[Avida-SVN] r1560 - in development: . source/main tests tests/avida_GA_lim_res tests/avida_GA_lim_res/config tests/optimize_task_lim_res tests/optimize_task_lim_res/config tests/string_match_embed3 tests/string_match_embed3/config
goingssh at myxo.css.msu.edu
goingssh at myxo.css.msu.edu
Wed May 16 13:40:29 PDT 2007
Author: goingssh
Date: 2007-05-16 16:40:29 -0400 (Wed, 16 May 2007)
New Revision: 1560
Added:
development/tests/avida_GA_lim_res/
development/tests/avida_GA_lim_res/config/
development/tests/avida_GA_lim_res/config/avida.cfg
development/tests/avida_GA_lim_res/config/default-classic.org
development/tests/avida_GA_lim_res/config/environment.cfg
development/tests/avida_GA_lim_res/config/events.cfg
development/tests/avida_GA_lim_res/config/instset-classic.cfg
development/tests/avida_GA_lim_res/test_list
development/tests/optimize_task_lim_res/
development/tests/optimize_task_lim_res/config/
development/tests/optimize_task_lim_res/config/103-aacrp.org
development/tests/optimize_task_lim_res/config/avida.cfg
development/tests/optimize_task_lim_res/config/default-classic.org
development/tests/optimize_task_lim_res/config/environment.cfg
development/tests/optimize_task_lim_res/config/events.cfg
development/tests/optimize_task_lim_res/config/instset-classic.cfg
development/tests/optimize_task_lim_res/test_list
development/tests/string_match_embed3/
development/tests/string_match_embed3/config/
development/tests/string_match_embed3/config/avida.cfg
development/tests/string_match_embed3/config/environment.cfg
development/tests/string_match_embed3/config/events.cfg
development/tests/string_match_embed3/config/inst_set.default
development/tests/string_match_embed3/config/organism.default
development/tests/string_match_embed3/test_list
Modified:
development/Avida.sln
development/Avida.vcproj
development/source/main/cTaskLib.cc
Log:
Adding consistency tests for avida as GA, optimize task, and string match function, with twists like limited resources, using events to turn off mutations, inject specially created orgs, etc...
Modified: development/Avida.sln
===================================================================
--- development/Avida.sln 2007-05-16 00:18:59 UTC (rev 1559)
+++ development/Avida.sln 2007-05-16 20:40:29 UTC (rev 1560)
@@ -1,24 +1,19 @@
-
Microsoft Visual Studio Solution File, Format Version 9.00
# Visual Studio 2005
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Avida", "Avida.vcproj", "{E1C1D683-833F-40D9-A952-CEC54FE40EFC}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Avida", "Avida.vcproj", "{0A7F34A9-645B-11B1-871E-B8C06AED84B3}"
EndProject
-Project("{54435603-DBB4-11D2-8724-00A0C9A8B90C}") = "Installer", "Installer\Installer.vdproj", "{9E776A2E-5D27-4900-9856-F5AF0C8FC84A}"
-EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
- Debug|Win32 = Debug|Win32
Release|Win32 = Release|Win32
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {E1C1D683-833F-40D9-A952-CEC54FE40EFC}.Debug|Win32.ActiveCfg = Debug|Win32
- {E1C1D683-833F-40D9-A952-CEC54FE40EFC}.Debug|Win32.Build.0 = Debug|Win32
- {E1C1D683-833F-40D9-A952-CEC54FE40EFC}.Release|Win32.ActiveCfg = Release|Win32
- {E1C1D683-833F-40D9-A952-CEC54FE40EFC}.Release|Win32.Build.0 = Release|Win32
- {9E776A2E-5D27-4900-9856-F5AF0C8FC84A}.Debug|Win32.ActiveCfg = Debug
- {9E776A2E-5D27-4900-9856-F5AF0C8FC84A}.Release|Win32.ActiveCfg = Release
+ {0A7F34A9-645B-11B1-871E-B8C06AED84B3}.Release|Win32.ActiveCfg = Release|Win32
+ {0A7F34A9-645B-11B1-871E-B8C06AED84B3}.Release|Win32.Build.0 = Release|Win32
EndGlobalSection
GlobalSection(SolutionProperties) = preSolution
HideSolutionNode = FALSE
EndGlobalSection
EndGlobal
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+bXEFVQVXaW4zMnEGVQd2YXJpYW50cQdoAXVicy4=
+
Modified: development/Avida.vcproj
===================================================================
--- development/Avida.vcproj 2007-05-16 00:18:59 UTC (rev 1559)
+++ development/Avida.vcproj 2007-05-16 20:40:29 UTC (rev 1560)
@@ -1,183 +1,39 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="Windows-1252"?>
<VisualStudioProject
ProjectType="Visual C++"
Version="8.00"
Name="Avida"
- ProjectGUID="{E1C1D683-833F-40D9-A952-CEC54FE40EFC}"
+ ProjectGUID="{0A7F34A9-645B-11B1-871E-B8C06AED84B3}"
+ SccProjectName=""
+ SccLocalPath=""
RootNamespace="Avida"
- Keyword="Win32Proj"
- >
+ Keyword="MakeFileProj">
<Platforms>
<Platform
