[Avida-SVN] r3361 - in branches/goings: . source/classification source/main
goingssh at myxo.css.msu.edu
goingssh at myxo.css.msu.edu
Thu Aug 6 17:40:58 PDT 2009
Author: goingssh
Date: 2009-08-06 20:40:58 -0400 (Thu, 06 Aug 2009)
New Revision: 3361
Modified:
branches/goings/Avida.sln
branches/goings/Avida.vcproj
branches/goings/source/classification/cClassificationManager.cc
branches/goings/source/classification/cGenotype.cc
branches/goings/source/classification/cGenotype.h
branches/goings/source/main/cPopulation.cc
branches/goings/source/main/cPopulation.h
Log:
Changed fitness sharing so uses more cpu time (does distance calc every time new org is born with every other org in population), but less memory (just one pop_size x pop_size grid of ints, at pop size 3600 this is <60mb), so even with extra cpu time runs much faster because not pushing memory limits!
Modified: branches/goings/Avida.sln
===================================================================
--- branches/goings/Avida.sln 2009-08-05 19:49:15 UTC (rev 3360)
+++ branches/goings/Avida.sln 2009-08-07 00:40:58 UTC (rev 3361)
@@ -1,31 +1,31 @@
Microsoft Visual Studio Solution File, Format Version 10.00
# Visual Studio 2008
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ALL_BUILD", ".\ALL_BUILD.vcproj", "{08B649F7-2C22-4A22-A7CB-B227102ACCC7}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ALL_BUILD", ".\ALL_BUILD.vcproj", "{61C4DAB5-929F-4791-9C41-B4847CBBF58D}"
ProjectSection(ProjectDependencies) = postProject
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA} = {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D} = {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677} = {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C} = {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2} = {6A554B77-0482-4ABC-885D-FC3F599CE4C2}
+ {74757819-5F00-47ED-9DE0-553FFECEE045} = {74757819-5F00-47ED-9DE0-553FFECEE045}
EndProjectSection
EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "INSTALL", ".\INSTALL.vcproj", "{EE73950F-F4A8-4E5C-92B4-D9DFD79352FD}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "INSTALL", ".\INSTALL.vcproj", "{1D6BBBBD-11A2-4B3C-B862-97F4B5E0EACC}"
ProjectSection(ProjectDependencies) = postProject
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7} = {08B649F7-2C22-4A22-A7CB-B227102ACCC7}
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA} = {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D} = {61C4DAB5-929F-4791-9C41-B4847CBBF58D}
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C} = {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}
EndProjectSection
EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ZERO_CHECK", ".\ZERO_CHECK.vcproj", "{4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "ZERO_CHECK", ".\ZERO_CHECK.vcproj", "{6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}"
ProjectSection(ProjectDependencies) = postProject
EndProjectSection
EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "avida", ".\avida.vcproj", "{260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "avida", ".\avida.vcproj", "{6A554B77-0482-4ABC-885D-FC3F599CE4C2}"
ProjectSection(ProjectDependencies) = postProject
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677} = {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA} = {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}
+ {74757819-5F00-47ED-9DE0-553FFECEE045} = {74757819-5F00-47ED-9DE0-553FFECEE045}
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C} = {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}
EndProjectSection
EndProject
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "avidacore", ".\avidacore.vcproj", "{BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}"
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "avidacore", ".\avidacore.vcproj", "{74757819-5F00-47ED-9DE0-553FFECEE045}"
ProjectSection(ProjectDependencies) = postProject
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA} = {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C} = {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}
EndProjectSection
EndProject
Global
@@ -36,42 +36,42 @@
RelWithDebInfo|Win32 = RelWithDebInfo|Win32
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7}.Debug|Win32.ActiveCfg = Debug|Win32
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7}.Debug|Win32.Build.0 = Debug|Win32
