03:15:26 UTC (rev 1911)
@@ -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
@@ -53,40 +57,41 @@
### 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)
-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).
+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
@@ -103,15 +108,16 @@
### 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.
-IMPLICIT_REPRO_BONUS 0 # Immediately call Inst_Repro to divide when upon achieving this bonus. 0 = OFF
-IMPLICIT_REPRO_TIME 0 # Immediately call Inst_Repro after this many cpu cycles. 0 = OFF
+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.
+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
### MUTATION_GROUP ###
# Mutations
@@ -120,6 +126,8 @@
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)
@@ -173,6 +181,8 @@
# (-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)
@@ -187,6 +197,7 @@
# (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
@@ -196,7 +207,11 @@
# 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_MERIT 0 # Pre-calculate merit at birth (unlimited resources only).
+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.
### GENEOLOGY_GROUP ###
# Geneology
@@ -258,9 +273,9 @@
### ANALYZE_GROUP ###
# Analysis Settings
-MAX_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
@@ -275,7 +290,6 @@
# 0 = on divide
# 1 = on completion of task
# 2 = on sleep
-ENERGY_VERBOSE 0 # Print energy and merit values. 0/1 (off/on)
LOG_SLEEP_TIMES 0 # Log sleep start and end times. 0/1 (off/on)
# WARNING: may use lots of memory.
@@ -304,3 +318,24 @@
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)
+
+### 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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