- Name="Win32"
- />
+ Name="Win32"/>
</Platforms>
<ToolFiles>
</ToolFiles>
<Configurations>
<Configuration
- Name="Debug|Win32"
- OutputDirectory="Debug"
- IntermediateDirectory="Debug"
- ConfigurationType="1"
- >
- <Tool
- Name="VCPreBuildEventTool"
- />
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="0"
- AdditionalIncludeDirectories=""$(ProjectDir)source\tools";"$(ProjectDir)source\targets\avida-viewer";"$(ProjectDir)source\platform\msvc2005";"$(ProjectDir)source\platform\msvc2005\pdcurses";"$(ProjectDir)source\main";"$(ProjectDir)source\drivers";"$(ProjectDir)source\cpu";"$(ProjectDir)source\classification";"$(ProjectDir)source\analyze";"$(ProjectDir)source\actions";"$(ProjectDir)source""
- PreprocessorDefinitions="NOMACROS;DEBUG;WIN32;_WIN32"
- MinimalRebuild="true"
- BasicRuntimeChecks="3"
- RuntimeLibrary="1"
- UsePrecompiledHeader="0"
- WarningLevel="2"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="4"
- ForcedIncludeFiles=""
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- LinkIncremental="2"
- IgnoreDefaultLibraryNames="LIBCMT"
- GenerateDebugInformation="true"
- SubSystem="1"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
- />
- <Tool
- Name="VCManifestTool"
- />
- <Tool
- Name="VCXDCMakeTool"
- />
- <Tool
- Name="VCBscMakeTool"
- />
- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
- </Configuration>
- <Configuration
Name="Release|Win32"
- OutputDirectory="Release"
- IntermediateDirectory="Release"
- ConfigurationType="1"
+ ConfigurationType="0"
+ UseOfMFC="0"
+ ATLMinimizesCRunTimeLibraryUsage="false"
>
<Tool
- Name="VCPreBuildEventTool"
+ Name="VCNMakeTool"
+ BuildCommandLine="echo Starting SCons && "C:\Program Files\Python2-5\python.exe" "C:\Documents and Settings\sherri\My Documents\Research\avidaDevel\BuildAvida.py" -C "C:\Documents and Settings\sherri\My Documents\Research\avidaDevel" -f "SConstruct" C:\Documents and Settings\sherri\My Documents\Research\avidaDevel\build-Release-MemTrack\targets\avida\avida.exe"
+ ReBuildCommandLine="echo Starting SCons && "C:\Program Files\Python2-5\python.exe" "C:\Documents and Settings\sherri\My Documents\Research\avidaDevel\BuildAvida.py" -C "C:\Documents and Settings\sherri\My Documents\Research\avidaDevel" -f "SConstruct" C:\Documents and Settings\sherri\My Documents\Research\avidaDevel\build-Release-MemTrack\targets\avida\avida.exe"
+ CleanCommandLine="echo Starting SCons && "C:\Program Files\Python2-5\python.exe" "C:\Documents and Settings\sherri\My Documents\Research\avidaDevel\BuildAvida.py" -C "C:\Documents and Settings\sherri\My Documents\Research\avidaDevel" -f "SConstruct" -c C:\Documents and Settings\sherri\My Documents\Research\avidaDevel\build-Release-MemTrack\targets\avida\avida.exe"
+ Output="C:\Documents and Settings\sherri\My Documents\Research\avidaDevel\build-Release-MemTrack\targets\avida\avida.exe"
+ PreprocessorDefinitions=""
+ IncludeSearchPath=""
+ ForcedIncludes=""
+ AssemblySearchPath=""
+ ForcedUsingAssemblies=""
+ CompileAsManaged=""
/>
- <Tool
- Name="VCCustomBuildTool"
- />
- <Tool
- Name="VCXMLDataGeneratorTool"
- />
- <Tool
- Name="VCWebServiceProxyGeneratorTool"
- />
- <Tool
- Name="VCMIDLTool"
- />
- <Tool
- Name="VCCLCompilerTool"
- Optimization="3"
- InlineFunctionExpansion="2"
- EnableIntrinsicFunctions="true"
- FavorSizeOrSpeed="1"
- OmitFramePointers="true"
- WholeProgramOptimization="true"
- AdditionalIncludeDirectories=""$(ProjectDir)source\tools";"$(ProjectDir)source\targets\avida-viewer";"$(ProjectDir)source\platform\msvc2005";"$(ProjectDir)source\platform\msvc2005\pdcurses";"$(ProjectDir)source\main";"$(ProjectDir)source\drivers";"$(ProjectDir)source\cpu";"$(ProjectDir)source\classification";"$(ProjectDir)source\analyze";"$(ProjectDir)source\actions";"$(ProjectDir)source""
- PreprocessorDefinitions="NOMACROS;NDEBUG;WIN32;_WIN32"
- ExceptionHandling="1"
- RuntimeLibrary="0"
- BufferSecurityCheck="false"
- EnableEnhancedInstructionSet="1"
- FloatingPointModel="2"
- UsePrecompiledHeader="0"
- WarningLevel="2"
- Detect64BitPortabilityProblems="true"
- DebugInformationFormat="3"
- ForcedIncludeFiles=""
- />
- <Tool
- Name="VCManagedResourceCompilerTool"
- />
- <Tool
- Name="VCResourceCompilerTool"
- />
- <Tool
- Name="VCPreLinkEventTool"
- />
- <Tool
- Name="VCLinkerTool"
- Version="2.6.2"
- LinkIncremental="1"
- GenerateDebugInformation="false"
- SubSystem="1"
- OptimizeReferences="2"
