[Avida-SVN] r1432 - in development: Avida.xcodeproj tests tests/default_classic_100u/config tests/default_transsmt_100u/config tests/midrun_classsic_30u/config tests/task_sort_analyze tests/task_sort_analyze/config tests/task_sort_analyze/expected tests/task_sort_analyze/expected/data
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Mon Mar 26 06:29:34 PDT 2007
Author: brysonda
Date: 2007-03-26 09:29:34 -0400 (Mon, 26 Mar 2007)
New Revision: 1432
Added:
development/tests/task_sort_analyze/
development/tests/task_sort_analyze/config/
development/tests/task_sort_analyze/config/analyze.cfg
development/tests/task_sort_analyze/config/avida.cfg
development/tests/task_sort_analyze/config/basic-10-sorter.org
development/tests/task_sort_analyze/config/environment.cfg
development/tests/task_sort_analyze/config/events.cfg
development/tests/task_sort_analyze/config/instset-classic.cfg
development/tests/task_sort_analyze/expected/
development/tests/task_sort_analyze/expected/data/
development/tests/task_sort_analyze/expected/data/detail.dat
development/tests/task_sort_analyze/test_list
Modified:
development/Avida.xcodeproj/project.pbxproj
development/tests/default_classic_100u/config/environment.cfg
development/tests/default_classic_100u/config/events.cfg
development/tests/default_classic_100u/config/instset-classic.cfg
development/tests/default_transsmt_100u/config/environment.cfg
development/tests/default_transsmt_100u/config/events.cfg
development/tests/default_transsmt_100u/config/instset-transsmt.cfg
development/tests/midrun_classsic_30u/config/environment.cfg
development/tests/midrun_classsic_30u/config/events.cfg
development/tests/midrun_classsic_30u/config/instset-classic.cfg
Log:
Add new consistency test that verifies sorting task functionality. It does this through analyze mode, also testing LOAD_ORGANISM, RECALCULATE, and DETAIL.
Update all other consistency test configurations to remove some of the comments to save a little space.
Modified: development/Avida.xcodeproj/project.pbxproj
===================================================================
--- development/Avida.xcodeproj/project.pbxproj 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/Avida.xcodeproj/project.pbxproj 2007-03-26 13:29:34 UTC (rev 1432)
@@ -452,7 +452,7 @@
700E12610A097A0800B604CD /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
700E12630A097A1700B604CD /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
700E28CF0859FFD700CF158A /* tObjectFactory.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tObjectFactory.h; sourceTree = "<group>"; };
- 700E2B83085DE50C00CF158A /* avida-viewer */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = "avida-viewer"; sourceTree = BUILT_PRODUCTS_DIR; };
+ 700E2B83085DE50C00CF158A /* avida-viewer */ = {isa = PBXFileReference; includeInIndex = 0; lastKnownFileType = "compiled.mach-o.executable"; path = "avida-viewer"; sourceTree = BUILT_PRODUCTS_DIR; };
7013845F09028B3E0087ED2E /* cAvidaConfig.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cAvidaConfig.h; sourceTree = "<group>"; };
7013846009028B3E0087ED2E /* cAvidaConfig.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cAvidaConfig.cc; sourceTree = "<group>"; };
701384A10902A16F0087ED2E /* defs.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = defs.h; sourceTree = "<group>"; };
@@ -923,7 +923,7 @@
DCC315CF076253A5008F7A48 /* Makefile */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.make; path = Makefile; sourceTree = "<group>"; };
DCC315D0076253A5008F7A48 /* task_event_gen.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.cc; sourceTree = "<group>"; };
DCC315D1076253A5008F7A48 /* task_event_gen.old.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.old.cc; sourceTree = "<group>"; };
- DCC3164D07626CF3008F7A48 /* avida */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = avida; sourceTree = BUILT_PRODUCTS_DIR; };
+ DCC3164D07626CF3008F7A48 /* avida */ = {isa = PBXFileReference; includeInIndex = 0; lastKnownFileType = "compiled.mach-o.executable"; path = avida; sourceTree = BUILT_PRODUCTS_DIR; };
/* End PBXFileReference section */
/* Begin PBXFrameworksBuildPhase section */
Modified: development/tests/default_classic_100u/config/environment.cfg
===================================================================
--- development/tests/default_classic_100u/config/environment.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/default_classic_100u/config/environment.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -1,17 +1,3 @@
-##############################################################################
-#
-# 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/
-#
-##############################################################################
-
REACTION NOT not process:value=1.0:type=pow requisite:max_count=1
REACTION NAND nand process:value=1.0:type=pow requisite:max_count=1
REACTION AND and process:value=2.0:type=pow requisite:max_count=1
Modified: development/tests/default_classic_100u/config/events.cfg
===================================================================
--- development/tests/default_classic_100u/config/events.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/default_classic_100u/config/events.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -1,18 +1,3 @@
-##############################################################################
-#
-# This is the setup file for the events system. From here, you can
-# configure any actions that you want to have happen during the course of
-# an experiment, including setting the times for data collection.
