[Avida-SVN] r3433 - in development: . Avida.xcodeproj source/cpu source/main support/config support/config/misc tests/analyze_dumplandscape/config tests/analyze_fulllandscape_1step/config tests/analyze_fulllandscape_2step/config tests/analyze_truncate_lineage/config tests/analyze_truncate_lineage_fulllandscape/config tests/avida_GA_lim_res/config tests/avida_GA_sex/config tests/default_classic_500u/config tests/demes_germline/config tests/demes_grid_repl/config tests/demes_torus_repl/config tests/midrun_classic_30u/config tests/optimize_multivar_lim_res/config tests/reaction_ordering/config tests/resources_9r/config tests/spatial_res_100u/config tests/task_sort_analyze/config
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Wed Sep 30 08:34:40 PDT 2009
Author: brysonda
Date: 2009-09-30 11:34:39 -0400 (Wed, 30 Sep 2009)
New Revision: 3433
Added:
development/support/config/default-heads-sex.org
development/support/config/default-heads.org
development/support/config/instset-heads-sex.cfg
development/support/config/instset-heads.cfg
development/support/config/misc/environment-2paths.cfg
development/support/config/misc/environment-9resource.cfg
development/support/config/misc/environment-all-logic.cfg
development/support/config/misc/environment-cascade.cfg
development/support/config/misc/instset-heads-30-parasite.cfg
development/support/config/misc/instset-heads-32-oldsearch.cfg
development/support/config/misc/instset-no-heads-19-short.cfg
development/support/config/misc/instset-no-heads-24.cfg
development/support/config/misc/instset-no-heads-27-no-nops.cfg
development/support/config/misc/instset-no-heads-27-parasite-no-inject.cfg
development/support/config/misc/instset-no-heads-28-base.cfg
development/support/config/misc/instset-no-heads-28-const.cfg
development/support/config/misc/instset-no-heads-29-memsize.cfg
development/support/config/misc/instset-no-heads-29-multithreaded.cfg
development/support/config/misc/instset-no-heads-31-multithreaded.cfg
development/support/config/misc/organism-heads-100.org
development/support/config/misc/organism-heads-15-template.org
development/support/config/misc/organism-heads-50.org
development/support/config/misc/organism-heads-multi-birth.org
development/support/config/misc/organism-heads-parasite-host.org
development/support/config/misc/organism-heads-parasite-host2.org
development/support/config/misc/organism-heads-parasite-infected.org
development/support/config/misc/organism-heads-parasite-infected2.org
development/support/config/misc/organism-no-heads.org
development/tests/analyze_dumplandscape/config/instset-heads.cfg
development/tests/analyze_fulllandscape_1step/config/instset-heads.cfg
development/tests/analyze_fulllandscape_2step/config/instset-heads.cfg
development/tests/analyze_truncate_lineage/config/instset-heads.cfg
development/tests/analyze_truncate_lineage_fulllandscape/config/instset-heads.cfg
development/tests/avida_GA_lim_res/config/instset-heads.cfg
development/tests/avida_GA_sex/config/instset-heads.cfg
development/tests/default_classic_500u/config/instset-heads.cfg
development/tests/demes_germline/config/instset-heads.cfg
development/tests/demes_grid_repl/config/instset-heads.cfg
development/tests/demes_torus_repl/config/instset-heads.cfg
development/tests/midrun_classic_30u/config/instset-heads.cfg
development/tests/optimize_multivar_lim_res/config/instset-heads.cfg
development/tests/reaction_ordering/config/instset-heads.cfg
development/tests/resources_9r/config/instset-heads.cfg
development/tests/spatial_res_100u/config/instset-heads.cfg
development/tests/task_sort_analyze/config/instset-heads.cfg
Removed:
development/support/config/default-classic.org
development/support/config/default-sex-classic.org
development/support/config/instset-classic.cfg
development/support/config/instset-sex-classic.cfg
development/support/config/misc/environment.2paths
development/support/config/misc/environment.9resource
development/support/config/misc/environment.all_logic
development/support/config/misc/environment.cascade
development/support/config/misc/inst_set.19.short
development/support/config/misc/inst_set.24.old
development/support/config/misc/inst_set.26.default
development/support/config/misc/inst_set.27.multi
development/support/config/misc/inst_set.27.no-nop
development/support/config/misc/inst_set.27.parasite
development/support/config/misc/inst_set.28.base
development/support/config/misc/inst_set.28.const
development/support/config/misc/inst_set.29.base_memsize
development/support/config/misc/inst_set.31.multi
development/support/config/misc/inst_set.32.heads
development/support/config/misc/inst_set.heads.parasite
development/support/config/misc/organism.heads.100
development/support/config/misc/organism.heads.15
development/support/config/misc/organism.heads.50
development/support/config/misc/organism.host
development/support/config/misc/organism.host2
development/support/config/misc/organism.infected
development/support/config/misc/organism.infected2
development/support/config/misc/organism.multi-birth
development/support/config/misc/organism.noheads
development/support/config/misc/template-classic.org
development/tests/analyze_dumplandscape/config/instset-classic.cfg
development/tests/analyze_fulllandscape_1step/config/instset-classic.cfg
development/tests/analyze_fulllandscape_2step/config/instset-classic.cfg
development/tests/analyze_truncate_lineage/config/instset-classic.cfg
development/tests/analyze_truncate_lineage_fulllandscape/config/instset-classic.cfg
development/tests/avida_GA_lim_res/config/instset-classic.cfg
development/tests/avida_GA_sex/config/instset-classic.cfg
development/tests/default_classic_500u/config/instset-classic.cfg
development/tests/demes_germline/config/instset-classic.cfg
development/tests/demes_grid_repl/config/instset-classic.cfg
development/tests/demes_torus_repl/config/instset-classic.cfg
development/tests/midrun_classic_30u/config/instset-classic.cfg
development/tests/optimize_multivar_lim_res/config/instset-classic.cfg
development/tests/reaction_ordering/config/instset-classic.cfg
development/tests/resources_9r/config/instset-classic.cfg
development/tests/spatial_res_100u/config/instset-classic.cfg
development/tests/task_sort_analyze/config/instset-classic.cfg
Modified:
development/Avida.xcodeproj/project.pbxproj
development/CMakeLists.txt
development/source/cpu/cHardwareCPU.h
development/source/main/cAvidaConfig.h
development/support/config/avida.cfg
development/support/config/events.cfg
Log:
The Great Configuration Update of 2009!
- Renamed 'classic' organisms and instruction sets to more appropriately named 'heads'
- Updated, commented, and renamed various instruction sets in the support/misc directory so that it is more clear what exactly the instruction sets do
- Renamed environment files and organism files using current file extension conventions.
- Refresh the avida.cfg file so that it contains a dump of the latest additions and default settings
- Clean up default events.cfg file use of deprecated exit action
This CAN break consistency, in that the default file for an unnamed cHardwareCPU instruction set is now called 'instset-heads.cfg'. Renaming the file or setting the name explicitly in avida.cfg will fix the problem.
Modified: development/Avida.xcodeproj/project.pbxproj
===================================================================
--- development/Avida.xcodeproj/project.pbxproj 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/Avida.xcodeproj/project.pbxproj 2009-09-30 15:34:39 UTC (rev 3433)
@@ -200,18 +200,20 @@
70447CA80F83DB5600E1BF72 /* cBirthMateSelectHandler.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70447CA60F83DB5600E1BF72 /* cBirthMateSelectHandler.cc */; };
70447CAB0F83DBC100E1BF72 /* cBirthDemeHandler.h in Headers */ = {isa = PBXBuildFile; fileRef = 70447CA90F83DBC100E1BF72 /* cBirthDemeHandler.h */; };
70447CAC0F83DBC100E1BF72 /* cBirthDemeHandler.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70447CAA0F83DBC100E1BF72 /* cBirthDemeHandler.cc */; };
- 7049F3560A66A8F500640512 /* instset-classic.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7049F3520A66A8F500640512 /* instset-classic.cfg */; };
- 7049F3570A66A8F500640512 /* instset-sex-classic.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7049F3530A66A8F500640512 /* instset-sex-classic.cfg */; };
7049F3580A66A8F500640512 /* instset-smt.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7049F3540A66A8F500640512 /* instset-smt.cfg */; };
7049F3590A66A8F500640512 /* instset-transsmt.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7049F3550A66A8F500640512 /* instset-transsmt.cfg */; };
- 7049F3700A66AD7E00640512 /* default-classic.org in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7049F36C0A66AD7E00640512 /* default-classic.org */; };
- 7049F3710A66AD7E00640512 /* default-sex-classic.org in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7049F36D0A66AD7E00640512 /* default-sex-classic.org */; };
7049F3720A66AD7E00640512 /* default-smt.org in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7049F36E0A66AD7E00640512 /* default-smt.org */; };
7049F3730A66AD7E00640512 /* default-transsmt.org in CopyFiles */ = {isa = PBXBuildFile; fileRef = 7049F36F0A66AD7E00640512 /* default-transsmt.org */; };
704C21DC0C28C3980038F1A5 /* libtcmalloc.a in Frameworks */ = {isa = PBXBuildFile; fileRef = 70AA941909D486AE006A24C8 /* libtcmalloc.a */; };
7050E6780D74C36F008B3CA0 /* AvidaScript.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7050E6770D74C36F008B3CA0 /* AvidaScript.cc */; };
7050E69F0D74CFED008B3CA0 /* cDumpASTVisitor.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7050E69D0D74CFEB008B3CA0 /* cDumpASTVisitor.cc */; };
7050E7D70D7DC979008B3CA0 /* cDirectInterpretASTVisitor.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7050E7D60D7DC96E008B3CA0 /* cDirectInterpretASTVisitor.cc */; };
+ 705B103C1073AEF1002242E6 /* default-gx.org in CopyFiles */ = {isa = PBXBuildFile; fileRef = 705B10311073AC1F002242E6 /* default-gx.org */; };
+ 705B103D1073AEF1002242E6 /* default-heads-sex.org in CopyFiles */ = {isa = PBXBuildFile; fileRef = 705B10321073AC1F002242E6 /* default-heads-sex.org */; };
+ 705B103E1073AEF1002242E6 /* default-heads.org in CopyFiles */ = {isa = PBXBuildFile; fileRef = 705B10331073AC1F002242E6 /* default-heads.org */; };
+ 705B103F1073AF05002242E6 /* instset-gx.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 705B10341073AC1F002242E6 /* instset-gx.cfg */; };
+ 705B10401073AF05002242E6 /* instset-heads-sex.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 705B10351073AC1F002242E6 /* instset-heads-sex.cfg */; };
+ 705B10411073AF05002242E6 /* instset-heads.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = 705B10361073AC1F002242E6 /* instset-heads.cfg */; };
70658C5A085DF67D00486BED /* libncurses.5.4.dylib in Frameworks */ = {isa = PBXBuildFile; fileRef = 70658C59085DF67D00486BED /* libncurses.5.4.dylib */; };
7073972E0D725B9F003855D3 /* cSemanticASTVisitor.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7073972C0D725B9D003855D3 /* cSemanticASTVisitor.cc */; };
7076FEB00D347FD000556CAF /* cAnalyzeTreeStats_CumulativeStemminess.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7076FEAE0D347FD000556CAF /* cAnalyzeTreeStats_CumulativeStemminess.cc */; };
@@ -350,17 +352,19 @@
dstPath = work;
dstSubfolderSpec = 16;
files = (
+ 705B103F1073AF05002242E6 /* instset-gx.cfg in CopyFiles */,
+ 705B10401073AF05002242E6 /* instset-heads-sex.cfg in CopyFiles */,
+ 705B10411073AF05002242E6 /* instset-heads.cfg in CopyFiles */,
+ 705B103C1073AEF1002242E6 /* default-gx.org in CopyFiles */,
+ 705B103D1073AEF1002242E6 /* default-heads-sex.org in CopyFiles */,
+ 705B103E1073AEF1002242E6 /* default-heads.org in CopyFiles */,
700E2996085A1F6000CF158A /* avida in CopyFiles */,
7039884D09F00D020052ACE7 /* analyze.cfg in CopyFiles */,
7039884E09F00D030052ACE7 /* avida.cfg in CopyFiles */,
7039884F09F00D060052ACE7 /* environment.cfg in CopyFiles */,
7039885009F00D080052ACE7 /* events.cfg in CopyFiles */,
- 7049F3560A66A8F500640512 /* instset-classic.cfg in CopyFiles */,
- 7049F3570A66A8F500640512 /* instset-sex-classic.cfg in CopyFiles */,
7049F3580A66A8F500640512 /* instset-smt.cfg in CopyFiles */,
7049F3590A66A8F500640512 /* instset-transsmt.cfg in CopyFiles */,
- 7049F3700A66AD7E00640512 /* default-classic.org in CopyFiles */,
- 7049F3710A66AD7E00640512 /* default-sex-classic.org in CopyFiles */,
7049F3720A66AD7E00640512 /* default-smt.org in CopyFiles */,
7049F3730A66AD7E00640512 /* default-transsmt.org in CopyFiles */,
70B1A7430B7E3FFD00067486 /* instset-experimental.cfg in CopyFiles */,
@@ -512,12 +516,8 @@
7048A9A40EA431140087B7BD /* cASCPPParameter_NativeObjectSupport.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cASCPPParameter_NativeObjectSupport.h; sourceTree = "<group>"; };
7049F2D70A66859300640512 /* cHardwareTransSMT.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cHardwareTransSMT.cc; sourceTree = "<group>"; };
7049F2D80A66859300640512 /* cHardwareTransSMT.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cHardwareTransSMT.h; sourceTree = "<group>"; };
- 7049F3520A66A8F500640512 /* instset-classic.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "instset-classic.cfg"; sourceTree = "<group>"; };
- 7049F3530A66A8F500640512 /* instset-sex-classic.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "instset-sex-classic.cfg"; sourceTree = "<group>"; };
7049F3540A66A8F500640512 /* instset-smt.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "instset-smt.cfg"; sourceTree = "<group>"; };
7049F3550A66A8F500640512 /* instset-transsmt.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "instset-transsmt.cfg"; sourceTree = "<group>"; };
- 7049F36C0A66AD7E00640512 /* default-classic.org */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "default-classic.org"; sourceTree = "<group>"; };
- 7049F36D0A66AD7E00640512 /* default-sex-classic.org */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "default-sex-classic.org"; sourceTree = "<group>"; };
7049F36E0A66AD7E00640512 /* default-smt.org */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "default-smt.org"; sourceTree = "<group>"; };
7049F36F0A66AD7E00640512 /* default-transsmt.org */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "default-transsmt.org"; sourceTree = "<group>"; };
704ADBC30A6EEFC300666970 /* DriverActions.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = DriverActions.h; sourceTree = "<group>"; };
@@ -559,6 +559,36 @@
705ABB180A8A6A6000A6A80E /* EnvironmentActions.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = EnvironmentActions.cc; sourceTree = "<group>"; };
705ACD4C0A13FED4002D5BA0 /* PrintActions.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = PrintActions.h; sourceTree = "<group>"; };
705ACD4D0A13FED4002D5BA0 /* PrintActions.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = PrintActions.cc; sourceTree = "<group>"; };
+ 705B100E1073AB58002242E6 /* environment-2paths.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "environment-2paths.cfg"; sourceTree = "<group>"; };
+ 705B100F1073AB58002242E6 /* environment-9resource.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "environment-9resource.cfg"; sourceTree = "<group>"; };
+ 705B10101073AB58002242E6 /* environment-all-logic.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "environment-all-logic.cfg"; sourceTree = "<group>"; };
+ 705B10111073AB58002242E6 /* environment-cascade.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "environment-cascade.cfg"; sourceTree = "<group>"; };
+ 705B10121073AB58002242E6 /* instset-heads-30-parasite.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-heads-30-parasite.cfg"; sourceTree = "<group>"; };
+ 705B10131073AB58002242E6 /* instset-heads-32-oldsearch.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-heads-32-oldsearch.cfg"; sourceTree = "<group>"; };