- EnableCOMDATFolding="2"
- LinkTimeCodeGeneration="1"
- TargetMachine="1"
- />
- <Tool
- Name="VCALinkTool"
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- <Tool
- Name="VCManifestTool"
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- <Tool
- Name="VCXDCMakeTool"
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- <Tool
- Name="VCBscMakeTool"
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- <Tool
- Name="VCFxCopTool"
- />
- <Tool
- Name="VCAppVerifierTool"
- />
- <Tool
- Name="VCWebDeploymentTool"
- />
- <Tool
- Name="VCPostBuildEventTool"
- />
</Configuration>
</Configurations>
<References>
@@ -185,1355 +41,1239 @@
<Files>
<Filter
Name="Header Files"
- Filter="h;hpp;hxx;hm;inl;inc;xsd"
- UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
- >
+ Filter="h;hpp;hxx;hm;inl">
+ <Filter
+ Name="actions"
+ Filter="">
<File
- RelativePath=".\source\main\avida.h"
- >
+ RelativePath="source\actions\cAction.h">
</File>
<File
- RelativePath=".\source\actions\cAction.h"
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+ RelativePath="source\actions\cActionLibrary.h">
</File>
<File
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+ RelativePath="source\actions\DriverActions.h">
</File>
<File
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+ RelativePath="source\actions\EnvironmentActions.h">
</File>
<File
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+ RelativePath="source\actions\LandscapeActions.h">
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<File
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</File>
<File
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+ RelativePath="source\actions\PrintActions.h">
</File>
<File
- RelativePath=".\source\analyze\cAnalyzeCommandDefBase.h"
- >
+ RelativePath="source\actions\SaveLoadActions.h">
</File>
+ </Filter>
+ <Filter
+ Name="analyze"
+ Filter="">
<File
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+ RelativePath="source\analyze\cAnalyze.h">
</File>
<File
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</File>
<File
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+ RelativePath="source\analyze\cAnalyzeCommandAction.h">
</File>
<File
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</File>
<File
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</File>
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+ RelativePath="source\analyze\cAnalyzeFunction.h">
</File>
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</File>
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<File
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</File>
<File
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</File>
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</File>
<File
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<File
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<File
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+-->
Modified: development/source/main/cTaskLib.cc
===================================================================
--- development/source/main/cTaskLib.cc 2007-05-16 00:18:59 UTC (rev 1559)
+++ development/source/main/cTaskLib.cc 2007-05-16 20:40:29 UTC (rev 1560)
@@ -2238,7 +2238,7 @@
// possible fraction they'll be below minimum allowed consumed and will consume nothing
if (quality > 1)
- cout << "\n\nquality > 1, wtf?!\n\n";
+ cout << "\n\nquality > 1!\n\n";
if (quality < .001)
return .001;
else
Added: development/tests/avida_GA_lim_res/config/avida.cfg
===================================================================
--- development/tests/avida_GA_lim_res/config/avida.cfg (rev 0)
+++ development/tests/avida_GA_lim_res/config/avida.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -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 50 # Width of the Avida world
+WORLD_Y 40 # 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 default-classic.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 1.0 # 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 0.0025 # 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 0.0 # Insertion rate (per divide)
+DIVIDE_DEL_PROB 0.0 # 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 0 # 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/avida_GA_lim_res/config/default-classic.org
===================================================================
--- development/tests/avida_GA_lim_res/config/default-classic.org (rev 0)