-#
-# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
-#
-# This file is currently setup to record key information every 100 updates.
-#
-# For information on how to use this file, see: doc/events.html
-# For other sample event configurations, see: support/config/
-#
-##############################################################################
-
# Print all of the standard data files...
u 0:10:end PrintAverageData # Save info about they average genotypes
u 0:10:end PrintDominantData # Save info about most abundant genotypes
Modified: development/tests/default_classic_100u/config/instset-classic.cfg
===================================================================
--- development/tests/default_classic_100u/config/instset-classic.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/default_classic_100u/config/instset-classic.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -26,27 +26,3 @@
if-label 1 # y
set-flow 1 # z Move flow-head to address in ?CX?
-#adv-head 1
-#jump-f 1
-#jump-b 1
-#call 1
-#return 1
-#if-bit-1 1
-#get 1
-#put 1
-#h-read 1
-#h-write 1
-#set-head 1
-#search-f 1
-#search-b 1
-
-
-# Works on multiple nops: pop push inc dec IO adv-head
-
-# What if we add a new head. Search will return the location of something,
-# and put the new head there. Then set-head will move another head to that
-# point. In the case of the copy loop, it only needs to be set once and
-# this will speed up the code quite a bit!
-
-# Search with no template returns current position (abs line number) in
-# genome.
\ No newline at end of file
Modified: development/tests/default_transsmt_100u/config/environment.cfg
===================================================================
--- development/tests/default_transsmt_100u/config/environment.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/default_transsmt_100u/config/environment.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -1,17 +1,3 @@
-##############################################################################
-#
-# 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/
-#
-##############################################################################
-
REACTION NOT not process:value=1.0:type=pow requisite:max_count=1
REACTION NAND nand process:value=1.0:type=pow requisite:max_count=1
REACTION AND and process:value=2.0:type=pow requisite:max_count=1
Modified: development/tests/default_transsmt_100u/config/events.cfg
===================================================================
--- development/tests/default_transsmt_100u/config/events.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/default_transsmt_100u/config/events.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -1,18 +1,3 @@
-##############################################################################
-#
-# This is the setup file for the events system. From here, you can
-# configure any actions that you want to have happen during the course of
-# an experiment, including setting the times for data collection.
-#
-# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
-#
-# This file is currently setup to record key information every 100 updates.
-#
-# For information on how to use this file, see: doc/events.html
-# For other sample event configurations, see: support/config/
-#
-##############################################################################
-
# Print all of the standard data files...
u 0:10:end PrintAverageData # Save info about they average genotypes
u 0:10:end PrintDominantData # Save info about most abundant genotypes
Modified: development/tests/default_transsmt_100u/config/instset-transsmt.cfg
===================================================================
--- development/tests/default_transsmt_100u/config/instset-transsmt.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/default_transsmt_100u/config/instset-transsmt.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -31,20 +31,3 @@
Val-Delete 1 #30 (D)
Val-Copy 1 #31 (E)
IO 1 #32 (F)
-
-# Additional Instructions - Disabled by Default
-#Nop-X 1 #33 ()
-#Thread-Create 1 #34 ()
-#Thread-Cancel 1 #35 ()
-#Thread-Kill 1 #36 ()
-#Inject 1 #37 ()
-#Apoptosis 1 #38 ()
-#Net-Get 1 #39 ()
-#Net-Send 1 #40 ()
-#Net-Receive 1 #41 ()
-#Net-Last 1 #42 ()
-#Rotate-Left 1 #43 ()
-#Rotate-Right 1 #44 ()
-#Call-Flow 1 #45 ()
-#Call-Label 1 #46 ()
-#Return 1 #47 ()
Modified: development/tests/midrun_classsic_30u/config/environment.cfg
===================================================================
--- development/tests/midrun_classsic_30u/config/environment.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/midrun_classsic_30u/config/environment.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -1,17 +1,3 @@
-##############################################################################
-#
-# 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/
-#
-##############################################################################
-
REACTION NOT not process:value=1.0:type=pow requisite:max_count=1
REACTION NAND nand process:value=1.0:type=pow requisite:max_count=1
REACTION AND and process:value=2.0:type=pow requisite:max_count=1
Modified: development/tests/midrun_classsic_30u/config/events.cfg
===================================================================
--- development/tests/midrun_classsic_30u/config/events.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/midrun_classsic_30u/config/events.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -1,18 +1,3 @@
-##############################################################################
-#
-# This is the setup file for the events system. From here, you can
-# configure any actions that you want to have happen during the course of
-# an experiment, including setting the times for data collection.