+ 705B10141073AB58002242E6 /* instset-no-heads-19-short.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-19-short.cfg"; sourceTree = "<group>"; };
+ 705B10151073AB58002242E6 /* instset-no-heads-24.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-24.cfg"; sourceTree = "<group>"; };
+ 705B10161073AB58002242E6 /* instset-no-heads-27-no-nops.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-27-no-nops.cfg"; sourceTree = "<group>"; };
+ 705B10171073AB58002242E6 /* instset-no-heads-27-parasite-no-inject.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-27-parasite-no-inject.cfg"; sourceTree = "<group>"; };
+ 705B10181073AB58002242E6 /* instset-no-heads-28-base.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-28-base.cfg"; sourceTree = "<group>"; };
+ 705B10191073AB58002242E6 /* instset-no-heads-28-const.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-28-const.cfg"; sourceTree = "<group>"; };
+ 705B101A1073AB58002242E6 /* instset-no-heads-29-memsize.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-29-memsize.cfg"; sourceTree = "<group>"; };
+ 705B101B1073AB58002242E6 /* instset-no-heads-29-multithreaded.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-29-multithreaded.cfg"; sourceTree = "<group>"; };
+ 705B101C1073AB58002242E6 /* instset-no-heads-31-multithreaded.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-no-heads-31-multithreaded.cfg"; sourceTree = "<group>"; };
+ 705B101D1073AB58002242E6 /* organism-heads-15-template.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-heads-15-template.org"; sourceTree = "<group>"; };
+ 705B101E1073AB58002242E6 /* organism-heads-50.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-heads-50.org"; sourceTree = "<group>"; };
+ 705B101F1073AB58002242E6 /* organism-heads-100.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-heads-100.org"; sourceTree = "<group>"; };
+ 705B10201073AB58002242E6 /* organism-heads-multi-birth.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-heads-multi-birth.org"; sourceTree = "<group>"; };
+ 705B10211073AB58002242E6 /* organism-heads-parasite-host.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-heads-parasite-host.org"; sourceTree = "<group>"; };
+ 705B10221073AB58002242E6 /* organism-heads-parasite-host2.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-heads-parasite-host2.org"; sourceTree = "<group>"; };
+ 705B10231073AB58002242E6 /* organism-heads-parasite-infected.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-heads-parasite-infected.org"; sourceTree = "<group>"; };
+ 705B10241073AB58002242E6 /* organism-heads-parasite-infected2.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-heads-parasite-infected2.org"; sourceTree = "<group>"; };
+ 705B10251073AB58002242E6 /* organism-no-heads.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "organism-no-heads.org"; sourceTree = "<group>"; };
+ 705B10311073AC1F002242E6 /* default-gx.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "default-gx.org"; sourceTree = "<group>"; };
+ 705B10321073AC1F002242E6 /* default-heads-sex.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "default-heads-sex.org"; sourceTree = "<group>"; };
+ 705B10331073AC1F002242E6 /* default-heads.org */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "default-heads.org"; sourceTree = "<group>"; };
+ 705B10341073AC1F002242E6 /* instset-gx.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-gx.cfg"; sourceTree = "<group>"; };
+ 705B10351073AC1F002242E6 /* instset-heads-sex.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-heads-sex.cfg"; sourceTree = "<group>"; };
+ 705B10361073AC1F002242E6 /* instset-heads.cfg */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = "instset-heads.cfg"; sourceTree = "<group>"; };
70658C59085DF67D00486BED /* libncurses.5.4.dylib */ = {isa = PBXFileReference; lastKnownFileType = "compiled.mach-o.dylib"; name = libncurses.5.4.dylib; path = /usr/lib/libncurses.5.4.dylib; sourceTree = "<absolute>"; };
7069470C0EE8FA2700AD67C0 /* tArrayUtils.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tArrayUtils.h; sourceTree = "<group>"; };
706C6F480B83E69D003174C1 /* cSaleItem.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cSaleItem.h; sourceTree = "<group>"; };
@@ -586,30 +616,6 @@
707AF2D509EE8501001AEA89 /* avida.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = avida.cfg; sourceTree = "<group>"; };
707AF2D709EE8501001AEA89 /* environment.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.cfg; sourceTree = "<group>"; };
707AF2D809EE8501001AEA89 /* events.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = events.cfg; sourceTree = "<group>"; };
- 707AF2DE09EE8501001AEA89 /* environment.2paths */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.2paths; sourceTree = "<group>"; };
- 707AF2DF09EE8501001AEA89 /* environment.9resource */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.9resource; sourceTree = "<group>"; };
- 707AF2E009EE8501001AEA89 /* environment.all_logic */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.all_logic; sourceTree = "<group>"; };
- 707AF2E109EE8501001AEA89 /* environment.cascade */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.cascade; sourceTree = "<group>"; };
- 707AF2E209EE8501001AEA89 /* inst_set.19.short */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.19.short; sourceTree = "<group>"; };
- 707AF2E309EE8501001AEA89 /* inst_set.24.old */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.24.old; sourceTree = "<group>"; };
- 707AF2E409EE8501001AEA89 /* inst_set.26.default */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.26.default; sourceTree = "<group>"; };
- 707AF2E509EE8501001AEA89 /* inst_set.27.multi */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.27.multi; sourceTree = "<group>"; };
- 707AF2E609EE8501001AEA89 /* inst_set.27.no-nop */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "inst_set.27.no-nop"; sourceTree = "<group>"; };
- 707AF2E709EE8501001AEA89 /* inst_set.27.parasite */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.27.parasite; sourceTree = "<group>"; };
- 707AF2E809EE8501001AEA89 /* inst_set.28.base */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.28.base; sourceTree = "<group>"; };
- 707AF2E909EE8501001AEA89 /* inst_set.28.const */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.28.const; sourceTree = "<group>"; };
- 707AF2EA09EE8501001AEA89 /* inst_set.29.base_memsize */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.29.base_memsize; sourceTree = "<group>"; };
- 707AF2EB09EE8501001AEA89 /* inst_set.31.multi */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.31.multi; sourceTree = "<group>"; };
- 707AF2EC09EE8501001AEA89 /* inst_set.32.heads */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.32.heads; sourceTree = "<group>"; };
- 707AF2ED09EE8501001AEA89 /* inst_set.heads.parasite */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = inst_set.heads.parasite; sourceTree = "<group>"; };
- 707AF2EE09EE8501001AEA89 /* organism.heads.100 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.100; sourceTree = "<group>"; };
- 707AF2EF09EE8501001AEA89 /* organism.heads.15 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.15; sourceTree = "<group>"; };
- 707AF2F009EE8501001AEA89 /* organism.heads.50 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.heads.50; sourceTree = "<group>"; };
- 707AF2F109EE8501001AEA89 /* organism.host */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.host; sourceTree = "<group>"; };
- 707AF2F209EE8501001AEA89 /* organism.host2 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.host2; sourceTree = "<group>"; };
- 707AF2F309EE8501001AEA89 /* organism.infected */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.infected; sourceTree = "<group>"; };
- 707AF2F409EE8501001AEA89 /* organism.infected2 */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.infected2; sourceTree = "<group>"; };
- 707AF2F509EE8501001AEA89 /* organism.noheads */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = organism.noheads; sourceTree = "<group>"; };
707CE51D0A9E49A50022D19C /* config.html */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text.html.documentation; path = config.html; sourceTree = "<group>"; };
707CE7490AA333060022D19C /* actions.html */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text.html.documentation; path = actions.html; sourceTree = "<group>"; };
707CE7500AA334120022D19C /* analyze.html */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text.html.documentation; path = analyze.html; sourceTree = "<group>"; };
@@ -1136,18 +1142,20 @@
707AF2D209EE8501001AEA89 /* Support */ = {
isa = PBXGroup;
children = (
+ 705B10311073AC1F002242E6 /* default-gx.org */,
+ 705B10321073AC1F002242E6 /* default-heads-sex.org */,
+ 705B10331073AC1F002242E6 /* default-heads.org */,
+ 705B10341073AC1F002242E6 /* instset-gx.cfg */,
+ 705B10351073AC1F002242E6 /* instset-heads-sex.cfg */,
+ 705B10361073AC1F002242E6 /* instset-heads.cfg */,
70B1A7590B7E431F00067486 /* experimental.org */,
70B1A7420B7E3FFD00067486 /* instset-experimental.cfg */,
- 7049F36C0A66AD7E00640512 /* default-classic.org */,
- 7049F36D0A66AD7E00640512 /* default-sex-classic.org */,
7049F36E0A66AD7E00640512 /* default-smt.org */,
7049F36F0A66AD7E00640512 /* default-transsmt.org */,
707AF2D309EE8501001AEA89 /* analyze.cfg */,
707AF2D509EE8501001AEA89 /* avida.cfg */,
707AF2D709EE8501001AEA89 /* environment.cfg */,
707AF2D809EE8501001AEA89 /* events.cfg */,
- 7049F3520A66A8F500640512 /* instset-classic.cfg */,
- 7049F3530A66A8F500640512 /* instset-sex-classic.cfg */,
7049F3540A66A8F500640512 /* instset-smt.cfg */,
7049F3550A66A8F500640512 /* instset-transsmt.cfg */,
707AF2DD09EE8501001AEA89 /* misc */,
@@ -1159,30 +1167,30 @@
707AF2DD09EE8501001AEA89 /* misc */ = {
isa = PBXGroup;
children = (
- 707AF2DE09EE8501001AEA89 /* environment.2paths */,
- 707AF2DF09EE8501001AEA89 /* environment.9resource */,
- 707AF2E009EE8501001AEA89 /* environment.all_logic */,
- 707AF2E109EE8501001AEA89 /* environment.cascade */,
- 707AF2E209EE8501001AEA89 /* inst_set.19.short */,
- 707AF2E309EE8501001AEA89 /* inst_set.24.old */,
- 707AF2E409EE8501001AEA89 /* inst_set.26.default */,
- 707AF2E509EE8501001AEA89 /* inst_set.27.multi */,
- 707AF2E609EE8501001AEA89 /* inst_set.27.no-nop */,
- 707AF2E709EE8501001AEA89 /* inst_set.27.parasite */,
- 707AF2E809EE8501001AEA89 /* inst_set.28.base */,
- 707AF2E909EE8501001AEA89 /* inst_set.28.const */,
- 707AF2EA09EE8501001AEA89 /* inst_set.29.base_memsize */,
- 707AF2EB09EE8501001AEA89 /* inst_set.31.multi */,
- 707AF2EC09EE8501001AEA89 /* inst_set.32.heads */,
- 707AF2ED09EE8501001AEA89 /* inst_set.heads.parasite */,
- 707AF2EE09EE8501001AEA89 /* organism.heads.100 */,
- 707AF2EF09EE8501001AEA89 /* organism.heads.15 */,
- 707AF2F009EE8501001AEA89 /* organism.heads.50 */,
- 707AF2F109EE8501001AEA89 /* organism.host */,
- 707AF2F209EE8501001AEA89 /* organism.host2 */,
- 707AF2F309EE8501001AEA89 /* organism.infected */,
- 707AF2F409EE8501001AEA89 /* organism.infected2 */,
- 707AF2F509EE8501001AEA89 /* organism.noheads */,
+ 705B100E1073AB58002242E6 /* environment-2paths.cfg */,
+ 705B100F1073AB58002242E6 /* environment-9resource.cfg */,
+ 705B10101073AB58002242E6 /* environment-all-logic.cfg */,
+ 705B10111073AB58002242E6 /* environment-cascade.cfg */,
+ 705B10121073AB58002242E6 /* instset-heads-30-parasite.cfg */,
+ 705B10131073AB58002242E6 /* instset-heads-32-oldsearch.cfg */,
+ 705B10141073AB58002242E6 /* instset-no-heads-19-short.cfg */,
+ 705B10151073AB58002242E6 /* instset-no-heads-24.cfg */,
+ 705B10161073AB58002242E6 /* instset-no-heads-27-no-nops.cfg */,
+ 705B10171073AB58002242E6 /* instset-no-heads-27-parasite-no-inject.cfg */,
+ 705B10181073AB58002242E6 /* instset-no-heads-28-base.cfg */,
+ 705B10191073AB58002242E6 /* instset-no-heads-28-const.cfg */,
+ 705B101A1073AB58002242E6 /* instset-no-heads-29-memsize.cfg */,
+ 705B101B1073AB58002242E6 /* instset-no-heads-29-multithreaded.cfg */,
+ 705B101C1073AB58002242E6 /* instset-no-heads-31-multithreaded.cfg */,
+ 705B101D1073AB58002242E6 /* organism-heads-15-template.org */,
+ 705B101E1073AB58002242E6 /* organism-heads-50.org */,
+ 705B101F1073AB58002242E6 /* organism-heads-100.org */,
+ 705B10201073AB58002242E6 /* organism-heads-multi-birth.org */,
+ 705B10211073AB58002242E6 /* organism-heads-parasite-host.org */,
+ 705B10221073AB58002242E6 /* organism-heads-parasite-host2.org */,
+ 705B10231073AB58002242E6 /* organism-heads-parasite-infected.org */,
+ 705B10241073AB58002242E6 /* organism-heads-parasite-infected2.org */,
+ 705B10251073AB58002242E6 /* organism-no-heads.org */,
);
path = misc;
sourceTree = "<group>";
Modified: development/CMakeLists.txt
===================================================================
--- development/CMakeLists.txt 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/CMakeLists.txt 2009-09-30 15:34:39 UTC (rev 3433)
@@ -661,12 +661,14 @@
${CFG_FILES_DIR}/avida.cfg
${CFG_FILES_DIR}/environment.cfg
${CFG_FILES_DIR}/events.cfg
- ${CFG_FILES_DIR}/instset-classic.cfg
- ${CFG_FILES_DIR}/instset-sex-classic.cfg
+ ${CFG_FILES_DIR}/instset-gx.cfg
+ ${CFG_FILES_DIR}/instset-heads.cfg
+ ${CFG_FILES_DIR}/instset-heads-sex.cfg
${CFG_FILES_DIR}/instset-smt.cfg
${CFG_FILES_DIR}/instset-transsmt.cfg
- ${CFG_FILES_DIR}/default-classic.org
- ${CFG_FILES_DIR}/default-sex-classic.org
+ ${CFG_FILES_DIR}/default-gx.org
+ ${CFG_FILES_DIR}/default-heads.org
+ ${CFG_FILES_DIR}/default-heads-sex.org
${CFG_FILES_DIR}/default-smt.org
${CFG_FILES_DIR}/default-transsmt.org
)
Modified: development/source/cpu/cHardwareCPU.h
===================================================================
--- development/source/cpu/cHardwareCPU.h 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/source/cpu/cHardwareCPU.h 2009-09-30 15:34:39 UTC (rev 3433)
@@ -262,7 +262,7 @@
~cHardwareCPU() { ; }
static tInstLib<tMethod>* GetInstLib() { return s_inst_slib; }
- static cString GetDefaultInstFilename() { return "instset-classic.cfg"; }
+ static cString GetDefaultInstFilename() { return "instset-heads.cfg"; }
bool SingleProcess(cAvidaContext& ctx, bool speculative = false);
void ProcessBonusInst(cAvidaContext& ctx, const cInstruction& inst);
Modified: development/source/main/cAvidaConfig.h
===================================================================
--- development/source/main/cAvidaConfig.h 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/source/main/cAvidaConfig.h 2009-09-30 15:34:39 UTC (rev 3433)
@@ -300,7 +300,7 @@
CONFIG_ADD_VAR(EVENT_FILE, cString, "events.cfg", "File containing list of events during run");
CONFIG_ADD_VAR(ANALYZE_FILE, cString, "analyze.cfg", "File used for analysis mode");
CONFIG_ADD_VAR(ENVIRONMENT_FILE, cString, "environment.cfg", "File that describes the environment");
- CONFIG_ADD_VAR(START_CREATURE, cString, "default-classic.org", "Organism to seed the soup");
+ CONFIG_ADD_VAR(START_CREATURE, cString, "default-heads.org", "Organism to seed the soup");
CONFIG_ADD_GROUP(DEME_GROUP, "Demes and Germlines");
CONFIG_ADD_VAR(NUM_DEMES, int, 1, "Number of independent groups in the\npopulation (default=1).");
Modified: development/support/config/avida.cfg
===================================================================
--- development/support/config/avida.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/avida.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -20,44 +20,51 @@
### ARCH_GROUP ###
# Architecture Variables
-WORLD_X 60 # Width of the Avida world
-WORLD_Y 60 # Height of the Avida world
-WORLD_Z 1 # Depth of the Avida world
-WORLD_GEOMETRY 2 # 1 = Bounded Grid
- # 2 = Torus
- # 3 = Clique
- # 4 = Hexagonal grid
- # 5 = Lattice
-RANDOM_SEED 0 # Random number seed (0 for based on time)
-HARDWARE_TYPE 0 # 0 = Original CPUs
- # 1 = New SMT CPUs
- # 2 = Transitional SMT
- # 3 = Experimental CPU
- # 4 = Gene Expression CPU
-SPECULATIVE 1 # Enable speculative execution
-TRACE_EXECUTION 0 # Trace the execution of all organisms in the population (default=off,SLOW!)