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7}.Release|Win32.ActiveCfg = Release|Win32
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7}.Release|Win32.Build.0 = Release|Win32
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7}.MinSizeRel|Win32.Build.0 = MinSizeRel|Win32
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
- {08B649F7-2C22-4A22-A7CB-B227102ACCC7}.RelWithDebInfo|Win32.Build.0 = RelWithDebInfo|Win32
- {EE73950F-F4A8-4E5C-92B4-D9DFD79352FD}.Debug|Win32.ActiveCfg = Debug|Win32
- {EE73950F-F4A8-4E5C-92B4-D9DFD79352FD}.Release|Win32.ActiveCfg = Release|Win32
- {EE73950F-F4A8-4E5C-92B4-D9DFD79352FD}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
- {EE73950F-F4A8-4E5C-92B4-D9DFD79352FD}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}.Debug|Win32.ActiveCfg = Debug|Win32
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}.Debug|Win32.Build.0 = Debug|Win32
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}.Release|Win32.ActiveCfg = Release|Win32
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}.Release|Win32.Build.0 = Release|Win32
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}.MinSizeRel|Win32.Build.0 = MinSizeRel|Win32
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
- {4C8DCFE4-D4A0-421D-A0C0-BDE023FDDEBA}.RelWithDebInfo|Win32.Build.0 = RelWithDebInfo|Win32
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}.Debug|Win32.ActiveCfg = Debug|Win32
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}.Debug|Win32.Build.0 = Debug|Win32
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}.Release|Win32.ActiveCfg = Release|Win32
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}.Release|Win32.Build.0 = Release|Win32
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}.MinSizeRel|Win32.Build.0 = MinSizeRel|Win32
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
- {260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}.RelWithDebInfo|Win32.Build.0 = RelWithDebInfo|Win32
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}.Debug|Win32.ActiveCfg = Debug|Win32
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}.Debug|Win32.Build.0 = Debug|Win32
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}.Release|Win32.ActiveCfg = Release|Win32
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}.Release|Win32.Build.0 = Release|Win32
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}.MinSizeRel|Win32.Build.0 = MinSizeRel|Win32
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
- {BDCCEEFA-8177-4D5F-AA74-4C17EB92D677}.RelWithDebInfo|Win32.Build.0 = RelWithDebInfo|Win32
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D}.Debug|Win32.ActiveCfg = Debug|Win32
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D}.Debug|Win32.Build.0 = Debug|Win32
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D}.Release|Win32.ActiveCfg = Release|Win32
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D}.Release|Win32.Build.0 = Release|Win32
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D}.MinSizeRel|Win32.Build.0 = MinSizeRel|Win32
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
+ {61C4DAB5-929F-4791-9C41-B4847CBBF58D}.RelWithDebInfo|Win32.Build.0 = RelWithDebInfo|Win32
+ {1D6BBBBD-11A2-4B3C-B862-97F4B5E0EACC}.Debug|Win32.ActiveCfg = Debug|Win32
+ {1D6BBBBD-11A2-4B3C-B862-97F4B5E0EACC}.Release|Win32.ActiveCfg = Release|Win32
+ {1D6BBBBD-11A2-4B3C-B862-97F4B5E0EACC}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
+ {1D6BBBBD-11A2-4B3C-B862-97F4B5E0EACC}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}.Debug|Win32.ActiveCfg = Debug|Win32
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}.Debug|Win32.Build.0 = Debug|Win32
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}.Release|Win32.ActiveCfg = Release|Win32
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}.Release|Win32.Build.0 = Release|Win32
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}.MinSizeRel|Win32.Build.0 = MinSizeRel|Win32
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
+ {6E0FA05C-85A0-4FDA-83A9-014A4797DD0C}.RelWithDebInfo|Win32.Build.0 = RelWithDebInfo|Win32
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2}.Debug|Win32.ActiveCfg = Debug|Win32
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2}.Debug|Win32.Build.0 = Debug|Win32