+++ development/tests/avida_GA_lim_res/config/default-classic.org 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,17 @@
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+IObuf-add1
+repro
Added: development/tests/avida_GA_lim_res/config/environment.cfg
===================================================================
--- development/tests/avida_GA_lim_res/config/environment.cfg (rev 0)
+++ development/tests/avida_GA_lim_res/config/environment.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,23 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This file is currently setup to reward 9 tasks, all of which use the
+# "infinite" resource, which is undepletable.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+RESOURCE resOPT1:inflow=1000:outflow=.01
+RESOURCE resOPT2:inflow=1000:outflow=.01
+
+REACTION OPT1 optimize:function=7,binary=1,varlength=20,basepow=1.3 process:resource=resOPT1:type=pow:value=3.0:frac=.0005:max=5:min=.025 requisite:divide_only=1
+REACTION OPT2 optimize:function=8,binary=1,varlength=20,basepow=1.3 process:resource=resOPT2:type=pow:value=3.0:frac=.0005:max=5:min=.025 requisite:divide_only=1
+REACTION OPT1 optimize:function=6,binary=1,varlength=20,basepow=1.3 process:resource=resOPT1:type=pow:value=3.0:frac=.0005:max=5:min=.025 requisite:divide_only=1
+REACTION OPT2 optimize:function=5,binary=1,varlength=20,basepow=1.3 process:resource=resOPT2:type=pow:value=3.0:frac=.0005:max=5:min=.025 requisite:divide_only=1
+REACTION OPT1 optimize:function=4,binary=1,varlength=20,basepow=1.3 process:resource=resOPT1:type=pow:value=3.0:frac=.0005:max=5:min=.025 requisite:divide_only=1
+REACTION OPT2 optimize:function=1,binary=1,varlength=20,basepow=1.3 process:resource=resOPT2:type=pow:value=3.0:frac=.0005:max=5:min=.025 requisite:divide_only=1
+
Added: development/tests/avida_GA_lim_res/config/events.cfg
===================================================================
--- development/tests/avida_GA_lim_res/config/events.cfg (rev 0)
+++ development/tests/avida_GA_lim_res/config/events.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,39 @@
+##############################################################################
+#
+# 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 inject_all_random_repro 40
+
+# Print all of the standard data files...
+u 0:100:end PrintAverageData # Save info about they average genotypes
+u 0:100:end PrintDominantData # Save info about most abundant genotypes
+u 0:100:end PrintStatsData # Collect satistics about entire pop.
+u 0:100:end PrintCountData # Count organisms, genotypes, species, etc.
+u 0:100:end PrintTasksData # Save organisms counts for each task.
+u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
+u 0:100:end PrintResourceData # Track resource abundance.
+
+# A few data files not printed by default
+u 0:100 PrintDominantGenotype # Save the most abundant genotypes
+# u 100:100:end PrintErrorData # Std. Error on averages.
+# u 100:100:end PrintVarianceData # Variance on averages.
+# u 100:100:end PrintTotalsData # Total counts over entire run.
+#u 100:100:end PrintTasksExeData # Num. times tasks have been executed.
+u 0:100:end PrintTasksQualData # Task quality information
+
+# Setup the exit time and full population data collection.
+u 100:100 SavePopulation # Save current state of population.
+u 100:100 SaveHistoricPopulation # Save ancestors of current population.
+u 100 exit # exit
+
Added: development/tests/avida_GA_lim_res/config/instset-classic.cfg
===================================================================
--- development/tests/avida_GA_lim_res/config/instset-classic.cfg (rev 0)
+++ development/tests/avida_GA_lim_res/config/instset-classic.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,3 @@
+IObuf-add0 1 #a
+IObuf-add1 1 #b
+repro 0 #c
Added: development/tests/avida_GA_lim_res/test_list
===================================================================
--- development/tests/avida_GA_lim_res/test_list (rev 0)
+++ development/tests/avida_GA_lim_res/test_list 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,35 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+args = -s 100 ; Command line arguments to pass to the application
+app = %(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 = Sherri Goings ; Who created the test
+email = goingssh 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.