-BCAST_HOPS 1 # Number of hops to broadcast an alarm
-ALARM_SELF 0 # Does sending an alarm move sender IP to alarm label?
- # 0=no
- # 1=yes
-IO_EXPIRE 1 # Is the expiration functionality of '-expire' I/O instructions enabled?
+WORLD_X 60 # Width of the Avida world
+WORLD_Y 60 # Height of the Avida world
+WORLD_Z 1 # Depth of the Avida world
+WORLD_GEOMETRY 2 # 1 = Bounded Grid
+ # 2 = Torus
+ # 3 = Clique
+ # 4 = Hexagonal grid
+ # 5 = Lattice
+SCALE_FREE_M 3 # Number of connections to add per cell when using a scale-free geometry.
+SCALE_FREE_ALPHA 1.0 # Attachment power (1=linear).
+SCALE_FREE_ZERO_APPEAL 0.0 # Appeal of cells with zero connections.
+RANDOM_SEED 0 # Random number seed (0 for based on time)
+HARDWARE_TYPE 0 # 0 = Original CPUs
+ # 1 = New SMT CPUs
+ # 2 = Transitional SMT
+ # 3 = Experimental CPU
+ # 4 = Gene Expression CPU
+SPECULATIVE 1 # Enable speculative execution
+TRACE_EXECUTION 0 # Trace the execution of all organisms in the population (default=off,SLOW!)
+BCAST_HOPS 1 # Number of hops to broadcast an alarm
+ALARM_SELF 0 # Does sending an alarm move sender IP to alarm label?
+ # 0=no
+ # 1=yes
+IO_EXPIRE 1 # Is the expiration functionality of '-expire' I/O instructions enabled?
### CONFIG_FILE_GROUP ###
# Configuration Files
-DATA_DIR data # Directory in which config files are found
-INST_SET - # File containing instruction set
-INST_SET_FORMAT 0 # Instruction set file format.
- # 0 = Default
- # 1 = New Style
-EVENT_FILE events.cfg # File containing list of events during run
-ANALYZE_FILE analyze.cfg # File used for analysis mode
-ENVIRONMENT_FILE environment.cfg # File that describes the environment
-START_CREATURE default-classic.org # Organism to seed the soup
+DATA_DIR data # Directory in which config files are found
+INST_SET - # File containing instruction set
+INST_SET_FORMAT 0 # Instruction set file format.
+ # 0 = Default
+ # 1 = New Style
+EVENT_FILE events.cfg # File containing list of events during run
+ANALYZE_FILE analyze.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment.cfg # File that describes the environment
+START_CREATURE default-heads.org # Organism to seed the soup
### DEME_GROUP ###
# Demes and Germlines
NUM_DEMES 1 # Number of independent groups in the
# population (default=1).
+DEMES_COMPETITION_STYLE 0 # Select how the demes compete
+ # 0=Fitness proportional
+ # 1=Tournament
+DEMES_TOURNAMENT_SIZE 0 # Number of demes that participate in a tournament
DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline (default=0).
DEMES_PREVENT_STERILE 0 # Whether to prevent sterile demes from
# replicating (default=0 or no).
@@ -115,6 +122,7 @@
# 0=all other demes
# 1=eight adjacent neighbors
# 2=two adjacent demes in list
+ # 3=proportional based on the number of points
DEMES_NUM_X 0 # Simulated number of demes in X dimension. Only used for migration.
DEMES_SEED_METHOD 0 # Deme seeding method.
# 0=maintain old consistency
@@ -129,6 +137,8 @@
# For use with DEMES_DIVIDE_METHOD 2.
# <0 = OFF
DEMES_PREFER_EMPTY 0 # Give empty demes preference as targets of deme replication?
+DEMES_PROTECTION_POINTS 0 # The number of points a deme receives for each suicide.
+POINT_DECAY_PERCENT 0 # The percentage of points decayed each time cActionDecayPoints is called.
### REPRODUCTION_GROUP ###
# Birth and Death
@@ -144,8 +154,10 @@
# 8 = Next grid cell (id+1)
# 9 = Largest energy used in entire population
# 10 = Largest energy used in neighborhood
+ # 11 = Local neighborhood dispersal
PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
ALLOW_PARENT 1 # Allow births to replace the parent organism?
+DISPERSAL_RATE 0.0 # Rate of dispersal under birth method 11 (poisson distributed random connection list hops)
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)
@@ -179,20 +191,23 @@
### 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
+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
+ALLOW_MATE_SELECTION 0 # Allow organisms to select mates (requires instruction set support)
+LEGACY_GRID_LOCAL_SELECTION 0 # Enable legacy grid local mate selection (ignores population structure)
### DIVIDE_GROUP ###
# Divide Restrictions
CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
+ # (Checked BEFORE mutations applied on divide.)
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.
MIN_GENOME_SIZE 0 # Minimum number of instructions allowed in a genome. 0 = OFF
@@ -202,6 +217,7 @@
IMMUNITY_TASK -1 # Task providing immunity from the required task.
REQUIRED_REACTION -1 # Reaction ID required for successful divide.
REQUIRED_BONUS 0.0 # Required bonus to divide.
+REQUIRE_EXACT_COPY 0 # Require offspring to be an exact copy (only divide mutations allowed).
IMPLICIT_REPRO_BONUS 0 # Call Inst_Repro to divide upon achieving this bonus. 0 = OFF
IMPLICIT_REPRO_CPU_CYCLES 0 # Call Inst_Repro after this many cpu cycles. 0 = OFF
IMPLICIT_REPRO_TIME 0 # Call Inst_Repro after this time used. 0 = OFF
@@ -210,36 +226,44 @@
### MUTATION_GROUP ###
# Mutations
-POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
-COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
-COPY_INS_PROB 0.0 # Insertion rate (per copy)
-COPY_DEL_PROB 0.0 # Deletion rate (per copy)
-COPY_UNIFORM_PROB 0.0 # Uniform mutation probability (per copy)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-COPY_SLIP_PROB 0.0 # Slip rate (per copy)
-DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
-DIV_INS_PROB 0.0 # Insertion rate (per site, applied on divide)
-DIV_DEL_PROB 0.0 # Deletion rate (per site, applied on divide)
-DIV_UNIFORM_PROB 0.0 # Uniform mutation probability (per site, applied on divide)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-DIV_SLIP_PROB 0.0 # Slip rate
-DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
-DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
-DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
-DIVIDE_UNIFORM_PROB 0.0 # Uniform mutation probability (per divide)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
-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)
-SLIP_FILL_MODE 0 # Fill insertions from slip mutations with 0=duplication, 1=nop-X, 2=random, 3=scrambled
-PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
-SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
-META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
-META_STD_DEV 0.0 # Standard deviation of meta mutation size.
-MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
- # 2 = Mutation rates inherited from parent.
-MIGRATION_RATE 0.0 # Uniform probability of offspring migrating to a new deme.
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
+COPY_INS_PROB 0.0 # Insertion rate (per copy)
+COPY_DEL_PROB 0.0 # Deletion rate (per copy)
+COPY_UNIFORM_PROB 0.0 # Uniform mutation probability (per copy)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+COPY_SLIP_PROB 0.0 # Slip rate (per copy)
+DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
+DIV_INS_PROB 0.0 # Insertion rate (per site, applied on divide)
+DIV_DEL_PROB 0.0 # Deletion rate (per site, applied on divide)
+DIV_UNIFORM_PROB 0.0 # Uniform mutation probability (per site, applied on divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+DIV_SLIP_PROB 0.0 # Slip rate (per site, applied on divide)
+DIVIDE_MUT_PROB 0.0 # Mutation rate (max one, per divide)
+DIVIDE_INS_PROB 0.05 # Insertion rate (max one, per divide)
+DIVIDE_DEL_PROB 0.05 # Deletion rate (max one, per divide)
+DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
+DIVIDE_POISSON_MUT_MEAN 0.0 # Mutation rate (Poisson distributed, per divide)
+DIVIDE_POISSON_INS_MEAN 0.0 # Insertion rate (Poisson distributed, per divide)
+DIVIDE_POISSON_DEL_MEAN 0.0 # Deletion rate (Poisson distributed, per divide)
+DIVIDE_POISSON_SLIP_MEAN 0.0 # Slip rate (Poisson distributed, per divide)
+DIVIDE_UNIFORM_PROB 0.0 # Uniform mutation probability (per divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+DEATH_PROB 0.0 # Death rate (parent organism, per divide)
+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)
+SLIP_FILL_MODE 0 # Fill insertions from slip mutations with 0=duplication, 1=nop-X, 2=random, 3=scrambled, 4=nop-C
+SLIP_COPY_MODE 0 # How to handle 'on-copy' slip mutations:
+ # 0 = actual read head slip
+ # 1 = instant large mutation (obeys slip mode)
+PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
+META_STD_DEV 0.0 # Standard deviation of meta mutation size.
+MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
+ # 2 = Mutation rates inherited from parent.
+MIGRATION_RATE 0.0 # Uniform probability of offspring migrating to a new deme.
### REVERSION_GROUP ###
# Mutation Reversion
@@ -248,10 +272,12 @@
REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
REVERT_NEUTRAL 0.0 #
REVERT_BENEFICIAL 0.0 #
+REVERT_TASKLOSS 0.0 # should org be reverted if loses task(s) without gaining other(s)?
STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
STERILIZE_DETRIMENTAL 0.0 #
STERILIZE_NEUTRAL 0.0 #
STERILIZE_BENEFICIAL 0.0 #
+STERILIZE_TASKLOSS 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
@@ -261,63 +287,70 @@
### 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.
- # 3 = DemeProbabalistic, each deme gets the same number of CPU cycles, which are awarded probabalistically within each deme.
- # 4 = ProbDemeProbabalistic, each deme gets CPU cycles proportional to its living population size, which are awarded probabalistically within each deme.
- # 5 = CONSTANT BURST: all organisms get default, in SLICING_BURST_SIZE chunks
-SLICING_BURST_SIZE 1 # Sets the scheduler burst size, when supported.
-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
- # 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
-BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
-DEFAULT_BONUS 1.0 # Initial bonus before any tasks
-MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by this default bonus
- # rather than the accumulated bonus of the parent? 0 = off
-MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
- # (-1 = none, 0 = First in INST_SET.)
-MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
- # per instruction (-1 = penalty, 0 = no effect.)
-FITNESS_METHOD 0 # 0 = default, >=1 = experimental
-FITNESS_COEFF_1 1.0 # 1st FITNESS_METHOD parameter
-FITNESS_COEFF_2 1.0 # 2nd FITNESS_METHOD parameter
-FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from
- # FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # (0 = off, 1 = on)
-FITNESS_VALLEY_START 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
- # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # get fitness 1 (lowest)
-FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
- # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # get fitness 1 (lowest)
-MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
-THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
- # (num_threads-1) * THREAD_SLICING_METHOD + 1
- # 0 = One thread executed per time slice.