-#
-# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
-#
-# This file is currently setup to record key information every 100 updates.
-#
-# For information on how to use this file, see: doc/events.html
-# For other sample event configurations, see: support/config/
-#
-##############################################################################
-
# Print all of the standard data files...
u begin LoadPopulation detail-50000.pop
u 0:5:end PrintAverageData # Save info about they average genotypes
Modified: development/tests/midrun_classsic_30u/config/instset-classic.cfg
===================================================================
--- development/tests/midrun_classsic_30u/config/instset-classic.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/midrun_classsic_30u/config/instset-classic.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -24,29 +24,5 @@
jmp-head 1 # w Move ?IP? head by fixed amount in CX. Set old pos in CX.
get-head 1 # x Get position of specified head in CX.
if-label 1 # y
-set-flow 1 # z Move flow-head to address in ?CX?
+set-flow 1 # z Move flow-head to address in ?CX?
-#adv-head 1
-#jump-f 1
-#jump-b 1
-#call 1
-#return 1
-#if-bit-1 1
-#get 1
-#put 1
-#h-read 1
-#h-write 1
-#set-head 1
-#search-f 1
-#search-b 1
-
-
-# Works on multiple nops: pop push inc dec IO adv-head
-
-# What if we add a new head. Search will return the location of something,
-# and put the new head there. Then set-head will move another head to that
-# point. In the case of the copy loop, it only needs to be set once and
-# this will speed up the code quite a bit!
-
-# Search with no template returns current position (abs line number) in
-# genome.
\ No newline at end of file
Added: development/tests/task_sort_analyze/config/analyze.cfg
===================================================================
--- development/tests/task_sort_analyze/config/analyze.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/task_sort_analyze/config/analyze.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -0,0 +1,4 @@
+LOAD_ORGANISM basic-10-sorter.org
+RECALCULATE
+DETAIL detail.dat length viable copy_length exe_length merit comp_merit gest_time efficiency fitness task.0 task.0:binary
+
Added: development/tests/task_sort_analyze/config/avida.cfg
===================================================================
--- development/tests/task_sort_analyze/config/avida.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/task_sort_analyze/config/avida.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -0,0 +1,216 @@
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.7.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 0 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 1 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+VERBOSITY 1 # Control output verbosity
+
+### ARCH_GROUP ###
+# Architecture Variables
+WORLD_X 60 # Width of the Avida world
+WORLD_Y 60 # Height of the Avida world
+WORLD_GEOMETRY 2 # 1 = Bounded Grid
+ # 2 = Torus
+NUM_DEMES 0 # Number of independed groups in the population; 0=off
+RANDOM_SEED 0 # Random number seed (0 for based on time)
+HARDWARE_TYPE 0 # 0 = Original CPUs
+ # 1 = New SMT CPUs
+ # 2 = Transitional SMT
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET - # File containing instruction set
+EVENT_FILE events.cfg # File containing list of events during run
+ANALYZE_FILE analyze.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment.cfg # File that describes the environment
+START_CREATURE basic-10-sorter.org # Organism to seed the soup
+
+### 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)
+PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
+DEATH_METHOD 2 # 0 = Never die of old age.
+ # 1 = Die when inst executed = AGE_LIMIT (+deviation)
+ # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
+AGE_LIMIT 20 # Modifies DEATH_METHOD
+AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
+ALLOC_METHOD 0 # (Orignal CPU Only)
+ # 0 = Allocated space is set to default instruction.