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2}.Release|Win32.ActiveCfg = Release|Win32
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2}.Release|Win32.Build.0 = Release|Win32
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2}.MinSizeRel|Win32.Build.0 = MinSizeRel|Win32
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
+ {6A554B77-0482-4ABC-885D-FC3F599CE4C2}.RelWithDebInfo|Win32.Build.0 = RelWithDebInfo|Win32
+ {74757819-5F00-47ED-9DE0-553FFECEE045}.Debug|Win32.ActiveCfg = Debug|Win32
+ {74757819-5F00-47ED-9DE0-553FFECEE045}.Debug|Win32.Build.0 = Debug|Win32
+ {74757819-5F00-47ED-9DE0-553FFECEE045}.Release|Win32.ActiveCfg = Release|Win32
+ {74757819-5F00-47ED-9DE0-553FFECEE045}.Release|Win32.Build.0 = Release|Win32
+ {74757819-5F00-47ED-9DE0-553FFECEE045}.MinSizeRel|Win32.ActiveCfg = MinSizeRel|Win32
+ {74757819-5F00-47ED-9DE0-553FFECEE045}.MinSizeRel|Win32.Build.0 = MinSizeRel|Win32
+ {74757819-5F00-47ED-9DE0-553FFECEE045}.RelWithDebInfo|Win32.ActiveCfg = RelWithDebInfo|Win32
+ {74757819-5F00-47ED-9DE0-553FFECEE045}.RelWithDebInfo|Win32.Build.0 = RelWithDebInfo|Win32
EndGlobalSection
GlobalSection(ExtensibilityGlobals) = postSolution
EndGlobalSection
Modified: branches/goings/Avida.vcproj
===================================================================
--- branches/goings/Avida.vcproj 2009-08-05 19:49:15 UTC (rev 3360)
+++ branches/goings/Avida.vcproj 2009-08-07 00:40:58 UTC (rev 3361)
@@ -3,7 +3,7 @@
ProjectType="Visual C++"
Version="9.00"
Name="avida"
- ProjectGUID="{260D06F7-2BB8-48C5-8C67-0D9E0FA1A07D}"
+ ProjectGUID="{6A554B77-0482-4ABC-885D-FC3F599CE4C2}"
Keyword="Win32Proj">
<Platforms>
<Platform
@@ -21,7 +21,7 @@
<Tool
Name="VCCLCompilerTool"
AdditionalOptions=" /Zm1000"
- AdditionalIncludeDirectories=""C:\Documents and Settings\Sherri Goings\Desktop\development\source";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\actions";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\analyze";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\classification";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\viewer-core";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\viewer-coreGUI";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\cpu";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\drivers";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\main";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\platform";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\tools&q!
uot;;"
+ AdditionalIncludeDirectories="Z:\Documents\Research\EcoEvo\FitShare\source;Z:\Documents\Research\EcoEvo\FitShare\source\actions;Z:\Documents\Research\EcoEvo\FitShare\source\analyze;Z:\Documents\Research\EcoEvo\FitShare\source\classification;Z:\Documents\Research\EcoEvo\FitShare\source\viewer-core;Z:\Documents\Research\EcoEvo\FitShare\source\viewer-coreGUI;Z:\Documents\Research\EcoEvo\FitShare\source\cpu;Z:\Documents\Research\EcoEvo\FitShare\source\drivers;Z:\Documents\Research\EcoEvo\FitShare\source\main;Z:\Documents\Research\EcoEvo\FitShare\source\platform;Z:\Documents\Research\EcoEvo\FitShare\source\tools;"
BasicRuntimeChecks="3"
CompileAs="2"
DebugInformationFormat="3"
@@ -34,13 +34,13 @@
PreprocessorDefinitions="WIN32,_WINDOWS,_DEBUG,CMAKE_INTDIR=\"Debug\""
AssemblerListingLocation="Debug"
ObjectFile="$(IntDir)\"
- ProgramDataBaseFileName="C:/Documents and Settings/Sherri Goings/Desktop/development/bin/Debug/avida.pdb"
+ ProgramDataBaseFileName="Z:/Documents/Research/EcoEvo/FitShare/bin/Debug/avida.pdb"
/>
<Tool
Name="VCCustomBuildTool"/>
<Tool
Name="VCResourceCompilerTool"
- AdditionalIncludeDirectories=""C:\Documents and Settings\Sherri Goings\Desktop\development\source";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\actions";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\analyze";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\classification";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\viewer-core";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\viewer-coreGUI";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\cpu";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\drivers";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\main";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\platform";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\tools&q!