- # 1 = All threads executed each time slice.
-NO_CPU_CYCLE_TIME 0 # Don't count each CPU cycle as part of gestation time
-MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
-MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
-MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
-MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
-MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
-MIN_GB_DONATE_THRESHOLD -1 # threshold green beard donates only to orgs above this
- # donation attempt threshold; -1=no thresh
-DONATE_THRESH_QUANTA 10 # The size of steps between quanta donate thresholds
-MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
-PRECALC_PHENOTYPE 0 # 0 = Disabled
- # 1 = Assign precalculated merit at birth (unlimited resources only)
- # 2 = Assign precalculated gestation time
- # 3 = Assign precalculated merit AND gestation time.
- # Fitness will be evaluated for organism based on these settings.
-FASTFORWARD_UPDATES 0 # Fast-forward if the average generation has not changed in this many updates. (0 = off)
-FASTFORWARD_NUM_ORGS 0 # Fast-forward if population is equal to this
+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.
+ # 3 = DemeProbabalistic, each deme gets the same number of CPU cycles, which are awarded probabalistically within each deme.
+ # 4 = ProbDemeProbabalistic, each deme gets CPU cycles proportional to its living population size, which are awarded probabalistically within each deme.
+ # 5 = CONSTANT BURST: all organisms get default, in SLICING_BURST_SIZE chunks
+SLICING_BURST_SIZE 1 # Sets the scheduler burst size, when supported.
+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
+ # 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
+BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
+DEFAULT_BONUS 1.0 # Initial bonus before any tasks
+MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by this default bonus
+ # rather than the accumulated bonus of the parent? 0 = off
+MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
+ # (-1 = none, 0 = First in INST_SET.)
+MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
+ # per instruction (-1 = penalty, 0 = no effect.)
+MERIT_INC_APPLY_IMMEDIATE 0 # Should merit increases (above current) be applied immediately, or delayed until divide?
+FITNESS_METHOD 0 # 0 = default, >=1 = experimental
+FITNESS_COEFF_1 1.0 # 1st FITNESS_METHOD parameter
+FITNESS_COEFF_2 1.0 # 2nd FITNESS_METHOD parameter
+FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from
+ # FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # (0 = off, 1 = on)
+FITNESS_VALLEY_START 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+MAX_CPU_THREADS 1 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
+ # (num_threads-1) * THREAD_SLICING_METHOD + 1
+ # 0 = One thread executed per time slice.
+ # 1 = All threads executed each time slice.
+NO_CPU_CYCLE_TIME 0 # Don't count each CPU cycle as part of gestation time
+MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
+MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
+MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
+MIN_GB_DONATE_THRESHOLD -1 # threshold green beard donates only to orgs above this
+ # donation attempt threshold; -1=no thresh
+DONATE_THRESH_QUANTA 10 # The size of steps between quanta donate thresholds
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+PRECALC_PHENOTYPE 0 # 0 = Disabled
+ # 1 = Assign precalculated merit at birth (unlimited resources only)
+ # 2 = Assign precalculated gestation time
+ # 3 = Assign precalculated merit AND gestation time.
+ # 4 = Assign last instruction counts
+ # 5 = Assign last instruction counts and merit
+ # 6 = Assign last instruction counts and gestation time
+ # 7 = Assign everything currently supported
+ # Fitness will be evaluated for organism based on these settings.
+FASTFORWARD_UPDATES 0 # Fast-forward if the average generation has not changed in this many updates. (0 = off)
+FASTFORWARD_NUM_ORGS 0 # Fast-forward if population is equal to this
+GENOTYPE_PHENPLAST_CALC 100 # Number of times to test a genotype's
+ # plasticity during runtime.
### GENEOLOGY_GROUP ###
# Geneology
@@ -332,6 +365,7 @@
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)
+TRACK_PARENT_DIST 0 # Track parent distance during run. This is unnecessary when track main lineage is on.
### LOG_GROUP ###
# Log Files
@@ -386,10 +420,10 @@
SELL_PRICE 0 # price offered by organisms attempting to sell
### HOARD_RESOURCE_GROUP ###
-# Resource Hoarding Parameters
+# Resource Hoarding Parameters
USE_RESOURCE_BINS 0 # Enable resource bin use. This serves as a guard on most resource hoarding code.
-ABSORB_RESOURCE_FRACTION .0025 # Fraction of available environmental resource an organism absorbs with the collect instruction.
-MULTI_ABSORB_TYPE 0 # What to do if collect is called on a range of resources.
+ABSORB_RESOURCE_FRACTION .0025 # Fraction of available environmental resource an organism absorbs.
+MULTI_ABSORB_TYPE 0 # What to do if a collect instruction is called on a range of resources.
# 0 = absorb a random resource in the range
# 1 = absorb the first resource in the range
# 2 = absorb the last resource in the range
@@ -415,12 +449,13 @@
FRAC_PARENT_ENERGY_GIVEN_TO_DEME_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring deme.
FRAC_ENERGY_DECAY_AT_ORG_BIRTH 0.0 # Fraction of energy lost due to decay during organism reproduction.
FRAC_ENERGY_DECAY_AT_DEME_BIRTH 0.0 # Fraction of energy lost due to decay during deme reproduction.
-NUM_INST_EXC_BEFORE_0_ENERGY 0 # Number of instructions executed before energy is exhausted.
+NUM_CYCLES_EXC_BEFORE_0_ENERGY 0 # Number of virtual CPU cycles executed before energy is exhausted.
ENERGY_CAP -1.0 # Maximum amount of energy that can be stored in an organism. -1 means the cap is set to Max Double
APPLY_ENERGY_METHOD 0 # When should rewarded energy be applied to current energy?
# 0 = on divide
# 1 = on completion of task
# 2 = on sleep
+FIX_METABOLIC_RATE -1.0 # Fix organism metobolic rate to value. This value is static. Feature disabled by default (value == -1)
FRAC_ENERGY_TRANSFER 0.0 # Fraction of replaced organism's energy take by new resident
LOG_SLEEP_TIMES 0 # Log sleep start and end times. 0/1 (off/on)
# WARNING: may use lots of memory.
@@ -432,13 +467,16 @@
ATTACK_DECAY_RATE 0.0 # Percent of cell's energy decayed by attack
ENERGY_THRESH_LOW .33 # Threshold percent below which energy level is considered low. Requires ENERGY_CAP.
ENERGY_THRESH_HIGH .75 # Threshold percent above which energy level is considered high. Requires ENERGY_CAP.
+ENERGY_COMPARISON_EPSILON 0.0 # Percent difference (relative to executing organism) required in energy level comparisons
### ENERGY_SHARING_GROUP ###
# Energy Sharing Settings
-ENERGY_SHARING_METHOD 0 # Method for sharing energy. 0=receiver must actively receive/request, 1=energy pushed on receiver
-ENERGY_SHARING_PCT 0.0 # Percent of energy to share
-ENERGY_SHARING_INCREMENT 0.01 # Amount to change percent energy shared
-ENERGY_SHARING_LOSS 0.0 # Percent of shared energy lost in transfer
+ENERGY_SHARING_METHOD 0 # Method for sharing energy. 0=receiver must actively receive/request, 1=energy pushed on receiver
+ENERGY_SHARING_PCT 0.0 # Percent of energy to share
+ENERGY_SHARING_INCREMENT 0.01 # Amount to change percent energy shared
+RESOURCE_SHARING_LOSS 0.0 # Fraction of shared resource lost in transfer
+ENERGY_SHARING_UPDATE_METABOLIC 0 # 0/1 (off/on) - Whether to update an organism's metabolic rate on donate or reception/application of energy
+LOG_ENERGY_SHARING 0 # Whether or not to log energy shares. 0/1 (off/on)
### SECOND_PASS_GROUP ###
# Tracking metrics known after the running experiment previously
@@ -524,3 +562,72 @@
SYNC_FITNESS_WINDOW 100 # Number of updates over which to calculate fitness (default=100).
SYNC_FLASH_LOSSRATE 0.0 # P() to lose a flash send (0.0==off).
SYNC_TEST_FLASH_ARRIVAL -1 # CPU cycle at which an organism will receive a flash (off=-1, default=-1, analyze mode only.)
+
+### CONSENSUS_GROUP ###
+# Consensus settings
+CONSENSUS_HOLD_TIME 1 # Number of updates that consensus must be held for.
+
+### REPUTATION_GROUP ###
+# Reputation Settings
+RAW_MATERIAL_AMOUNT 100 # Number of raw materials an organism starts with
+AUTO_REPUTATION 0 # Is an organism's reputation automatically computed based on its donations
+ # 0=no
+ # 1=increment for each donation + standing
+ # 2=+1 for donations given -1 for donations received
+ # 3=1 for donors -1 for recivers who have not donated
+ # 4=+1 for donors
+ # 5=+1 for donors during task check
+ALT_BENEFIT 1.00 # Number multiplied by the number of raw materials received from another organism to compute reward
+ALT_COST 1.00 # Number multiplied by the number of your raw materials
+ROTATE_ON_DONATE 0 # Rotate an organism to face its donor 0/1 (off/on)
+REPUTATION_REWARD 0 # Reward an organism for having a good reputation
+DONATION_FAILURE_PERCENT 0 # Percentage of times that a donation fails
+RANDOMIZE_RAW_MATERIAL_AMOUNT 0 # Should all the organisms receive the same amount 0/1 (off/on)
+DONATION_RESTRICTIONS 0 # 0=none
+ # 1=inter-species only
+ # 2=different tag only
+INHERIT_REPUTATION 0 # 0=reputations are not inherited
+ # 1=reputations are inherited
+ # 2=tags are inherited
+SPECIALISTS 0 # 0=generalists allowed
+ # 1=only specialists
+STRING_AMOUNT_CAP -1 # -1=no cap on string amounts
+ # #=CAP
+MATCH_ALREADY_PRODUCED 0 # 0=off
+ # 1=on
+
+### GROUP_FORMATION_GROUP ###
+# Group Formation Settings
+USE_FORM_GROUPS 0 # Enable organisms to form groups. 0=off,
+ # 1=on no restrict,
+ # 2=on restrict to defined
+
+### DEME_NETWORK_GROUP ###
+# Deme network settings
+DEME_NETWORK_TYPE 0 # 0=topology, structure of network determines fitness.
+DEME_NETWORK_REQUIRES_CONNECTEDNESS 1 # Whether the deme's network must be connected before an actual fitness is calculated.
+DEME_NETWORK_TOPOLOGY_FITNESS 0 # Network measure used to determine fitness; see cDemeTopologyNetwork.h.
+
+### HGT_GROUP ###
+# Horizontal gene transfer settings
+ENABLE_HGT 0 # Whether HGT is enabled; 0=false (default),
+ # 1=true.
+HGT_FRAGMENT_SIZE_MEAN 10 # Mean size of fragments (drawn from a normal
+ # dist., default=10).
+HGT_FRAGMENT_SIZE_VARIANCE 2 # Variance of fragments (drawn from a normal
+ # dist., default=2).
+HGT_MAX_FRAGMENTS_PER_CELL 100 # Max. allowed number of fragments
+ # per cell (default=100).
+HGT_DIFFUSION_METHOD 0 # Method to use for diffusion of genome
+ # fragments (0=none [default]).
+HGT_INSERTION_PROB 0.0 # Probability that a genome fragment
+ # will be inserted during a copy (default=0.0).
+HGT_LOOKAHEAD_LENGTH 4 # Number of instructions forward from the
+ # read head that will be used to calculate
+ # the liklihood of HGT.
+
+### INST_RES_GROUP ###
+# Resource-Dependent Instructions Settings
+INST_RES # Resource upon which the execution of certain instruction depends
+INST_RES_FLOOR 0.0 # Assumed lower level of resource in environment. Used for probability dist.
+INST_RES_CEIL 0.0 # Assumed upper level of resource in environment. Used for probability dist.
Deleted: development/support/config/default-classic.org
===================================================================
--- development/support/config/default-classic.org 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/default-classic.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,100 +0,0 @@
-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 #
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-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 #
Copied: development/support/config/default-heads-sex.org (from rev 3430, development/support/config/default-sex-classic.org)
===================================================================
--- development/support/config/default-heads-sex.org (rev 0)
+++ development/support/config/default-heads-sex.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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 #
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+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 #
+divide-sex # ...divide (with sex...)!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Copied: development/support/config/default-heads.org (from rev 3430, development/support/config/default-classic.org)
===================================================================
--- development/support/config/default-heads.org (rev 0)
+++ development/support/config/default-heads.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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 #
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+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 #
Deleted: development/support/config/default-sex-classic.org
===================================================================
--- development/support/config/default-sex-classic.org 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/default-sex-classic.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,100 +0,0 @@
-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 #
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-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 #
-divide-sex # ...divide (with sex...)!
-mov-head # Otherwise, loop back to the beginning of the copy loop.
-nop-A # End label.
-nop-B #
Modified: development/support/config/events.cfg
===================================================================
--- development/support/config/events.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/events.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -23,7 +23,7 @@
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 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.
@@ -33,4 +33,4 @@
# Setup the exit time and full population data collection.
u 50000:50000 SavePopulation # Save current state of population.
u 50000:50000 SaveHistoricPopulation # Save ancestors of current population.