+ # 1 = Set to section of dead genome (Necrophilia)
+ # 2 = Allocated space is set to random instruction.
+DIVIDE_METHOD 1 # 0 = Divide leaves state of mother untouched.
+ # 1 = Divide resets state of mother
+ # (after the divide, we have 2 children)
+ # 2 = Divide resets state of current thread only
+ # (does not touch possible parasite threads)
+GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
+ # increased on divide.
+ # 1 = Both the generation of the mother and child are
+ # increased on divide (good with DIVIDE_METHOD 1).
+
+### RECOMBINATION_GROUP ###
+# Sexual Recombination and Modularity
+RECOMBINATION_PROB 1.0 # probability of recombination in div-sex
+MAX_BIRTH_WAIT_TIME -1 # Updates incipiant orgs can wait for crossover
+MODULE_NUM 0 # number of modules in the genome
+CONT_REC_REGS 1 # are (modular) recombination regions continuous
+CORESPOND_REC_REGS 1 # are (modular) recombination regions swapped randomly
+ # or with corresponding positions?
+TWO_FOLD_COST_SEX 0 # 1 = only one recombined offspring is born.
+ # 2 = both offspring are born
+SAME_LENGTH_SEX 0 # 0 = recombine with any genome
+ # 1 = only recombine w/ same length
+
+### DIVIDE_GROUP ###
+# Divide Restrictions
+CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
+MIN_COPIED_LINES 0.5 # Code fraction which must be copied before divide.
+MIN_EXE_LINES 0.5 # Code fraction which must be executed before divide.
+REQUIRE_ALLOCATE 1 # (Original CPU Only) Require allocate before divide?
+REQUIRED_TASK -1 # Task ID required for successful divide.
+IMMUNITY_TASK -1 # Task providing immunity from the required task.
+REQUIRED_REACTION -1 # Reaction ID required for successful divide.
+REQUIRED_BONUS 0 # The bonus that an organism must accumulate to divide.
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
+INS_MUT_PROB 0.0 # Insertion rate (per site, applied on divide)
+DEL_MUT_PROB 0.0 # Deletion rate (per site, applied on divide)
+DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
+DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
+DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
+DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
+PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+INJECT_INS_PROB 0.0 # Insertion rate (per site, applied on inject)
+INJECT_DEL_PROB 0.0 # Deletion rate (per site, applied on inject)
+INJECT_MUT_PROB 0.0 # Mutation rate (per site, applied on inject)
+
+### REVERSION_GROUP ###
+# Mutation Reversion
+# These slow down avida a lot, and should be set to 0.0 normally.
+REVERT_FATAL 0.0 # Should any mutations be reverted on birth?
+REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
+REVERT_NEUTRAL 0.0 #
+REVERT_BENEFICIAL 0.0 #
+STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
+STERILIZE_DETRIMENTAL 0.0 #
+STERILIZE_NEUTRAL 0.0 #
+STERILIZE_BENEFICIAL 0.0 #
+FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
+ # be eliminated?
+NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness to be considered neutral.
+NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness to be considered neutral.
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
+ # 1 = Merit proportional to copied size
+ # 2 = Merit prop. to executed size
+ # 3 = Merit prop. to full size
+ # 4 = Merit prop. to min of executed or copied size
+ # 5 = Merit prop. to sqrt of the minimum size
+BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
+DEFAULT_BONUS 1.0 # Initial bonus before any tasks
+MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by the default bonus
+ # rather than the accumulated bonus of the parent?
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
+ # (num_threads-1) * THREAD_SLICING_METHOD + 1
+ # 0 = One thread executed per time slice.
+ # 1 = All threads executed each time slice.
+MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
+DONATE_SIZE 5.0 # Amount of merit donated with 'donate' command
+DONATE_MULT 10.0 # Multiple of merit given that the target receives.
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on edit distance for donate; -1=no max
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+
+### GENEOLOGY_GROUP ###
+# Geneology
+TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
+ # 0=no, 1=yes, 2=yes,w/sexual population
+THRESHOLD 3 # Number of organisms in a genotype needed for it
+ # to be considered viable.
+GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
+GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
+ # this many updates. (0 = off)
+SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
+SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
+SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
+TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
+
+### LOG_GROUP ###
+# Log Files
+LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
+LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
+LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
+LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
+
+### LINEAGE_GROUP ###
+# Lineage
+# NOTE: This should probably be called "Clade"
+# This one can slow down avida a lot. It is used to get an idea of how
+# often an advantageous mutation arises, and where it goes afterwards.
+# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
+# 0 = manual creation (on inject, use successive integers as lineage labels).
+# 1 = when a child's (potential) fitness is higher than that of its parent.
+# 2 = when a child's (potential) fitness is higher than max in population.
+# 3 = when a child's (potential) fitness is higher than max in dom. lineage
+# *and* the child is in the dominant lineage, or (2)
+# 4 = when a child's (potential) fitness is higher than max in dom. lineage
+# (and that of its own lineage)
+# 5 = same as child's (potential) fitness is higher than that of the
+# currently dominant organism, and also than that of any organism
+# currently in the same lineage.
+# 6 = when a child's (potential) fitness is higher than any organism
+# currently in the same lineage.
+# 7 = when a child's (potential) fitness is higher than that of any
+# organism in its line of descent
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
+
+### ORGANISM_NETWORK_GROUP ###
+# Organism Network Communication
+NET_ENABLED 0 # Enable Network Communication Support
+NET_DROP_PROB 0.0 # Message drop rate
+NET_MUT_PROB 0.0 # Message corruption probability
+NET_MUT_TYPE 0 # Type of message corruption. 0 = Random Single Bit, 1 = Always Flip Last
+NET_STYLE 0 # Communication Style. 0 = Random Next, 1 = Receiver Facing
+
+### BUY_SELL_GROUP ###
+# Buying and Selling Parameters
+SAVE_RECEIVED 0 # Enable storage of all inputs bought from other orgs
+BUY_PRICE 0 # price offered by organisms attempting to buy
+SELL_PRICE 0 # price offered by organisms attempting to sell
+
+### ANALYZE_GROUP ###
+# Analysis Settings
+MT_CONCURRENCY 1 # Number of concurrent analyze threads
+ANALYZE_OPTION_1 # String variable accessible from analysis scripts
+ANALYZE_OPTION_2 # String variable accessible from analysis scripts
Added: development/tests/task_sort_analyze/config/basic-10-sorter.org
===================================================================
--- development/tests/task_sort_analyze/config/basic-10-sorter.org 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/task_sort_analyze/config/basic-10-sorter.org 2007-03-26 13:29:34 UTC (rev 1432)
@@ -0,0 +1,132 @@
+IO # five IO's gets all of the input values
+push
+IO
+push
+IO
+push
+IO
+push
+IO
+push
+IO # five IO's gets all of the input values
+push
+IO
+push
+IO
+push
+IO
+push
+IO
+push
+
+nop-B # main routine, searches for least value
+nop-A
+nop-A
+h-search
+nop-A
+nop-A
+nop-C
+pop
+pop
+nop-C
+if-n-equ
+nop-C
+mov-head
+
+swap-stk # switch todo stack as the new source
+IO # output found min
+h-search
+nop-A
+nop-C
+nop-C
+pop
+push
+if-n-equ
+nop-A
+mov-head
+
+h-search # exit sorting routine
+nop-A
+nop-C
+nop-A
+mov-head
+
+nop-A # push value, return to start
+nop-B
+nop-B
+push
+push
+nop-C
+h-search
+nop-A
+nop-C
+nop-C
+mov-head # try next value
+dec
+
+nop-B # check value, looking for min
+nop-B
+nop-A
+swap-stk # change to the todo stack
+push # save both values becaus h-search screws up reg-B and reg-C
+push
+nop-C
+h-search
+nop-A
+nop-A
+nop-A
+pop # restore values
+nop-C
+pop
+if-less
+mov-head
+
+# if reg-C is <= reg-B
+push # save reg-B on todo stack
+swap-stk # flip back to source stack
+push # put reg-C back onto the source stack
+nop-C
+h-search
+nop-A
+nop-C
+nop-C
+mov-head # try next value
+dec
+
+# if reg-B is < reg-C
+nop-B
+nop-B
+nop-B
+push # save reg-C on todo stack
+nop-C
+swap-stk # flip back to source stack
+push # put reg-B back onto the source stack
+h-search
+nop-A
+nop-C
+nop-C
+mov-head # try next value
+dec
+
+# main replication routine
+nop-B
+nop-A
+nop-B
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-B #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+h-search # Mark the beginning of the copy loop
+h-copy # Do the copy
+if-label # If we're done copying....