uot;;"
+ AdditionalIncludeDirectories="Z:\Documents\Research\EcoEvo\FitShare\source;Z:\Documents\Research\EcoEvo\FitShare\source\actions;Z:\Documents\Research\EcoEvo\FitShare\source\analyze;Z:\Documents\Research\EcoEvo\FitShare\source\classification;Z:\Documents\Research\EcoEvo\FitShare\source\viewer-core;Z:\Documents\Research\EcoEvo\FitShare\source\viewer-coreGUI;Z:\Documents\Research\EcoEvo\FitShare\source\cpu;Z:\Documents\Research\EcoEvo\FitShare\source\drivers;Z:\Documents\Research\EcoEvo\FitShare\source\main;Z:\Documents\Research\EcoEvo\FitShare\source\platform;Z:\Documents\Research\EcoEvo\FitShare\source\tools;"
PreprocessorDefinitions="WIN32,_WINDOWS,_DEBUG,CMAKE_INTDIR=\"Debug\""/>
<Tool
Name="VCMIDLTool"
@@ -64,15 +64,15 @@
Name="VCLinkerTool"
AdditionalOptions=" /STACK:10000000 /machine:I386 /debug"
AdditionalDependencies="$(NOINHERIT) kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib lib\Debug\avidacore.lib "
- OutputFile="C:\Documents and Settings\Sherri Goings\Desktop\development\bin\Debug\avida.exe"
+ OutputFile="Z:\Documents\Research\EcoEvo\FitShare\bin\Debug\avida.exe"
Version="0.0"
GenerateManifest="TRUE"
LinkIncremental="2"
AdditionalLibraryDirectories=""
- ProgramDataBaseFile="C:/Documents and Settings/Sherri Goings/Desktop/development/bin/Debug/avida.pdb"
+ ProgramDataBaseFile="Z:/Documents/Research/EcoEvo/FitShare/bin/Debug/avida.pdb"
GenerateDebugInformation="TRUE"
SubSystem="1"
- ImportLibrary="C:\Documents and Settings\Sherri Goings\Desktop\development\bin\Debug\avida.lib"/>
+ ImportLibrary="Z:\Documents\Research\EcoEvo\FitShare\bin\Debug\avida.lib"/>
</Configuration>
<Configuration
Name="Release|Win32"
@@ -85,7 +85,7 @@
<Tool
Name="VCCLCompilerTool"
AdditionalOptions=" /Zm1000"
- AdditionalIncludeDirectories=""C:\Documents and Settings\Sherri Goings\Desktop\development\source";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\actions";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\analyze";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\classification";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\viewer-core";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\viewer-coreGUI";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\cpu";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\drivers";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\main";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\platform";"C:\Documents and Settings\Sherri Goings\Desktop\development\source\tools&q!
uot;;"
+ AdditionalIncludeDirectories="Z:\Documents\Research\EcoEvo\FitShare\source;Z:\Documents\Research\EcoEvo\FitShare\source\actions;Z:\Documents\Research\EcoEvo\FitShare\source\analyze;Z:\Documents\Research\EcoEvo\FitShare\source\classification;Z:\Documents\Research\EcoEvo\FitShare\source\viewer-core;Z:\Documents\Research\EcoEvo\FitShare\source\viewer-coreGUI;Z:\Documents\Research\EcoEvo\FitShare\source\cpu;Z:\Documents\Research\EcoEvo\FitShare\source\drivers;Z:\Documents\Research\EcoEvo\FitShare\source\main;Z:\Documents\Research\EcoEvo\FitShare\source\platform;Z:\Documents\Research\EcoEvo\FitShare\source\tools;"
CompileAs="2"
ExceptionHandling="1"
InlineFunctionExpansion="2"
@@ -96,13 +96,13 @@
PreprocessorDefinitions="WIN32,_WINDOWS,NDEBUG,CMAKE_INTDIR=\"Release\""
AssemblerListingLocation="Release"
ObjectFile="$(IntDir)\"
- ProgramDataBaseFileName="C:/Documents and Settings/Sherri Goings/Desktop/development/bin/Release/avida.pdb"
+ ProgramDataBaseFileName="Z:/Documents/Research/EcoEvo/FitShare/bin/Release/avida.pdb"
/>
<Tool
Name="VCCustomBuildTool"/>
<Tool
Name="VCResourceCompilerTool"
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uot;;"
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ocuments\Research\EcoEvo\FitShare\CMakeFiles\CMakeCXXPlatform.cmake;"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\Platform\cl.cmake";Z:\Documents\Research\EcoEvo\FitShare\CMakeFiles\CMakeRCCompiler.cmake;"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeRCInformation.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeCommonLanguageInclude.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeCXXInformation.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeCommonLanguageInclude.cmake";Z:\Documents\Research\EcoEvo\FitShare\CMakeLists.txt;"
Outputs="CMakeFiles\generate.stamp"/>
</FileConfiguration>
<FileConfiguration
Name="RelWithDebInfo|Win32">
<Tool
Name="VCCustomBuildTool"
- Description="Building Custom Rule C:/Documents and Settings/Sherri Goings/Desktop/development/CMakeLists.txt"
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- AdditionalDependencies=""C:\Documents and Settings\Sherri Goings\Desktop\development\CMakeLists.txt";"C:\Documents and Settings\Sherri Goings\Desktop\development\CMakeFiles\CMakeSystem.cmake";"C:\Documents and Settings\Sherri Goings\Desktop\development\CMakeFiles\CMakeCCompiler.cmake";"C:\Documents and Settings\Sherri Goings\Desktop\development\CMakeFiles\CMakeCXXCompiler.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeSystemSpecificInformation.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeGenericSystem.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\Platform\gcc.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\Platform\Windows.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\Platform\WindowsPaths.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeCInformation.cmake";"C:\Program Files\CMak!