-u 100000 exit # exit
+u 100000 Exit # exit
Deleted: development/support/config/instset-classic.cfg
===================================================================
--- development/support/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/support/config/instset-heads-sex.cfg (from rev 3430, development/support/config/instset-sex-classic.cfg)
===================================================================
--- development/support/config/instset-heads-sex.cfg (rev 0)
+++ development/support/config/instset-heads-sex.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,37 @@
+# No-ops
+nop-A 1 # a
+nop-B 1 # b
+nop-C 1 # c
+
+# Flow control operations
+if-n-equ 1 # d
+if-less 1 # e
+if-label 1 # f
+mov-head 1 # g
+jmp-head 1 # h
+get-head 1 # i
+set-flow 1 # j
+
+# Single Argument Math
+shift-r 1 # k
+shift-l 1 # l
+inc 1 # m
+dec 1 # n
+push 1 # o
+pop 1 # p
+swap-stk 1 # q
+swap 1 # r
+
+# Double Argument Math
+add 1 # s
+sub 1 # t
+nand 1 # u
+
+# Biological Operations
+h-copy 1 # v
+h-alloc 1 # w
+divide-sex 1 # x
+
+# I/O and Sensory
+IO 1 # y
+h-search 1 # z
Copied: development/support/config/instset-heads.cfg (from rev 3430, development/support/config/instset-classic.cfg)
===================================================================
--- development/support/config/instset-heads.cfg (rev 0)
+++ development/support/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,37 @@
+# No-ops
+nop-A 1 # a
+nop-B 1 # b
+nop-C 1 # c
+
+# Flow control operations
+if-n-equ 1 # d
+if-less 1 # e
+if-label 1 # f
+mov-head 1 # g
+jmp-head 1 # h
+get-head 1 # i
+set-flow 1 # j
+
+# Single Argument Math
+shift-r 1 # k
+shift-l 1 # l
+inc 1 # m
+dec 1 # n
+push 1 # o
+pop 1 # p
+swap-stk 1 # q
+swap 1 # r
+
+# Double Argument Math
+add 1 # s
+sub 1 # t
+nand 1 # u
+
+# Biological Operations
+h-copy 1 # v
+h-alloc 1 # w
+h-divide 1 # x
+
+# I/O and Sensory
+IO 1 # y
+h-search 1 # z
Deleted: development/support/config/instset-sex-classic.cfg
===================================================================
--- development/support/config/instset-sex-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/instset-sex-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,53 +0,0 @@
-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.
-divide-sex 1 # s Cuts off everything between the read and write heads and
- # submits to the birth chamber with sex flag on.
-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
Copied: development/support/config/misc/environment-2paths.cfg (from rev 3430, development/support/config/misc/environment.2paths)
===================================================================
--- development/support/config/misc/environment-2paths.cfg (rev 0)
+++ development/support/config/misc/environment-2paths.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,38 @@
+##############################################################################
+#
+# 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 environmental setup uses all 9 basic tasks, dividing them up into
+# two groups, with EQU available to both. Each organism can only derive
+# benefit from doing tasks in a single group, and hence the population as
+# a while will choose one pathway or the other.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+REACTION NOT
+REACTION NAND
+REACTION AND
+REACTION ORN
+REACTION OR
+REACTION ANDN
+REACTION NOR
+REACTION XOR
+REACTION EQU
+
+
+REACTION NOT not process:value=1.0 requisite:noreaction=NAND:noreaction=ORN:noreaction=OR:noreaction=XOR
+REACTION AND and process:value=2.0 requisite:noreaction=NAND:noreaction=ORN:noreaction=OR:noreaction=XOR
+REACTION ANDN andn process:value=4.0 requisite:noreaction=NAND:noreaction=ORN:noreaction=OR:noreaction=XOR
+REACTION NOR nor process:value=8.0 requisite:noreaction=NAND:noreaction=ORN:noreaction=OR:noreaction=XOR
+
+REACTION NAND nand process:value=1.0 requisite:noreaction=NOT:noreaction=AND:noreaction=ANDN:noreaction=NOR
+REACTION ORN orn process:value=2.0 requisite:noreaction=NOT:noreaction=AND:noreaction=ANDN:noreaction=NOR
+REACTION OR or process:value=4.0 requisite:noreaction=NOT:noreaction=AND:noreaction=ANDN:noreaction=NOR
+REACTION XOR xor process:value=8.0 requisite:noreaction=NOT:noreaction=AND:noreaction=ANDN:noreaction=NOR
+
+REACTION EQU equ process:value=16.0
Copied: development/support/config/misc/environment-9resource.cfg (from rev 3430, development/support/config/misc/environment.9resource)
===================================================================
--- development/support/config/misc/environment-9resource.cfg (rev 0)
+++ development/support/config/misc/environment-9resource.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,33 @@
+##############################################################################
+#
+# 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 environmental setup is that of a chemostat with 9 resources, each
+# with a unique task corresponding to them. All resources have a set inflow
+# of 100, and outflow rate of 0.01, setting their an equilibrium level at
+# 10,000. Given a maximum population size of 3600 and neighborhood size of
+# 9, the fraction of the resource absorbable in each reaction is simply
+# 9/3600 or 0.0025.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+RESOURCE resNOT:inflow=100:outflow=0.01 resNAND:inflow=100:outflow=0.01
+RESOURCE resAND:inflow=100:outflow=0.01 resORN:inflow=100:outflow=0.01
+RESOURCE resOR:inflow=100:outflow=0.01 resANDN:inflow=100:outflow=0.01
+RESOURCE resNOR:inflow=100:outflow=0.01 resXOR:inflow=100:outflow=0.01
+RESOURCE resEQU:inflow=100:outflow=0.01
+
+REACTION NOT not process:resource=resNOT:value=1.0:frac=0.0025:max=25
+REACTION NAND nand process:resource=resNAND:value=1.0:frac=0.0025:max=25
+REACTION AND and process:resource=resAND:value=2.0:frac=0.0025:max=25
+REACTION ORN orn process:resource=resORN:value=2.0:frac=0.0025:max=25
+REACTION OR or process:resource=resOR:value=4.0:frac=0.0025:max=25
+REACTION ANDN andn process:resource=resANDN:value=4.0:frac=0.0025:max=25
+REACTION NOR nor process:resource=resNOR:value=8.0:frac=0.0025:max=25
+REACTION XOR xor process:resource=resXOR:value=8.0:frac=0.0025:max=25
+REACTION EQU equ process:resource=resEQU:value=16.0:frac=0.0025:max=25
Copied: development/support/config/misc/environment-all-logic.cfg (from rev 3430, development/support/config/misc/environment.all_logic)
===================================================================
--- development/support/config/misc/environment-all-logic.cfg (rev 0)
+++ development/support/config/misc/environment-all-logic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,92 @@
+##############################################################################
+#
+# 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 environmental setup rewards all one-, two- and three-input logic
+# operations available.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+REACTION NOT not process:value=0.2:type=pow requisite:max_count=1
+REACTION NAND nand process:value=0.2:type=pow requisite:max_count=1
+REACTION AND and process:value=0.4:type=pow requisite:max_count=1
+REACTION ORN orn process:value=0.4:type=pow requisite:max_count=1
+REACTION OR or process:value=0.6:type=pow requisite:max_count=1
+REACTION ANDN andn process:value=0.6:type=pow requisite:max_count=1
+REACTION NOR nor process:value=0.8:type=pow requisite:max_count=1
+REACTION XOR xor process:value=0.8:type=pow requisite:max_count=1
+REACTION EQU equ process:value=1.0:type=pow requisite:max_count=1
+
+REACTION LOG3AA logic_3AA process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AB logic_3AB process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AC logic_3AC process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AD logic_3AD process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AE logic_3AE process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AF logic_3AF process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AG logic_3AG process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AH logic_3AH process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AI logic_3AI process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AJ logic_3AJ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AK logic_3AK process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AL logic_3AL process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AM logic_3AM process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AN logic_3AN process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AO logic_3AO process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AP logic_3AP process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AQ logic_3AQ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AR logic_3AR process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AS logic_3AS process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AT logic_3AT process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AU logic_3AU process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AV logic_3AV process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AW logic_3AW process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AX logic_3AX process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AY logic_3AY process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3AZ logic_3AZ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BA logic_3BA process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BB logic_3BB process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BC logic_3BC process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BD logic_3BD process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BE logic_3BE process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BF logic_3BF process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BG logic_3BG process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BH logic_3BH process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BI logic_3BI process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BJ logic_3BJ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BK logic_3BK process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BL logic_3BL process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BM logic_3BM process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BN logic_3BN process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BO logic_3BO process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BP logic_3BP process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BQ logic_3BQ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BR logic_3BR process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BS logic_3BS process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BT logic_3BT process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BU logic_3BU process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BV logic_3BV process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BW logic_3BW process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BX logic_3BX process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BY logic_3BY process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3BZ logic_3BZ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CA logic_3CA process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CB logic_3CB process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CC logic_3CC process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CD logic_3CD process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CE logic_3CE process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CF logic_3CF process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CG logic_3CG process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CH logic_3CH process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CI logic_3CI process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CJ logic_3CJ process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CK logic_3CK process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CL logic_3CL process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CM logic_3CM process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CN logic_3CN process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CO logic_3CO process:value=1.0:type=pow requisite:max_count=1
+REACTION LOG3CP logic_3CP process:value=1.0:type=pow requisite:max_count=1
Copied: development/support/config/misc/environment-cascade.cfg (from rev 3430, development/support/config/misc/environment.cascade)
===================================================================
--- development/support/config/misc/environment-cascade.cfg (rev 0)
+++ development/support/config/misc/environment-cascade.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,29 @@
+##############################################################################
+#
+# 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 environmental setup as an inflow of the resources for not and nand.
+# After that, all other resources are a cascade of products from the first,
+# requiring more and more complex tasks to make use of them.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+RESOURCE resNOT:inflow=100:outflow=0.01 resNAND:inflow=100:outflow=0.01
+RESOURCE resAND:outflow=0.01 resORN:outflow=0.01 resOR:outflow=0.01
+RESOURCE resANDN:outflow=0.01 resNOR:outflow=0.01 resXOR:outflow=0.01
+RESOURCE resEQU:outflow=0.01
+
+REACTION NOT not process:resource=resNOT:frac=0.0025:max=25:product=resAND
+REACTION NAND nand process:resource=resNAND:frac=0.0025:max=25:product=resORN
+REACTION AND and process:resource=resAND:frac=0.0025:max=25:product=resOR
+REACTION ORN orn process:resource=resORN:frac=0.0025:max=25:product=resANDN
+REACTION OR or process:resource=resOR:frac=0.0025:max=25:product=resNOR
+REACTION ANDN andn process:resource=resANDN:frac=0.0025:max=25:product=resXOR
+REACTION NOR nor process:resource=resNOR:frac=0.0025:max=25:product=resEQU
+REACTION XOR xor process:resource=resXOR:frac=0.0025:max=25:product=resEQU
+REACTION EQU equ process:resource=resEQU:frac=0.0025:max=25
Deleted: development/support/config/misc/environment.2paths
===================================================================
--- development/support/config/misc/environment.2paths 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/environment.2paths 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,38 +0,0 @@
-##############################################################################
-#
-# 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 environmental setup uses all 9 basic tasks, dividing them up into
-# two groups, with EQU available to both. Each organism can only derive
-# benefit from doing tasks in a single group, and hence the population as
-# a while will choose one pathway or the other.
-#
-# For information on how to use this file, see: doc/environment.html
-# For other sample environments, see: source/support/config/
-#
-##############################################################################
-
-REACTION NOT
-REACTION NAND
-REACTION AND
-REACTION ORN
-REACTION OR
-REACTION ANDN
-REACTION NOR
-REACTION XOR
-REACTION EQU
-
-
-REACTION NOT not process:value=1.0 requisite:noreaction=NAND:noreaction=ORN:noreaction=OR:noreaction=XOR
-REACTION AND and process:value=2.0 requisite:noreaction=NAND:noreaction=ORN:noreaction=OR:noreaction=XOR
-REACTION ANDN andn process:value=4.0 requisite:noreaction=NAND:noreaction=ORN:noreaction=OR:noreaction=XOR
-REACTION NOR nor process:value=8.0 requisite:noreaction=NAND:noreaction=ORN:noreaction=OR:noreaction=XOR
-
-REACTION NAND nand process:value=1.0 requisite:noreaction=NOT:noreaction=AND:noreaction=ANDN:noreaction=NOR
-REACTION ORN orn process:value=2.0 requisite:noreaction=NOT:noreaction=AND:noreaction=ANDN:noreaction=NOR
-REACTION OR or process:value=4.0 requisite:noreaction=NOT:noreaction=AND:noreaction=ANDN:noreaction=NOR
-REACTION XOR xor process:value=8.0 requisite:noreaction=NOT:noreaction=AND:noreaction=ANDN:noreaction=NOR
-
-REACTION EQU equ process:value=16.0
Deleted: development/support/config/misc/environment.9resource
===================================================================
--- development/support/config/misc/environment.9resource 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/environment.9resource 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,33 +0,0 @@
-##############################################################################
-#
-# 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 environmental setup is that of a chemostat with 9 resources, each
-# with a unique task corresponding to them. All resources have a set inflow
-# of 100, and outflow rate of 0.01, setting their an equilibrium level at
-# 10,000. Given a maximum population size of 3600 and neighborhood size of
-# 9, the fraction of the resource absorbable in each reaction is simply
-# 9/3600 or 0.0025.
-#
-# For information on how to use this file, see: doc/environment.html
-# For other sample environments, see: source/support/config/
-#
-##############################################################################
-
-RESOURCE resNOT:inflow=100:outflow=0.01 resNAND:inflow=100:outflow=0.01
-RESOURCE resAND:inflow=100:outflow=0.01 resORN:inflow=100:outflow=0.01
-RESOURCE resOR:inflow=100:outflow=0.01 resANDN:inflow=100:outflow=0.01
-RESOURCE resNOR:inflow=100:outflow=0.01 resXOR:inflow=100:outflow=0.01
-RESOURCE resEQU:inflow=100:outflow=0.01
-
-REACTION NOT not process:resource=resNOT:value=1.0:frac=0.0025:max=25
-REACTION NAND nand process:resource=resNAND:value=1.0:frac=0.0025:max=25
-REACTION AND and process:resource=resAND:value=2.0:frac=0.0025:max=25
-REACTION ORN orn process:resource=resORN:value=2.0:frac=0.0025:max=25
-REACTION OR or process:resource=resOR:value=4.0:frac=0.0025:max=25
-REACTION ANDN andn process:resource=resANDN:value=4.0:frac=0.0025:max=25
-REACTION NOR nor process:resource=resNOR:value=8.0:frac=0.0025:max=25
-REACTION XOR xor process:resource=resXOR:value=8.0:frac=0.0025:max=25
-REACTION EQU equ process:resource=resEQU:value=16.0:frac=0.0025:max=25
Deleted: development/support/config/misc/environment.all_logic
===================================================================
--- development/support/config/misc/environment.all_logic 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/environment.all_logic 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,92 +0,0 @@
-##############################################################################
-#
-# 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 environmental setup rewards all one-, two- and three-input logic
-# operations available.