+;
+; app
+; builddir
+; cpus
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
Added: development/tests/optimize_task_lim_res/config/103-aacrp.org
===================================================================
--- development/tests/optimize_task_lim_res/config/103-aacrp.org (rev 0)
+++ development/tests/optimize_task_lim_res/config/103-aacrp.org 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,130 @@
+# Thu Mar 22 20:46:24 2007
+# Filename........: archive/103-aacrp.org
+# Update Output...: 20000
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+# Update Created..: 10008
+# Genotype ID.....: 854126
+# Parent Gen ID...: 846720
+# Tree Depth......: 229
+# Parent Distance.: 4
+#
+# Generation: 0
+# Merit...........: 100.000000
+# Gestation Time..: 237
+# Fitness.........: 0.421941
+# Errors..........: 5
+# Genome Size.....: 103
+# Copied Size.....: 103
+# Executed Size...: 100
+# Offspring.......: SELF
+#
+# Tasks Performed:
+# optimize 1 (0.941115)
+# optimize 1 (0.470749)
+
+
+h-alloc
+h-search
+set-flow
+nop-A
+mov-head
+nop-C
+IO
+sub
+nop-A
+push
+add
+IO
+dec
+nop-B
+if-n-equ
+add
+h-search
+if-label
+get-head
+nop-B
+nop-C
+h-copy
+h-copy
+h-copy
+dec
+swap-stk
+nop-B
+if-less
+h-search
+dec
+nop-B
+inc
+nop-C
+if-less
+swap
+if-n-equ
+h-search
+inc
+nop-C
+add
+h-alloc
+IO
+pop
+nop-A
+sub
+dec
+swap
+dec
+nop-B
+h-copy
+if-less
+h-alloc
+push
+nop-A
+inc
+nop-A
+h-divide
+nand
+inc
+sub
+h-search
+push
+if-less
+swap
+h-copy
+h-divide
+h-copy
+inc
+h-copy
+h-alloc
+nop-C
+push
+if-n-equ
+nop-C
+get-head
+nop-A
+get-head
+sub
+nand
+if-less
+shift-r
+shift-l
+pop
+inc
+pop
+sub
+add
+if-label
+IO
+nop-C
+pop
+swap
+h-search
+h-copy
+h-copy
+h-copy
+if-label
+nop-C
+nop-A
+h-divide
+mov-head
+nop-A
+nop-B
Added: development/tests/optimize_task_lim_res/config/avida.cfg
===================================================================
--- development/tests/optimize_task_lim_res/config/avida.cfg (rev 0)
+++ development/tests/optimize_task_lim_res/config/avida.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -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 50 # Width of the Avida world
+WORLD_Y 50 # 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 default-classic.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/optimize_task_lim_res/config/default-classic.org
===================================================================
--- development/tests/optimize_task_lim_res/config/default-classic.org (rev 0)
+++ development/tests/optimize_task_lim_res/config/default-classic.org 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+h-search # Mark the beginning of the copy loop
+h-copy # Do the copy
+if-label # If we're done copying....
+nop-C #
+nop-A #
+h-divide # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Added: development/tests/optimize_task_lim_res/config/environment.cfg
===================================================================
--- development/tests/optimize_task_lim_res/config/environment.cfg (rev 0)
+++ development/tests/optimize_task_lim_res/config/environment.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,19 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This file is currently setup to reward 9 tasks, all of which use the
+# "infinite" resource, which is undepletable.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+RESOURCE resOPT1:inflow=4:outflow=.01
+RESOURCE resOPT4:inflow=4:outflow=.01
+
+REACTION OPT1 optimize:function=1 process:resource=resOPT1:type=pow:value=1.0:frac=.0625:max=25:min=.025 requisite:max_count=1
+REACTION OPT4 optimize:function=4 process:resource=resOPT4:type=pow:value=1.0:frac=.0625:max=25:min=.025 requisite:max_count=1
+
Added: development/tests/optimize_task_lim_res/config/events.cfg
===================================================================
--- development/tests/optimize_task_lim_res/config/events.cfg (rev 0)
+++ development/tests/optimize_task_lim_res/config/events.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,40 @@
+##############################################################################
+#
+# 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/
+#
+##############################################################################
+
+u 0 inject_all START_CREATURE
+u 80 zero_muts
+
+# Print all of the standard data files...
+u 0:100:end PrintAverageData # Save info about they average genotypes
+u 0:100:end PrintDominantData # Save info about most abundant genotypes
+u 0:100:end PrintStatsData # Collect satistics about entire pop.
+u 0:100:end PrintCountData # Count organisms, genotypes, species, etc.
+u 0:100:end PrintTasksData # Save organisms counts for each task.
+u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
+u 0:100:end PrintResourceData # Track resource abundance.
+
+# A few data files not printed by default
+u 0:100 PrintDominantGenotype # Save the most abundant genotypes
+# u 100:100:end PrintErrorData # Std. Error on averages.
+# u 100:100:end PrintVarianceData # Variance on averages.
+# u 100:100:end PrintTotalsData # Total counts over entire run.
+#u 100:100:end PrintTasksExeData # Num. times tasks have been executed.