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+ Description="Building Custom Rule Z:/Documents/Research/EcoEvo/FitShare/CMakeLists.txt"
+ CommandLine=""C:\Program Files\CMake 2.6\bin\cmake.exe" -HZ:/Documents/Research/EcoEvo/FitShare -BZ:/Documents/Research/EcoEvo/FitShare --check-stamp-file CMakeFiles/generate.stamp"
+ AdditionalDependencies="Z:\Documents\Research\EcoEvo\FitShare\CMakeLists.txt;Z:\Documents\Research\EcoEvo\FitShare\CMakeFiles\CMakeSystem.cmake;Z:\Documents\Research\EcoEvo\FitShare\CMakeFiles\CMakeCCompiler.cmake;Z:\Documents\Research\EcoEvo\FitShare\CMakeFiles\CMakeCXXCompiler.cmake;"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeSystemSpecificInformation.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeGenericSystem.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\Platform\gcc.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\Platform\Windows.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\Platform\WindowsPaths.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\CMakeCInformation.cmake";"C:\Program Files\CMake 2.6\share\cmake-2.6\Modules\Platform\Windows-cl.cmake";Z:\Documents\Research\EcoEvo\FitShare\CMakeFiles\CMakeCPlatform.cmake;Z:\D!
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Outputs="CMakeFiles\generate.stamp"/>
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</File>
@@ -307,7 +307,7 @@
Name="avida"
Filter="">
<File
- RelativePath="C:\Documents and Settings\Sherri Goings\Desktop\development\source\targets\avida\primitive.cc">
+ RelativePath="Z:\Documents\Research\EcoEvo\FitShare\source\targets\avida\primitive.cc">
</File>
</Filter>
</Filter>
Modified: branches/goings/source/classification/cClassificationManager.cc
===================================================================
--- branches/goings/source/classification/cClassificationManager.cc 2009-08-05 19:49:15 UTC (rev 3360)
+++ branches/goings/source/classification/cClassificationManager.cc 2009-08-07 00:40:58 UTC (rev 3361)
@@ -123,7 +123,7 @@
m_genotype_ctl->Insert(*in_genotype);
// for fitness sharing *SLG
- if (m_world->GetConfig().NICHE_RADIUS.Get() > 0)
+ /* if (m_world->GetConfig().NICHE_RADIUS.Get() > 0)
{
m_genotype_ctl->Reset(0);
for (int i = 0; i < m_genotype_ctl->GetSize(); i++) {
@@ -132,7 +132,7 @@
in_genotype->AddHDist(genotype, hd);
m_genotype_ctl->Next(0);
}
- }
+ }*/
m_world->GetStats().AddGenotype();
@@ -267,14 +267,17 @@
m_active_genotypes[list_num].Remove(&in_genotype);
m_genotype_ctl->Remove(in_genotype);
+ // for fitness sharing *SLG
+ /*if (m_world->GetConfig().NICHE_RADIUS.Get() > 0)
+ {
m_genotype_ctl->Reset(0);
- // for fitness sharing *SLG
for (int i = 0; i < m_genotype_ctl->GetSize(); i++) {
cGenotype * genotype = m_genotype_ctl->Get(0);
if (genotype!=NULL)
- genotype->RemHDist(&in_genotype);
+ genotype->RemHDist(&in_genotype);
m_genotype_ctl->Next(0);
}
+ }*/
in_genotype.Deactivate(m_world->GetStats().GetUpdate(), m_world->GetStats().GetTotCreatures());
if (m_world->GetConfig().TRACK_MAIN_LINEAGE.Get()) {
Modified: branches/goings/source/classification/cGenotype.cc