-#
-# For information on how to use this file, see: doc/environment.html
-# For other sample environments, see: source/support/config/
-#
-##############################################################################
-
-REACTION NOT not process:value=0.2:type=pow requisite:max_count=1
-REACTION NAND nand process:value=0.2:type=pow requisite:max_count=1
-REACTION AND and process:value=0.4:type=pow requisite:max_count=1
-REACTION ORN orn process:value=0.4:type=pow requisite:max_count=1
-REACTION OR or process:value=0.6:type=pow requisite:max_count=1
-REACTION ANDN andn process:value=0.6:type=pow requisite:max_count=1
-REACTION NOR nor process:value=0.8:type=pow requisite:max_count=1
-REACTION XOR xor process:value=0.8:type=pow requisite:max_count=1
-REACTION EQU equ process:value=1.0:type=pow requisite:max_count=1
-
-REACTION LOG3AA logic_3AA process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AB logic_3AB process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AC logic_3AC process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AD logic_3AD process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AE logic_3AE process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AF logic_3AF process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AG logic_3AG process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AH logic_3AH process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AI logic_3AI process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AJ logic_3AJ process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AK logic_3AK process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AL logic_3AL process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AM logic_3AM process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AN logic_3AN process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AO logic_3AO process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AP logic_3AP process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AQ logic_3AQ process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AR logic_3AR process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AS logic_3AS process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AT logic_3AT process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AU logic_3AU process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AV logic_3AV process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AW logic_3AW process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AX logic_3AX process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AY logic_3AY process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3AZ logic_3AZ process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BA logic_3BA process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BB logic_3BB process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BC logic_3BC process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BD logic_3BD process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BE logic_3BE process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BF logic_3BF process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BG logic_3BG process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BH logic_3BH process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BI logic_3BI process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BJ logic_3BJ process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BK logic_3BK process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BL logic_3BL process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BM logic_3BM process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BN logic_3BN process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BO logic_3BO process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BP logic_3BP process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BQ logic_3BQ process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BR logic_3BR process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BS logic_3BS process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BT logic_3BT process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BU logic_3BU process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BV logic_3BV process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BW logic_3BW process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BX logic_3BX process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BY logic_3BY process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3BZ logic_3BZ process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CA logic_3CA process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CB logic_3CB process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CC logic_3CC process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CD logic_3CD process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CE logic_3CE process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CF logic_3CF process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CG logic_3CG process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CH logic_3CH process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CI logic_3CI process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CJ logic_3CJ process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CK logic_3CK process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CL logic_3CL process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CM logic_3CM process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CN logic_3CN process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CO logic_3CO process:value=1.0:type=pow requisite:max_count=1
-REACTION LOG3CP logic_3CP process:value=1.0:type=pow requisite:max_count=1
Deleted: development/support/config/misc/environment.cascade
===================================================================
--- development/support/config/misc/environment.cascade 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/environment.cascade 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,29 +0,0 @@
-##############################################################################
-#
-# 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 environmental setup as an inflow of the resources for not and nand.
-# After that, all other resources are a cascade of products from the first,
-# requiring more and more complex tasks to make use of them.
-#
-# For information on how to use this file, see: doc/environment.html
-# For other sample environments, see: source/support/config/
-#
-##############################################################################
-
-RESOURCE resNOT:inflow=100:outflow=0.01 resNAND:inflow=100:outflow=0.01
-RESOURCE resAND:outflow=0.01 resORN:outflow=0.01 resOR:outflow=0.01
-RESOURCE resANDN:outflow=0.01 resNOR:outflow=0.01 resXOR:outflow=0.01
-RESOURCE resEQU:outflow=0.01
-
-REACTION NOT not process:resource=resNOT:frac=0.0025:max=25:product=resAND
-REACTION NAND nand process:resource=resNAND:frac=0.0025:max=25:product=resORN
-REACTION AND and process:resource=resAND:frac=0.0025:max=25:product=resOR
-REACTION ORN orn process:resource=resORN:frac=0.0025:max=25:product=resANDN
-REACTION OR or process:resource=resOR:frac=0.0025:max=25:product=resNOR
-REACTION ANDN andn process:resource=resANDN:frac=0.0025:max=25:product=resXOR
-REACTION NOR nor process:resource=resNOR:frac=0.0025:max=25:product=resEQU
-REACTION XOR xor process:resource=resXOR:frac=0.0025:max=25:product=resEQU
-REACTION EQU equ process:resource=resEQU:frac=0.0025:max=25
Deleted: development/support/config/misc/inst_set.19.short
===================================================================
--- development/support/config/misc/inst_set.19.short 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.19.short 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,19 +0,0 @@
-nop-A 1
-nop-B 1
-nop-C 1
-if-less 1
-jump-slf 1
-pop 1
-push 1
-shift-r 1
-shift-l 1
-inc 1
-dec 1
-add 1
-sub 1
-nand 1
-copy 1
-allocate 1
-divide 1
-get 1
-put 1
Deleted: development/support/config/misc/inst_set.24.old
===================================================================
--- development/support/config/misc/inst_set.24.old 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.24.old 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,39 +0,0 @@
-# No-ops
-nop-A 1
-nop-B 1
-nop-C 1
-
-# Flow control operations
-if-n-equ 1
-jump-f 1
-jump-b 1
-call 1
-return 1
-
-# Single Argument Math
-shift-r 1
-shift-l 1
-inc 1
-dec 1
-push 1
-pop 1
-
-# Double Argument Math
-add 1
-sub 1
-nand 1
-
-# Biological Operations
-copy 1
-allocate 1
-divide 1
-
-# I/O and Sensory
-get 1
-put 1
-search-f 1
-search-b 1
-
-# Other Commands
-rotate-l 0
-rotate-r 0
Deleted: development/support/config/misc/inst_set.26.default
===================================================================
--- development/support/config/misc/inst_set.26.default 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.26.default 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,53 +0,0 @@
-nop-A 1
-nop-B 1
-nop-C 1
-if-n-equ 1
-if-less 1
-pop 1
-push 1
-swap-stk 1
-swap 1
-shift-r 1
-shift-l 1
-inc 1
-dec 1
-add 1
-sub 1
-nand 1
-h-alloc 1 # Allocate as much memory as organism can use.
-h-divide 1 # Cuts off everything between the read and write heads
-IO 1 # Puts current contents of register and gets new.
-h-copy 1 # Combine h-read and h-write
-h-search 1 ### Search for matching template, set flow head, & return info.
- ## If no template, move flow-head here, set size&offset=0.
-mov-head 1 ### Move ?IP? head to flow control
-jmp-head 1 ### Move ?IP? head by fixed amount in CX. Set old pos in CX.
-get-head 1 ### Get position of specified head in CX.
-set-flow 1 ### Move flow-head to address in ?CX?
-
-
-if-label 1
-#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
Deleted: development/support/config/misc/inst_set.27.multi
===================================================================
--- development/support/config/misc/inst_set.27.multi 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.27.multi 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,71 +0,0 @@
-# No-ops
-nop-A 1
-nop-B 1
-nop-C 1
-nop-X 0
-
-# Flow control operations
-if-not-0 0
-if-n-equ 1
-if-bit-1 0
-jump-f 1
-jump-b 1
-jump-p 0
-call 1
-return 1
-
-# Single Argument Math
-shift-r 1
-shift-l 1
-bit-1 0
-inc 1
-dec 1
-push 1
-pop 1
-set-num 0
-zero 0 # Can use put instead.
-
-# Double Argument Math
-add 1
-sub 1
-nand 1
-nor 0
-order 0
-and 0
-not 0
-xor 0
-
-# Biological Operations
-copy 1
-read 0
-write 0
-allocate 1
-divide 1
-compare 0
-if-n-cpy 0
-c-alloc 0
-c-divide 0
-inject 0
-fork-th 1
-kill-th 1
-id-th 1
-
-# I/O and Sensory
-get 1
-put 1
-search-f 1
-search-b 1
-
-# Other Commands
-rotate-l 0
-rotate-r 0
-set-cmut 0
-mod-cmut 0
-
-# Direct Matching Template Commands
-dm-jp-f 0
-dm-jp-b 0
-
-# delete later
-if-less 1
-swap-stk 1
Deleted: development/support/config/misc/inst_set.27.no-nop
===================================================================
--- development/support/config/misc/inst_set.27.no-nop 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.27.no-nop 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,103 +0,0 @@
-nop-A 0
-nop-B 0
-nop-C 0
-nop-X 0
-if-equ-0 0
-if-not-0 0
-if-n-equ 1
-if-equ 0
-if-grt-0 0
-if-grt 0
-if->=-0 0
-if->= 0
-if-les-0 0
-if-less 1
-if-<=-0 0
-if-<= 0
-if-A!=B 0
-if-B!=C 0
-if-A!=C 0
-if-bit-1 1
-jump-f 1
-jump-b 1
-jump-p 0
-jump-slf 0
-call 1
-return 1
-pop 0
-push 0
-swap-stk 1
-flip-stk 0
-swap 1
-swap-AB 0
-swap-BC 0
-swap-AC 0
-copy-reg 0
-set_A=B 0
-set_A=C 0
-set_B=A 0
-set_B=C 0
-set_C=A 0
-set_C=B 0
-reset 0
-pop-A 1
-pop-B 1
-pop-C 1
-push-A 1
-push-B 1
-push-C 1
-shift-r 1
-shift-l 1
-bit-1 0
-set-num 0
-inc 1
-dec 1
-zero 0
-neg 0
-square 0
-sqrt 0
-not 0
-add 1
-sub 1
-mult 0
-div 0
-mod 0
-nand 1
-nor 0
-and 0
-order 0
-xor 0
-copy 1
-read 0
-write 0
-stk-read 0
-stk-writ 0
-compare 0
-if-n-cpy 0
-allocate 1
-divide 1
-c-alloc 0
-c-divide 0
-inject 0
-get 1
-stk-get 0
-stk-load 0
-put 1
-search-f 0
-search-b 0
-mem-size 0
-rotate-l 0
-rotate-r 0
-set-cmut 0
-mod-cmut 0
-fork-th 0
-kill-th 0
-id-th 0
-repro 0
-dm-jp-f 0
-dm-jp-b 0
-dm-sch-f 0
-dm-sch-b 0
-re-jp-f 0
-re-jp-b 0
-abs-jp 0
Deleted: development/support/config/misc/inst_set.27.parasite
===================================================================
--- development/support/config/misc/inst_set.27.parasite 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.27.parasite 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,60 +0,0 @@
-# No-ops
-nop-A 1
-nop-B 1
-nop-C 1
-nop-X 0
-
-# Flow control operations
-if-not-0 0
-if-n-equ 1
-if-bit-1 0
-jump-f 1
-jump-b 1
-jump-p 1
-call 1
-return 1
-
-# Single Argument Math
-shift-r 1
-shift-l 1
-bit-1 0
-inc 1
-dec 1
-push 1
-pop 1
-set-num 0
-zero 0 # Can use put instead.