+u 10:10:end PrintTasksQualData # Task quality information
+
+# Setup the exit time and full population data collection.
+u 100:100 SavePopulation # Save current state of population.
+u 100:100 SaveHistoricPopulation # Save ancestors of current population.
+u 100 exit # exit
+
Added: development/tests/optimize_task_lim_res/config/instset-classic.cfg
===================================================================
--- development/tests/optimize_task_lim_res/config/instset-classic.cfg (rev 0)
+++ development/tests/optimize_task_lim_res/config/instset-classic.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -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/optimize_task_lim_res/test_list
===================================================================
--- development/tests/optimize_task_lim_res/test_list (rev 0)
+++ development/tests/optimize_task_lim_res/test_list 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,35 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+args = -s 100 ; Command line arguments to pass to the application
+app = %(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 = Sherri Goings ; Who created the test
+email = goingssh 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.
+;
+; app
+; builddir
+; cpus
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
Added: development/tests/string_match_embed3/config/avida.cfg
===================================================================
--- development/tests/string_match_embed3/config/avida.cfg (rev 0)
+++ development/tests/string_match_embed3/config/avida.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,183 @@
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.5.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 0 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 0 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+POPULATION_FILE - # Population file to load
+
+### ARCH_GROUP ###
+# Architecture Variables
+MAX_UPDATES -1 # Maximum updates to run experiment (-1 = no limit)
+MAX_GENERATIONS -1 # Maximum generations to run experiment (-1 = no limit)
+END_CONDITION_MODE 0 # End run when ...
+ # 0 = MAX_UPDATES _OR_ MAX_GENERATIONS is reached
+ # 1 = MAX_UPDATES _AND_ MAX_GENERATIONS is reached
+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, Stack-based CPUs
+ # 2 = Newer -- Stacks, Memory, Threading
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET inst_set.default # 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 organism.default # Organism to seed the soup
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 0 # 0 = Replace random organism in neighborhood
+ # 1 = Replace oldest organism in neighborhood
+ # 2 = Replace largest Age/Merit in neighborhood
+ # 3 = Place only in empty cells in neighborhood
+ # 4 = Replace random from population (Mass Action)
+ # 5 = Replace oldest in entire population (like Tierra)
+ # 6 = Replace random within deme
+PREFER_EMPTY 1 # Are empty cells given 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_PROB 1.0 # probability that recombination will happen when div-sex is used
+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 at random or with corresponding ones, by location
+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 # (Origianl CPU Only) Is a an allocate required before a divide? (0/1)
+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.
+DIE_PROB 0.0 # probability of death when 'die' instruction is executed
+
+### 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
+
+### 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?
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 2 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+SIZE_MERIT_METHOD 4 # 0 = off (merit is 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
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing -> 1 + (num_organism_threads-1) * THREAD_SLICING_METHOD.
+ # 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
+BASE_SIZE_MERIT 100 # Base merit when size is *not* used
+DEFAULT_BONUS 1.0 # The bonus an organism gets before it has completed any tasks
+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
+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 #
Added: development/tests/string_match_embed3/config/environment.cfg
===================================================================
--- development/tests/string_match_embed3/config/environment.cfg (rev 0)
+++ development/tests/string_match_embed3/config/environment.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,217 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This file is currently setup to reward 9 tasks, all of which use the
+# "infinite" resource, which is undepletable.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+RESOURCE res0:inflow=10:outflow=.01
+RESOURCE res1:inflow=10:outflow=.01
+RESOURCE res2:inflow=10:outflow=.01
+RESOURCE res3:inflow=10:outflow=.01
+RESOURCE res4:inflow=10:outflow=.01
+RESOURCE res5:inflow=10:outflow=.01
+RESOURCE res6:inflow=10:outflow=.01
+RESOURCE res7:inflow=10:outflow=.01
+RESOURCE res8:inflow=10:outflow=.01
+RESOURCE res9:inflow=10:outflow=.01
+RESOURCE res10:inflow=10:outflow=.01
+RESOURCE res11:inflow=10:outflow=.01
+RESOURCE res12:inflow=10:outflow=.01
+RESOURCE res13:inflow=10:outflow=.01
+RESOURCE res14:inflow=10:outflow=.01
+RESOURCE res15:inflow=10:outflow=.01
+RESOURCE res16:inflow=10:outflow=.01
+RESOURCE res17:inflow=10:outflow=.01
+RESOURCE res18:inflow=10:outflow=.01
+RESOURCE res19:inflow=10:outflow=.01
+RESOURCE res20:inflow=10:outflow=.01
+RESOURCE res21:inflow=10:outflow=.01
+RESOURCE res22:inflow=10:outflow=.01
+RESOURCE res23:inflow=10:outflow=.01
+RESOURCE res24:inflow=10:outflow=.01
+RESOURCE res25:inflow=10:outflow=.01
+RESOURCE res26:inflow=10:outflow=.01
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+RESOURCE res97:inflow=10:outflow=.01
+RESOURCE res98:inflow=10:outflow=.01
+RESOURCE res99:inflow=10:outflow=.01
+
+REACTION MATCHPAT1 matchstr=919191919090909090909090 process:value=0.0
+REACTION MATCHPAT2 matchstr=919191919191919191919191 process:value=0.0
+REACTION MATCHPAT3 matchstr=909090909090909091919191 process:value=0.0