===================================================================
--- branches/goings/source/classification/cGenotype.cc 2009-08-05 19:49:15 UTC (rev 3360)
+++ branches/goings/source/classification/cGenotype.cc 2009-08-07 00:40:58 UTC (rev 3361)
@@ -40,6 +40,25 @@
using namespace std;
+//namespace
+//{
+// class cGenoCounter
+// {
+// public:
+// cGenoCounter() { m_nCount = 0; }
+// ~cGenoCounter()
+// {
+// cout << "Number of cGenotypes still present in memory: " << m_nCount << endl;
+// }
+// void Add() { m_nCount++; }
+// void Remove() { m_nCount--; }
+//
+// private:
+// int m_nCount;
+// };
+//
+// static cGenoCounter s_genoCounter;
+//}
cGenotype::cGenotype(cWorld* world, int in_update_born, int in_id)
: m_world(world)
@@ -62,6 +81,7 @@
, next(NULL)
, prev(NULL)
{
+ //s_genoCounter.Add();
}
cGenotype::~cGenotype()
@@ -79,6 +99,8 @@
if (m_phenplast != NULL)
delete m_phenplast;
+
+ //s_genoCounter.Remove();
}
bool cGenotype::SaveClone(ofstream& fp)
@@ -189,6 +211,7 @@
{
int dist = cGenomeUtil::FindHammingDistance(GetGenome(), gen->GetGenome(), 0);
hdists[gen] = dist;
+ //cout << hdists.size() << " : ";
return dist;
}
Modified: branches/goings/source/classification/cGenotype.h
===================================================================
--- branches/goings/source/classification/cGenotype.h 2009-08-05 19:49:15 UTC (rev 3360)
+++ branches/goings/source/classification/cGenotype.h 2009-08-07 00:40:58 UTC (rev 3361)
@@ -44,6 +44,8 @@
#include "cString.h"
#endif
#include <map>
+#include <iostream>
+using namespace std;
class cAvidaContext;
@@ -139,7 +141,7 @@
// for fitness sharing *SLG
int AddHDist(cGenotype* gen);
void AddHDist(cGenotype* gen, int dist) { hdists[gen] = dist; }
- void RemHDist(cGenotype* gen) { hdists.erase(gen); }
+ void RemHDist(cGenotype* gen) { int erased = hdists.erase(gen); if (erased==0) cout << "0"; }
double GetNicheVal();
// Test CPU info -- only used with limited options on.
Modified: branches/goings/source/main/cPopulation.cc
===================================================================
--- branches/goings/source/main/cPopulation.cc 2009-08-05 19:49:15 UTC (rev 3360)
+++ branches/goings/source/main/cPopulation.cc 2009-08-07 00:40:58 UTC (rev 3361)
@@ -94,6 +94,12 @@
int num_demes = m_world->GetConfig().NUM_DEMES.Get();
const int num_cells = world_x * world_y * world_z;
const int geometry = world->GetConfig().WORLD_GEOMETRY.Get();
+
+ if (m_world->GetConfig().NICHE_RADIUS.Get() > 0)
+ {
+ hdists.Resize(num_cells, num_cells);
+ hdists.SetAll(-1);
+ }
if(m_world->GetConfig().ENERGY_CAP.Get() == -1) {
m_world->GetConfig().ENERGY_CAP.Set(std::numeric_limits<double>::max());
@@ -395,8 +401,12 @@
}
// for fitness sharing *SLG
- double niche_val = parent_genotype->GetNicheVal();
+
+ double niche_val = 1;
+ if (m_world->GetConfig().NICHE_RADIUS.Get() > 0)
+ niche_val = GetNicheVal(parent_id);//parent_genotype->GetNicheVal();
parent_phenotype.SetMeritNicheVal(niche_val);
+
AdjustSchedule(parent_cell, parent_phenotype.GetMerit());
// In a local run, face the child toward the parent.