-
-# Double Argument Math
-add 1
-sub 1
-nand 1
-nor 0
-order 0
-and 0
-not 0
-xor 0
-
-# Biological Operations
-copy 1
-read 0
-write 0
-allocate 1
-divide 1
-compare 0
-if-n-cpy 0
-c-alloc 0
-c-divide 0
-inject 0
-
-# I/O and Sensory
-get 1
-put 1
-search-f 1
-search-b 1
-
-# Other Commands
-rotate-l 1
-rotate-r 1
-set-cmut 0
-mod-cmut 0
Deleted: development/support/config/misc/inst_set.28.base
===================================================================
--- development/support/config/misc/inst_set.28.base 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.28.base 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,103 +0,0 @@
-nop-A 1
-nop-B 1
-nop-C 1
-nop-X 0
-if-equ-0 0
-if-not-0 0
-if-n-equ 1
-if-equ 0
-if-grt-0 0
-if-grt 0
-if->=-0 0
-if->= 0
-if-les-0 0
-if-less 1
-if-<=-0 0
-if-<= 0
-if-A!=B 0
-if-B!=C 0
-if-A!=C 0
-if-bit-1 1
-jump-f 1
-jump-b 1
-jump-p 0
-jump-slf 0
-call 1
-return 1
-pop 1
-push 1
-swap-stk 1
-flip-stk 0
-swap 1
-swap-AB 0
-swap-BC 0
-swap-AC 0
-copy-reg 0
-set_A=B 0
-set_A=C 0
-set_B=A 0
-set_B=C 0
-set_C=A 0
-set_C=B 0
-reset 0
-pop-A 0
-pop-B 0
-pop-C 0
-push-A 0
-push-B 0
-push-C 0
-shift-r 1
-shift-l 1
-bit-1 0
-set-num 0
-inc 1
-dec 1
-zero 0
-neg 0
-square 0
-sqrt 0
-not 0
-add 1
-sub 1
-mult 0
-div 0
-mod 0
-nand 1
-nor 0
-and 0
-order 0
-xor 0
-copy 1
-read 0
-write 0
-stk-read 0
-stk-writ 0
-compare 0
-if-n-cpy 0
-allocate 1
-divide 1
-c-alloc 0
-c-divide 0
-inject 0
-get 1
-stk-get 0
-stk-load 0
-put 1
-search-f 1
-search-b 1
-mem-size 0
-rotate-l 0
-rotate-r 0
-set-cmut 0
-mod-cmut 0
-fork-th 0
-kill-th 0
-id-th 0
-repro 0
-dm-jp-f 0
-dm-jp-b 0
-dm-sch-f 0
-dm-sch-b 0
-re-jp-f 0
-re-jp-b 0
-abs-jp 0
Deleted: development/support/config/misc/inst_set.28.const
===================================================================
--- development/support/config/misc/inst_set.28.const 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.28.const 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,103 +0,0 @@
-nop-A 1
-nop-B 1
-nop-C 1
-nop-X 0
-if-equ-0 0
-if-not-0 0
-if-n-equ 1
-if-equ 0
-if-grt-0 0
-if-grt 0
-if->=-0 0
-if->= 0
-if-les-0 0
-if-less 1
-if-<=-0 0
-if-<= 0
-if-A!=B 0
-if-B!=C 0
-if-A!=C 0
-if-bit-1 1
-jump-f 1
-jump-b 1
-jump-p 0
-jump-slf 0
-call 1
-return 1
-pop 1
-push 1
-swap-stk 1
-flip-stk 0
-swap 1
-swap-AB 0
-swap-BC 0
-swap-AC 0
-copy-reg 0
-set_A=B 0
-set_A=C 0
-set_B=A 0
-set_B=C 0
-set_C=A 0
-set_C=B 0
-reset 0
-pop-A 0
-pop-B 0
-pop-C 0
-push-A 0
-push-B 0
-push-C 0
-shift-r 1
-shift-l 1
-bit-1 0
-set-num 0
-inc 1
-dec 1
-zero 0
-neg 0
-square 0
-sqrt 0
-not 0
-add 1
-sub 1
-mult 0
-div 0
-mod 0
-nand 1
-nor 0
-and 0
-order 0
-xor 0
-copy 1
-read 0
-write 0
-stk-read 0
-stk-writ 0
-compare 0
-if-n-cpy 0
-allocate 0
-divide 0
-c-alloc 1
-c-divide 1
-inject 0
-get 1
-stk-get 0
-stk-load 0
-put 1
-search-f 1
-search-b 1
-mem-size 0
-rotate-l 0
-rotate-r 0
-set-cmut 0
-mod-cmut 0
-fork-th 0
-kill-th 0
-id-th 0
-repro 0
-dm-jp-f 0
-dm-jp-b 0
-dm-sch-f 0
-dm-sch-b 0
-re-jp-f 0
-re-jp-b 0
-abs-jp 0
Deleted: development/support/config/misc/inst_set.29.base_memsize
===================================================================
--- development/support/config/misc/inst_set.29.base_memsize 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.29.base_memsize 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,103 +0,0 @@
-nop-A 1
-nop-B 1
-nop-C 1
-nop-X 0
-if-equ-0 0
-if-not-0 0
-if-n-equ 1
-if-equ 0
-if-grt-0 0
-if-grt 0
-if->=-0 0
-if->= 0
-if-les-0 0
-if-less 1
-if-<=-0 0
-if-<= 0
-if-A!=B 0
-if-B!=C 0
-if-A!=C 0
-if-bit-1 1
-jump-f 1
-jump-b 1
-jump-p 0
-jump-slf 0
-call 1
-return 1
-pop 1
-push 1
-swap-stk 1
-flip-stk 0
-swap 1
-swap-AB 0
-swap-BC 0
-swap-AC 0
-copy-reg 0
-set_A=B 0
-set_A=C 0
-set_B=A 0
-set_B=C 0
-set_C=A 0
-set_C=B 0
-reset 0
-pop-A 0
-pop-B 0
-pop-C 0
-push-A 0
-push-B 0
-push-C 0
-shift-r 1
-shift-l 1
-bit-1 0
-set-num 0
-inc 1
-dec 1
-zero 0
-neg 0
-square 0
-sqrt 0
-not 0
-add 1
-sub 1
-mult 0
-div 0
-mod 0
-nand 1
-nor 0
-and 0
-order 0
-xor 0
-copy 1
-read 0
-write 0
-stk-read 0
-stk-writ 0
-compare 0
-if-n-cpy 0
-allocate 1
-divide 1
-c-alloc 0
-c-divide 0
-inject 0
-get 1
-stk-get 0
-stk-load 0
-put 1
-search-f 1
-search-b 1
-mem-size 1
-rotate-l 0
-rotate-r 0
-set-cmut 0
-mod-cmut 0
-fork-th 0
-kill-th 0
-id-th 0
-repro 0
-dm-jp-f 0
-dm-jp-b 0
-dm-sch-f 0
-dm-sch-b 0
-re-jp-f 0
-re-jp-b 0
-abs-jp 0
Deleted: development/support/config/misc/inst_set.31.multi
===================================================================
--- development/support/config/misc/inst_set.31.multi 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.31.multi 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,103 +0,0 @@
-nop-A 1
-nop-B 1
-nop-C 1
-nop-X 0
-if-equ-0 0
-if-not-0 0
-if-n-equ 1
-if-equ 0
-if-grt-0 0
-if-grt 0
-if->=-0 0
-if->= 0
-if-les-0 0
-if-less 1
-if-<=-0 0
-if-<= 0
-if-A!=B 0
-if-B!=C 0
-if-A!=C 0
-if-bit-1 1
-jump-f 1
-jump-b 1
-jump-p 0
-jump-slf 0
-call 1
-return 1
-pop 1
-push 1
-swap-stk 1
-flip-stk 0
-swap 1
-swap-AB 0
-swap-BC 0
-swap-AC 0
-copy-reg 0
-set_A=B 0
-set_A=C 0
-set_B=A 0
-set_B=C 0
-set_C=A 0
-set_C=B 0
-reset 0
-pop-A 0
-pop-B 0
-pop-C 0
-push-A 0
-push-B 0
-push-C 0
-shift-r 1
-shift-l 1
-bit-1 0
-set-num 0
-inc 1
-dec 1
-zero 0
-neg 0
-square 0
-sqrt 0
-not 0
-add 1
-sub 1
-mult 0
-div 0
-mod 0
-nand 1
-nor 0
-and 0
-order 0
-xor 0
-copy 1
-read 0
-write 0
-stk-read 0
-stk-writ 0
-compare 0
-if-n-cpy 0
-allocate 1
-divide 1
-c-alloc 0
-c-divide 0
-inject 0
-get 1
-stk-get 0
-stk-load 0
-put 1
-search-f 1
-search-b 1
-mem-size 0
-rotate-l 0
-rotate-r 0
-set-cmut 0
-mod-cmut 0
-fork-th 1
-kill-th 1
-id-th 1
-repro 0
-dm-jp-f 0
-dm-jp-b 0
-dm-sch-f 0
-dm-sch-b 0
-re-jp-f 0
-re-jp-b 0
-abs-jp 0
Deleted: development/support/config/misc/inst_set.32.heads
===================================================================
--- development/support/config/misc/inst_set.32.heads 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.32.heads 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,110 +0,0 @@
-nop-A 1
-nop-B 1
-nop-C 1
-nop-X 0
-if-equ-0 0
-if-not-0 0
-if-n-equ 1
-if-equ 0
-if-grt-0 0
-if-grt 0
-if->=-0 0
-if->= 0
-if-les-0 0
-if-less 1
-if-<=-0 0
-if-<= 0
-if-A!=B 0
-if-B!=C 0
-if-A!=C 0
-if-bit-1 1
-jump-f 1
-jump-b 1
-jump-p 0
-jump-slf 0
-call 1
-return 1
-pop 1
-push 1
-swap-stk 1
-flip-stk 0
-swap 1
-swap-AB 0
-swap-BC 0
-swap-AC 0
-copy-reg 0
-set_A=B 0
-set_A=C 0
-set_B=A 0
-set_B=C 0
-set_C=A 0
-set_C=B 0
-reset 0
-pop-A 0
-pop-B 0
-pop-C 0
-push-A 0
-push-B 0
-push-C 0
-shift-r 1
-shift-l 1
-bit-1 0
-set-num 0
-inc 1
-dec 1
-zero 0
-neg 0
-square 0
-sqrt 0
-not 0
-add 1
-sub 1
-mult 0
-div 0
-mod 0
-nand 1
-nor 0
-and 0
-order 0
-xor 0
-copy 0
-read 0
-write 0
-stk-read 0
-stk-writ 0
-compare 0
-if-n-cpy 0
-allocate 0
-divide 0
-c-alloc 0
-c-divide 0
-inject 0
-get 1
-stk-get 0
-stk-load 0
-put 1
-search-f 1
-search-b 1
-mem-size 0
-rotate-l 0
-rotate-r 0
-set-cmut 0
-mod-cmut 0
-fork-th 0
-kill-th 0
-id-th 0
-repro 0
-dm-jp-f 0
-dm-jp-b 0
-dm-sch-f 0
-dm-sch-b 0
-re-jp-f 0
-re-jp-b 0
-abs-jp 0
-set-head 1
-adv-head 1
-if-label 1
-h-alloc 1
-h-divide 1
-h-read 1
-h-write 1
Deleted: development/support/config/misc/inst_set.heads.parasite
===================================================================
--- development/support/config/misc/inst_set.heads.parasite 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/inst_set.heads.parasite 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,54 +0,0 @@
-nop-A 1
-nop-B 1
-nop-C 1
-if-n-equ 1
-if-less 1
-pop 1
-push 1
-swap-stk 1
-swap 1
-shift-r 1
-shift-l 1
-inc 1
-dec 1
-add 1
-sub 1
-nand 1
-h-alloc 1
-h-divide 1
-IO 1 # Puts current contents of register and gets new.
-h-copy 1 # Combine h-read and h-write
-h-search 1 ### Search for matching template, set flow head, & return info.
- ## If no template, move flow-head here, set size&offset=0.
-mov-head 1 ### Move ?IP? head to flow control
-jmp-head 1 ### Move ?IP? head by fixed amount in CX
-#get-head 1 ### Get position of specified head in CX.
-set-flow 1 ### Move flow-head to address in ?CX?
-
-h-push 1
-h-pop 1
-
-if-label 1
-
-#inject-r 1
-inject 1
-rotate-l 1
-rotate-r 1
-
-#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
-
Copied: development/support/config/misc/instset-heads-30-parasite.cfg (from rev 3431, development/support/config/misc/inst_set.heads.parasite)
===================================================================
--- development/support/config/misc/instset-heads-30-parasite.cfg (rev 0)
+++ development/support/config/misc/instset-heads-30-parasite.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,43 @@
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-n-equ 1
+if-less 1
+if-label 1
+mov-head 1
+jmp-head 1
+set-flow 1
+h-push 1
+h-pop 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+swap-stk 1
+swap 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+h-copy 1
+h-alloc 1
+h-divide 1
+
+# I/O and Sensory
+IO 1
+h-search 1
+rotate-l 1
+rotate-r 1
+
+# Parasite Operations
+inject 1
Copied: development/support/config/misc/instset-heads-32-oldsearch.cfg (from rev 3431, development/support/config/misc/inst_set.32.heads)
===================================================================
--- development/support/config/misc/instset-heads-32-oldsearch.cfg (rev 0)
+++ development/support/config/misc/instset-heads-32-oldsearch.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,44 @@
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-n-equ 1
+if-less 1
+if-label 1
+if-bit-1 1
+jump-f 1
+jump-b 1
+call 1
+return 1
+set-head 1
+adv-head 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+swap-stk 1
+swap 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+h-read 1
+h-write 1
+h-alloc 1
+h-divide 1
+
+# I/O and Sensory
+get 1
+put 1
+search-f 1
+search-b 1
+
Copied: development/support/config/misc/instset-no-heads-19-short.cfg (from rev 3430, development/support/config/misc/inst_set.19.short)
===================================================================
--- development/support/config/misc/instset-no-heads-19-short.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-19-short.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,30 @@
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-less 1
+jump-slf 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+push 1
+pop 1
+inc 1
+dec 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+allocate 1
+divide 1
+
+# I/O and Sensory
+get 1
+put 1
Copied: development/support/config/misc/instset-no-heads-24.cfg (from rev 3431, development/support/config/misc/inst_set.24.old)
===================================================================
--- development/support/config/misc/instset-no-heads-24.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-24.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,35 @@
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-n-equ 1
+jump-f 1
+jump-b 1
+call 1
+return 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+allocate 1
+divide 1
+
+# I/O and Sensory
+get 1
+put 1
+search-f 1
+search-b 1
Copied: development/support/config/misc/instset-no-heads-27-no-nops.cfg (from rev 3431, development/support/config/misc/inst_set.27.no-nop)
===================================================================
--- development/support/config/misc/instset-no-heads-27-no-nops.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-27-no-nops.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,36 @@
+# Flow control operations
+if-n-equ 1
+if-less 1
+if-bit-1 1
+jump-f 1
+jump-b 1
+call 1
+return 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+pop-A 1
+pop-B 1
+pop-C 1
+push-A 1
+push-B 1
+push-C 1
+swap-stk 1
+swap 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+allocate 1
+divide 1
+
+# I/O and Sensory
+get 1
+put 1
Copied: development/support/config/misc/instset-no-heads-27-parasite-no-inject.cfg (from rev 3431, development/support/config/misc/inst_set.27.parasite)
===================================================================
--- development/support/config/misc/instset-no-heads-27-parasite-no-inject.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-27-parasite-no-inject.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,40 @@
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-n-equ 1
+jump-f 1
+jump-b 1
+jump-p 1
+call 1
+return 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+allocate 1
+divide 1
+
+# I/O and Sensory
+get 1
+put 1
+search-f 1
+search-b 1
+
+# Other Commands
+rotate-l 1
+rotate-r 1
Copied: development/support/config/misc/instset-no-heads-28-base.cfg (from rev 3431, development/support/config/misc/inst_set.28.base)
===================================================================
--- development/support/config/misc/instset-no-heads-28-base.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-28-base.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,39 @@
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-n-equ 1
+if-less 1
+if-bit-1 1
+jump-f 1
+jump-b 1
+call 1
+return 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+swap-stk 1
+swap 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+allocate 1
+divide 1
+
+# I/O and Sensory
+get 1
+put 1
+search-f 1
+search-b 1
Copied: development/support/config/misc/instset-no-heads-28-const.cfg (from rev 3431, development/support/config/misc/inst_set.28.const)
===================================================================
--- development/support/config/misc/instset-no-heads-28-const.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-28-const.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,39 @@
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-n-equ 1
+if-less 1
+if-bit-1 1
+jump-f 1
+jump-b 1
+call 1
+return 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+swap-stk 1
+swap 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+c-alloc 1
+c-divide 1
+
+# I/O and Sensory
+get 1
+put 1
+search-f 1
+search-b 1
Copied: development/support/config/misc/instset-no-heads-29-memsize.cfg (from rev 3431, development/support/config/misc/inst_set.29.base_memsize)
===================================================================
--- development/support/config/misc/instset-no-heads-29-memsize.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-29-memsize.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,40 @@
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-n-equ 1
+if-less 1
+if-bit-1 1
+jump-f 1
+jump-b 1
+call 1
+return 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+swap-stk 1
+swap 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+allocate 1
+divide 1
+
+# I/O and Sensory
+get 1
+put 1
+search-f 1
+search-b 1
+mem-size 1
Copied: development/support/config/misc/instset-no-heads-29-multithreaded.cfg (from rev 3431, development/support/config/misc/inst_set.27.multi)
===================================================================
--- development/support/config/misc/instset-no-heads-29-multithreaded.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-29-multithreaded.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,43 @@
+# This instruction set is the same as no-heads-24, but adds three instructions for working with multiple threads
+
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+# Flow control operations
+if-n-equ 1
+if-less 1
+jump-f 1
+jump-b 1
+call 1
+return 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+swap-stk 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+allocate 1
+divide 1
+fork-th 1
+kill-th 1
+id-th 1
+
+# I/O and Sensory
+get 1
+put 1
+search-f 1
+search-b 1
+
Copied: development/support/config/misc/instset-no-heads-31-multithreaded.cfg (from rev 3431, development/support/config/misc/inst_set.31.multi)
===================================================================
--- development/support/config/misc/instset-no-heads-31-multithreaded.cfg (rev 0)
+++ development/support/config/misc/instset-no-heads-31-multithreaded.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,44 @@
+
+# No-ops
+nop-A 1
+nop-B 1
+nop-C 1
+
+
+# Flow control operations
+if-n-equ 1
+if-less 1
+if-bit-1 1
+jump-f 1
+jump-b 1
+call 1
+return 1
+
+# Single Argument Math
+shift-r 1
+shift-l 1
+inc 1
+dec 1
+push 1
+pop 1
+swap-stk 1
+swap 1
+
+# Double Argument Math
+add 1
+sub 1
+nand 1
+
+# Biological Operations
+copy 1
+allocate 1
+divide 1
+fork-th 1
+kill-th 1
+id-th 1
+
+# I/O and Sensory
+get 1
+put 1
+search-f 1
+search-b 1
Copied: development/support/config/misc/organism-heads-100.org (from rev 3431, development/support/config/misc/organism.heads.100)
===================================================================
--- development/support/config/misc/organism-heads-100.org (rev 0)
+++ development/support/config/misc/organism-heads-100.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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 #
Copied: development/support/config/misc/organism-heads-15-template.org (from rev 3431, development/support/config/misc/template-classic.org)
===================================================================
--- development/support/config/misc/organism-heads-15-template.org (rev 0)
+++ development/support/config/misc/organism-heads-15-template.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,18 @@
+# --- Setup ---
+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 #
+
+# --- Copy Loop ---
+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 # End label.