+nop-C #
+nop-B #
+nop-A #
+h-divide # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-C #
+nop-B #
Added: development/tests/task_sort_analyze/config/environment.cfg
===================================================================
--- development/tests/task_sort_analyze/config/environment.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/task_sort_analyze/config/environment.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -0,0 +1,15 @@
+##############################################################################
+#
+# 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/
+#
+##############################################################################
+
+REACTION SORT sort_inputs:size=10,direction=-1,halflife=2.0 process:value=1024.0:type=mult requisite:divide_only=1
Added: development/tests/task_sort_analyze/config/events.cfg
===================================================================
--- development/tests/task_sort_analyze/config/events.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/task_sort_analyze/config/events.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -0,0 +1 @@
+u begin exit
Added: development/tests/task_sort_analyze/config/instset-classic.cfg
===================================================================
--- development/tests/task_sort_analyze/config/instset-classic.cfg 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/task_sort_analyze/config/instset-classic.cfg 2007-03-26 13:29:34 UTC (rev 1432)
@@ -0,0 +1,52 @@
+nop-A 1 # a
+nop-B 1 # b
+nop-C 1 # c
+if-n-equ 1 # d
+if-less 1 # e
+pop 1 # f
+push 1 # g
+swap-stk 1 # h
+swap 1 # i
+shift-r 1 # j
+shift-l 1 # k
+inc 1 # l
+dec 1 # m
+add 1 # n
+sub 1 # o
+nand 1 # p
+IO 1 # q Puts current contents of register and gets new.
+h-alloc 1 # r Allocate as much memory as organism can use.
+h-divide 1 # s Cuts off everything between the read and write heads
+h-copy 1 # t Combine h-read and h-write
+h-search 1 # u Search for matching template, set flow head & return info
+ # # if no template, move flow-head here, set size&offset=0.
+mov-head 1 # v Move ?IP? head to flow control.
+jmp-head 1 # w Move ?IP? head by fixed amount in CX. Set old pos in CX.
+get-head 1 # x Get position of specified head in CX.
+if-label 1 # y
+set-flow 1 # z Move flow-head to address in ?CX?
+
+#adv-head 1
+#jump-f 1
+#jump-b 1
+#call 1
+#return 1
+#if-bit-1 1
+#get 1
+#put 1
+#h-read 1
+#h-write 1
+#set-head 1
+#search-f 1
+#search-b 1
+
+
+# Works on multiple nops: pop push inc dec IO adv-head
+
+# What if we add a new head. Search will return the location of something,
+# and put the new head there. Then set-head will move another head to that
+# point. In the case of the copy loop, it only needs to be set once and
+# this will speed up the code quite a bit!
+
+# Search with no template returns current position (abs line number) in
+# genome.
\ No newline at end of file
Added: development/tests/task_sort_analyze/expected/data/detail.dat
===================================================================
--- development/tests/task_sort_analyze/expected/data/detail.dat 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/task_sort_analyze/expected/data/detail.dat 2007-03-26 13:29:34 UTC (rev 1432)
@@ -0,0 +1,17 @@
+#filetype genotype_data
+#format length viable copy_length exe_length merit comp_merit gest_time efficiency fitness task.0 task.0
+
+# Legend:
+# 1: Genome Length
+# 2: Is Viable (0/1)
+# 3: Copied Length
+# 4: Executed Length
+# 5: Merit
+# 6: Computational Merit
+# 7: Gestation Time
+# 8: Rep. Efficiency
+# 9: Fitness
+# 10: Sort Inputs
+# 11: Sort Inputs
+
+121 1 121 81 82944 1024 1295 0.0625483 64.0494 1 1
Added: development/tests/task_sort_analyze/test_list
===================================================================
--- development/tests/task_sort_analyze/test_list 2007-03-26 02:43:32 UTC (rev 1431)
+++ development/tests/task_sort_analyze/test_list 2007-03-26 13:29:34 UTC (rev 1432)
@@ -0,0 +1,11 @@
+[main]
+args = -a
+
+[consistency]
+enabled = yes
+long = no
+
+[performance]
+enabled = no
+long = no
+
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