+REACTION MATCH0 matchstr=000000000000100011011101 process:resource=res0:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH1 matchstr=101000001000000011110111 process:resource=res1:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH2 matchstr=100010000010001011010101 process:resource=res2:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH3 matchstr=101010101010001001010111 process:resource=res3:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH4 matchstr=101010000010001001011101 process:resource=res4:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH5 matchstr=001010001000100011010111 process:resource=res5:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH6 matchstr=101010101000101001110101 process:resource=res6:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH7 matchstr=001010000000100001010111 process:resource=res7:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH8 matchstr=001000101000100001010111 process:resource=res8:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH9 matchstr=001010000000100011011101 process:resource=res9:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH10 matchstr=000000001000101011111111 process:resource=res10:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH11 matchstr=100010100010100001110111 process:resource=res11:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH12 matchstr=001010000000100011011101 process:resource=res12:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH13 matchstr=001010000000000011111111 process:resource=res13:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH14 matchstr=100010000000100001011101 process:resource=res14:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH15 matchstr=100000100000100011010111 process:resource=res15:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH16 matchstr=000010101010100001110101 process:resource=res16:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH17 matchstr=101010100000101011111111 process:resource=res17:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH18 matchstr=001000000010000011010111 process:resource=res18:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH19 matchstr=100010000000101011010101 process:resource=res19:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH28 matchstr=100000001010100011010111 process:resource=res28:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH29 matchstr=101000101000000001010101 process:resource=res29:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH30 matchstr=100000100010100001010111 process:resource=res30:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH32 matchstr=000010100000000011010101 process:resource=res32:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH33 matchstr=011111010101010101111101 process:resource=res33:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH35 matchstr=011101010101010101111111 process:resource=res35:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH36 matchstr=010111011111111101010111 process:resource=res36:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH37 matchstr=111101010101011111010101 process:resource=res37:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH43 matchstr=111111011111010111010101 process:resource=res43:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH45 matchstr=011111011111010111010111 process:resource=res45:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH54 matchstr=010111110111111111110101 process:resource=res54:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH58 matchstr=011101010111010101010111 process:resource=res58:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH61 matchstr=010111010111010111111111 process:resource=res61:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH63 matchstr=011111110101111111111111 process:resource=res63:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH65 matchstr=010111110101110111111111 process:resource=res65:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH67 matchstr=011101010000000000100010 process:resource=res67:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH68 matchstr=010111011010000010101000 process:resource=res68:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH71 matchstr=111111011010000010100010 process:resource=res71:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH72 matchstr=011101111000001010101000 process:resource=res72:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH73 matchstr=010111110000101000001000 process:resource=res73:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH80 matchstr=111111111000000000000000 process:resource=res80:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH81 matchstr=010101010000000000000000 process:resource=res81:value=2.0:type=pow:frac=.0025:max=25
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+REACTION MATCH84 matchstr=010111110010001010001010 process:resource=res84:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH85 matchstr=111101110000000000100010 process:resource=res85:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH86 matchstr=010111110000101000000010 process:resource=res86:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH87 matchstr=011101110000101000101010 process:resource=res87:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH88 matchstr=011111010010001000100010 process:resource=res88:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH89 matchstr=011111110000101010000010 process:resource=res89:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH90 matchstr=110101011000000010101000 process:resource=res90:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH91 matchstr=111111010010000000101000 process:resource=res91:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH92 matchstr=011111010010000010000000 process:resource=res92:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH93 matchstr=111111110010001010001000 process:resource=res93:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH94 matchstr=011111110000001010100000 process:resource=res94:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH95 matchstr=110111111010000010100000 process:resource=res95:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH96 matchstr=011101010010100010100000 process:resource=res96:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH97 matchstr=010111111010101010101000 process:resource=res97:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH98 matchstr=111101011010000010001010 process:resource=res98:value=2.0:type=pow:frac=.0025:max=25
+REACTION MATCH99 matchstr=011101110010101000101000 process:resource=res99:value=2.0:type=pow:frac=.0025:max=25
\ No newline at end of file
Added: development/tests/string_match_embed3/config/events.cfg
===================================================================
--- development/tests/string_match_embed3/config/events.cfg (rev 0)
+++ development/tests/string_match_embed3/config/events.cfg 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,39 @@
+##############################################################################
+#
+# 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] [event] [arguments...]