@@ -552,22 +562,27 @@
m_world->GetClassificationManager().AdjustGenotype(*in_genotype);
// for fitness sharing *SLG
- double niche_val = in_genotype->GetNicheVal();
+ double niche_val = 1;
+ if (m_world->GetConfig().NICHE_RADIUS.Get() > 0)
+ {
+ UpdateHDists(target_cell.GetID(), in_genotype);
+ niche_val = GetNicheVal(target_cell.GetID());
+ }
in_organism->GetPhenotype().SetMeritNicheVal(niche_val);
-
+
// Initialize the time-slice for this new organism.
AdjustSchedule(target_cell, in_organism->GetPhenotype().GetMerit());
-
+
// Special handling for certain birth methods.
if (m_world->GetConfig().BIRTH_METHOD.Get() == POSITION_CHILD_FULL_SOUP_ELDEST) {
- reaper_queue.Push(&target_cell);
+ reaper_queue.Push(&target_cell);
}
-
+
// Keep track of statistics for organism counts...
num_organisms++;
-
+
if (deme_array.GetSize() > 0) {
- deme_array[target_cell.GetDemeID()].IncOrgCount();
+ deme_array[target_cell.GetDemeID()].IncOrgCount();
}
// Statistics...
@@ -914,6 +929,40 @@
}
}
+// maintain grid of hamming distances between each org in population and each other org
+// cell_id is cell we're about to place a new org, gen is its genotype
+void cPopulation::UpdateHDists(int cell_id, cGenotype* gen)
+{
+ for (int i=0; i<cell_array.GetSize(); i++)
+ {
+ int dist = m_world->GetConfig().NICHE_RADIUS.Get();
+ if (cell_array[i].GetOrganism())
+ dist = cGenomeUtil::FindHammingDistance(cell_array[i].GetOrganism()->GetGenome(), gen->GetGenome(), 0);
+ hdists[i][cell_id] = dist;
+ hdists[cell_id][i] = dist;
+ }
+}
+
+double cPopulation::GetNicheVal(int cell_id)
+{
+ double r = m_world->GetConfig().NICHE_RADIUS.Get();
+ if (r==0.0)
+ return 1.0;
+ double p = m_world->GetConfig().NICHE_SCALING.Get();
+
+ double sum = 0;
+ for(int i=0; i < hdists.GetNumCols(); i++)
+ {
+ double share = 0;
+ if (hdists[cell_id][i] < r)
+ share = 1 - pow((hdists[cell_id][i] / r),p);
+ sum += share;
+ }
+ if (sum<1)
+ sum = 1.0;
+ return sum;
+}
+
// CompeteDemes probabilistically copies demes into the next generation
// based on their fitness. How deme fitness is estimated is specified by
// competition_type input argument as:
Modified: branches/goings/source/main/cPopulation.h
===================================================================
--- branches/goings/source/main/cPopulation.h 2009-08-05 19:49:15 UTC (rev 3360)
+++ branches/goings/source/main/cPopulation.h 2009-08-07 00:40:58 UTC (rev 3361)
@@ -94,7 +94,7 @@
cResourceCount resource_count; // Global resources available
cBirthChamber birth_chamber; // Global birth chamber.
tArray<tList<cSaleItem> > market; // list of lists of items for sale, each list goes with 1 label
-
+ tMatrix<int> hdists; // grid with hamming distance between each cell and each other cell
tVector<pair<int,int> > *sleep_log;
// Data Tracking...
@@ -183,6 +183,8 @@
void AddSellValue(const int data, const int label, const int sell_price, const int org_id, const int cell_id);
int BuyValue(const int label, const int buy_price, const int cell_id);
void SwapCells(cPopulationCell & cell1, cPopulationCell & cell2);
+ void UpdateHDists(int cell_id, cGenotype* gen);
+ double GetNicheVal(int cell_id);
// Deme-related methods
//! Compete all demes with each other based on the given competition type.
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