+#
+# This file is currently setup to start off a population full of the
+# starting organism specified in genesis, and then record key information
+# every 100 updates.
+#
+# For information on how to use this file, see: doc/events.html
+# For other sample event configurations, see: source/support/config/
+#
+##############################################################################
+u 0 inject_all START_CREATURE
+# Print all of the standard data files...
+u 0:100 print_dom # Save the most abundant genotypes
+u 0:100:end print_average_data # Save info about they average genotypes
+u 0:100:end print_dominant_data # Save info about most abundant genotypes
+u 0:100:end print_stats_data # Collect satistics about entire pop.
+u 0:100:end print_count_data # Count organisms, genotypes, species, etc.
+u 0:100:end print_tasks_data # Save organisms counts for each task.
+u 0:100:end print_tasks_qual_data
+u 0:100:end print_time_data # Track time conversion (generations, etc.)
+u 0:100:end print_resource_data # Track resource abundance.
+
+# A few data files not printed by default
+# u 100:100:end print_error_data # Std. Error on averages.
+# u 100:100:end print_variance_data # Variance on averages.
+# u 100:100:end print_totals_data # Total counts over entire run.
+u 100:100:end print_tasks_exe_data # Num. times tasks have been executed.
+
+# Setup the exit time and full population data collection.
+u 100:100 detail_pop # Save current state of population.
+u 100:100 dump_historic_pop # Save ancestors of current population.
+u 100 exit # exit
+
Added: development/tests/string_match_embed3/config/inst_set.default
===================================================================
--- development/tests/string_match_embed3/config/inst_set.default (rev 0)
+++ development/tests/string_match_embed3/config/inst_set.default 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,54 @@
+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?
+match-strings 1 # A
+set-num 1 # B
+
+#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.
Added: development/tests/string_match_embed3/config/organism.default
===================================================================
--- development/tests/string_match_embed3/config/organism.default (rev 0)
+++ development/tests/string_match_embed3/config/organism.default 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,215 @@
+# Filename........: archive/091-aanxw
+# Update Output...: 50000
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+# Update Created..: 49888
+# Genotype ID.....: 7211085
+# Parent Gen ID...: 7208262
+# Tree Depth......: 1064
+# Parent Distance.: 1
+
+# Generation: 0
+# Merit...........: 89
+# Gestation Time..: 202
+# Fitness.........: 0.440594
+# Errors..........: 4
+# Genome Size.....: 91
+# Copied Size.....: 91
+# Executed Size...: 89
+# Offspring.......: SELF
+
+# matchstr 0
+# matchstr 0
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 1
+# matchstr 0
+# matchstr 0
+# matchstr 1
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 1
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 1
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 1
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 1
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 1
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+# matchstr 0
+
+dec
+add
+h-alloc
+set-num
+h-search
+nop-A
+inc
+add
+nand
+nop-A
+mov-head
+nop-C
+h-copy
+set-flow
+nop-C
+IO
+swap-stk
+if-label
+swap-stk
+nand
+nand
+h-copy
+swap
+dec
+shift-r
+nop-C
+if-n-equ
+sub
+nand
+inc
+nop-C
+swap
+shift-r
+h-search
+jmp-head
+nand
+nop-A
+swap
+shift-l
+get-head
+shift-r
+nop-A
+set-flow
+nand
+set-num
+swap
+pop
+nop-A
+set-num
+pop
+push
+inc
+if-label
+nand
+h-copy
+pop
+h-search
+add
+if-label
+shift-r
+push
+nop-C
+nand
+match-strings
+h-alloc
+jmp-head
+h-divide
+IO
+shift-l
+get-head
+IO
+h-search
+shift-r
+set-num
+inc
+if-n-equ
+h-divide
+h-divide
+h-search
+h-search
+h-copy
+h-copy
+h-copy
+h-copy
+if-label
+nop-C
+nop-A
+h-divide
+mov-head
+nop-A
+nop-B
Added: development/tests/string_match_embed3/test_list
===================================================================
--- development/tests/string_match_embed3/test_list (rev 0)
+++ development/tests/string_match_embed3/test_list 2007-05-16 20:40:29 UTC (rev 1560)
@@ -0,0 +1,35 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+args = -s 100 ; Command line arguments to pass to the application
+app = %(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 = Sherri Goings ; Who created the test
+email = goingssh 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.
+;
+; app
+; builddir
+; cpus
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
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