Copied: development/support/config/misc/organism-heads-50.org (from rev 3431, development/support/config/misc/organism.heads.50)
===================================================================
--- development/support/config/misc/organism-heads-50.org (rev 0)
+++ development/support/config/misc/organism-heads-50.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,53 @@
+# --- Setup ---
+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 #
+
+# --- Copy Loop ---
+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 #
Copied: development/support/config/misc/organism-heads-multi-birth.org (from rev 3431, development/support/config/misc/organism.multi-birth)
===================================================================
--- development/support/config/misc/organism-heads-multi-birth.org (rev 0)
+++ development/support/config/misc/organism-heads-multi-birth.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,103 @@
+# This organism will function under a DIVIDE_METHOD of 0 where it does not
+# get reset to initial conditions on divide.
+
+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 #
+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-search # Move flow head to divide routine...
+nop-A # Divide represented by single nop-B
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A #
+nop-C #
+nop-B # Start of divide routine
+h-divide # ...divide!
+nop-A # End label.
+nop-B #
Copied: development/support/config/misc/organism-heads-parasite-host.org (from rev 3431, development/support/config/misc/organism.host)
===================================================================
--- development/support/config/misc/organism-heads-parasite-host.org (rev 0)
+++ development/support/config/misc/organism-heads-parasite-host.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,65 @@
+# --- Setup ---
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+nop-B #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+
+# --- Not-so-Quick Tasks ---
+h-search # Mark beginning of task loop
+push # Push AX onto the stack to save it.
+nop-A
+swap-stk
+
+IO # Random stuff that might help in doing tasks...
+pop
+nop-C
+nand
+swap
+push
+IO
+swap
+nop-A
+pop
+nand
+push
+nop-C
+
+swap-stk # Restore AX and set BX to 0
+pop
+nop-A
+pop
+
+dec # Decriment AX. If it becomes zero, stop!
+nop-A
+if-n-equ
+nop-A
+mov-head
+
+# --- Copy Loop ---
+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 #
+nop-B #
+
+h-search # Set the next move to jump to the divide module...
+nop-C #
+nop-C #
+nop-C #
+
+mov-head # Jump to our "proper" destination.
+
+# --- Divide Module ---
+nop-A # Beginning marker
+nop-A #
+nop-A #
+h-divide # ...divide!
+
+nop-A # End label.
+nop-B #
+nop-C #
Copied: development/support/config/misc/organism-heads-parasite-host2.org (from rev 3431, development/support/config/misc/organism.host2)
===================================================================
--- development/support/config/misc/organism-heads-parasite-host2.org (rev 0)
+++ development/support/config/misc/organism-heads-parasite-host2.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,66 @@
+# --- Setup ---
+h-alloc # 1: Allocate space for child
+h-search # 2: Locate the end of the organism
+nop-C # 3:
+nop-A # 4:
+mov-head # 5: Place write-head at beginning of offspring.
+nop-C # 6:
+h-search # 7: Find the beginning of the copy loop.
+nop-A # 8:
+nop-A # 9:
+h-push # 10: Save the location of the current IP; move it to the flow head.
+
+# --- Post Copy ---
+IO # 11: Pull an input into BX
+IO # 12: Pull an input into CX
+nop-C # 13:
+
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+nop-C # FILLER
+
+
+nand # 14: Nand the two inputs together...
+IO # 15: ...and output the result.
+h-divide # 16: Finally divide!
+h-pop # 17: Jump back to the beginning of genome (pop 0 off stack...)
+
+# --- Copy Loop ---
+nop-B # 18: Mark the beginning of the copy loop.
+nop-B # 19:
+h-copy # 20: Do the copy
+if-label # 21: If we're done copying....
+nop-C # 22:
+nop-A # 23:
+h-pop # 24: ...jump out of the copy loop.
+mov-head # 25: Otherwise, loop back to the beginning of the copy loop.
+
+nop-A # 26: End label.
+nop-B # 27: End label.
Copied: development/support/config/misc/organism-heads-parasite-infected.org (from rev 3431, development/support/config/misc/organism.infected)
===================================================================
--- development/support/config/misc/organism-heads-parasite-infected.org (rev 0)
+++ development/support/config/misc/organism-heads-parasite-infected.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,127 @@
+# --- Setup ---
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+nop-B #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+
+# --- Not-so-Quick Tasks ---
+h-search # Mark beginning of task loop
+push # Push AX onto the stack to save it.
+nop-A
+swap-stk
+
+IO # Random stuff that might help in doing tasks...
+pop
+nop-C
+nand
+swap
+push
+IO
+swap
+nop-A
+pop
+nand
+push
+nop-C
+
+swap-stk # Restore AX and set BX to 0
+pop
+nop-A
+pop
+
+dec # Decriment BX. If it becomes zero, stop!
+nop-A
+if-n-equ
+nop-A
+mov-head
+
+# --- Copy Loop ---
+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 #
+nop-B #
+
+h-search # Set the next move to jump to the divide module...
+nop-C #
+nop-C #
+nop-C #
+
+mov-head # Jump to our "proper" destination.
+
+# --- Divide Module ---
+nop-A # Beginning marker
+nop-A #
+nop-A #
+
+#---- Infection --------------------------------------------------------
+
+nop-C # Extend template so other infections can't get in here
+h-search # Mark the beginning of the infection
+
+## Save the positions of the read/write heads so divide works later ##
+h-push # Back up the read head
+nop-B
+h-push # Back up the write head twice
+nop-C
+h-push # (second one for putting read head here later...)
+nop-C
+
+## Move the read head to the beginning of the infection... ##
+mov-head # Move the read head to the h-search above...
+nop-B
+dec # Decrement BX to -1
+dec # Decrement BX to -2
+swap # Put the -2 into CX
+jmp-head # Move read head back to "correct" begining of infection
+nop-B
+
+## Infection copy loop... ##
+h-search # Mark the beginning of the copy loop
+h-copy # Do the copy
+if-label # If we're done copying....
+nop-C #
+nop-C #
+h-search # ... reset the jump point to after the loop
+nop-C
+nop-B
+nop-B
+mov-head # Jump! (either back, or past...)
+nop-A # Copy loop end label
+nop-C #
+nop-C #
+
+## Setup and perform injection ##
+h-pop # Move read head to beginning of copy...
+nop-B
+rotate-r # Find a good host
+nop-C
+nop-C
+nop-C
+inject # Inject!!!
+nop-C
+nop-C
+nop-C
+
+## Restore state for host ##
+h-pop # Restore the write head...
+nop-C
+h-pop # Restore the read head...
+nop-B
+IO # Template divider...
+nop-A # End template of infection
+nop-A
+#---- End Infection ----------------------------------------------------
+
+
+# --- Real Divide
+h-divide # ...divide!
+
+nop-A # End label.
+nop-B #
+nop-C #
Copied: development/support/config/misc/organism-heads-parasite-infected2.org (from rev 3431, development/support/config/misc/organism.infected2)
===================================================================
--- development/support/config/misc/organism-heads-parasite-infected2.org (rev 0)
+++ development/support/config/misc/organism-heads-parasite-infected2.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,72 @@
+# --- Setup ---
+h-alloc # 1: Allocate space for child
+h-search # 2: Locate the end of the organism
+nop-C # 3:
+nop-A # 4:
+
+# --- Infection ---
+
+nop-C # I 1: ???Extend the template we targeted...
+mov-head # I 2: Place the write-head at the beginning of new infection
+nop-C # I 3:
+h-search # I 4: Find the beginning of the infection...
+nop-B # I 5: ...match the C:A before infection
+nop-C # I 6:
+mov-head # I 7: Place read-head at beginning of infection
+nop-B # I 8:
+h-search # I 9: Find the beginning of the copy loop
+nop-A # I10:
+nop-A # I11:
+h-push # I12: Save location of the current IP; move it to copy loop.
+
+h-search # I13: Fix placement of read head
+nop-C # I14:
+nop-A # I15:
+nop-C # I16:
+mov-head # I17:
+nop-B # I18:
+
+#inject-r # I19: We're done! Inject...
+rotate-r
+nop-B
+nop-C
+inject
+
+nop-B # I20: ... lock onto C:A template at beginning of host.
+nop-C # I21:
+h-pop # I22: Jump back to the beginning of the host.
+
+nop-A # I23: Infection end template
+nop-B # I24:
+
+# --- Host Setup Continued...
+mov-head # 5: Place write-head at beginning of offspring.
+nop-C # 6:
+h-search # 7: Find the beginning of the copy loop.
+nop-A # 8:
+nop-A # 9:
+h-push # 10: Save the location of the current IP; move it to the flow head.
+
+# --- Post Copy ---
+IO # 11: Pull an input into BX
+IO # 12: Pull an input into CX
+nop-C # 13:
+nand # 14: Nand the two inputs together...
+IO # 15: ...and output the result.
+h-divide # 16: Finally divide!
+h-pop # 17: Jump back to the beginning of genome (pop 0 off stack...)
+
+# --- Copy Loop ---
+nop-B # 18: Mark the beginning of the copy loop.
+nop-B # 19:
+h-copy # 20: Do the copy
+if-label # 21: If we're done copying....
+nop-C # 22:
+nop-A # 23:
+h-pop # 24: ...jump out of the copy loop.
+mov-head # 25: Otherwise, loop back to the beginning of the copy loop.
+
+nop-A # 26: End label.
+nop-B # 27: End label.
+
+
Copied: development/support/config/misc/organism-no-heads.org (from rev 3431, development/support/config/misc/organism.noheads)
===================================================================
--- development/support/config/misc/organism-no-heads.org (rev 0)
+++ development/support/config/misc/organism-no-heads.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,20 @@
+search-f # calc Size
+nop-A
+nop-A
+add
+inc
+allocate
+push # Move size into CX and clear BX
+nop-B
+pop
+nop-C
+sub
+nop-B # Copy Loop
+copy
+inc
+if-n-equ
+jump-b
+nop-A
+divide # And divide...
+nop-B
+nop-B
Deleted: development/support/config/misc/organism.heads.100
===================================================================
--- development/support/config/misc/organism.heads.100 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.heads.100 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,100 +0,0 @@
-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 #
Deleted: development/support/config/misc/organism.heads.15
===================================================================
--- development/support/config/misc/organism.heads.15 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.heads.15 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,18 +0,0 @@
-# --- Setup ---
-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 #
-
-# --- Copy Loop ---
-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 # End label.
Deleted: development/support/config/misc/organism.heads.50
===================================================================
--- development/support/config/misc/organism.heads.50 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.heads.50 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,53 +0,0 @@
-# --- Setup ---
-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 #
-
-# --- Copy Loop ---
-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 #
Deleted: development/support/config/misc/organism.host
===================================================================
--- development/support/config/misc/organism.host 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.host 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,65 +0,0 @@
-# --- Setup ---
-h-alloc # Allocate space for child
-h-search # Locate the end of the organism
-nop-C #
-nop-A #
-nop-B #
-mov-head # Place write-head at beginning of offspring.
-nop-C #
-
-# --- Not-so-Quick Tasks ---
-h-search # Mark beginning of task loop
-push # Push AX onto the stack to save it.
-nop-A
-swap-stk
-
-IO # Random stuff that might help in doing tasks...
-pop
-nop-C
-nand
-swap
-push
-IO
-swap
-nop-A
-pop
-nand
-push
-nop-C
-
-swap-stk # Restore AX and set BX to 0
-pop
-nop-A
-pop
-
-dec # Decriment AX. If it becomes zero, stop!
-nop-A
-if-n-equ
-nop-A
-mov-head
-
-# --- Copy Loop ---
-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 #
-nop-B #
-
-h-search # Set the next move to jump to the divide module...
-nop-C #
-nop-C #
-nop-C #
-
-mov-head # Jump to our "proper" destination.
-
-# --- Divide Module ---
-nop-A # Beginning marker
-nop-A #
-nop-A #
-h-divide # ...divide!
-
-nop-A # End label.
-nop-B #
-nop-C #
Deleted: development/support/config/misc/organism.host2
===================================================================
--- development/support/config/misc/organism.host2 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.host2 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,66 +0,0 @@
-# --- Setup ---
-h-alloc # 1: Allocate space for child
-h-search # 2: Locate the end of the organism
-nop-C # 3:
-nop-A # 4:
-mov-head # 5: Place write-head at beginning of offspring.
-nop-C # 6:
-h-search # 7: Find the beginning of the copy loop.
-nop-A # 8:
-nop-A # 9:
-h-push # 10: Save the location of the current IP; move it to the flow head.
-
-# --- Post Copy ---
-IO # 11: Pull an input into BX
-IO # 12: Pull an input into CX
-nop-C # 13:
-
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-nop-C # FILLER
-
-
-nand # 14: Nand the two inputs together...
-IO # 15: ...and output the result.
-h-divide # 16: Finally divide!
-h-pop # 17: Jump back to the beginning of genome (pop 0 off stack...)
-
-# --- Copy Loop ---
-nop-B # 18: Mark the beginning of the copy loop.
-nop-B # 19:
-h-copy # 20: Do the copy
-if-label # 21: If we're done copying....
-nop-C # 22:
-nop-A # 23:
-h-pop # 24: ...jump out of the copy loop.
-mov-head # 25: Otherwise, loop back to the beginning of the copy loop.
-
-nop-A # 26: End label.
-nop-B # 27: End label.
Deleted: development/support/config/misc/organism.infected
===================================================================
--- development/support/config/misc/organism.infected 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.infected 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,127 +0,0 @@
-# --- Setup ---
-h-alloc # Allocate space for child
-h-search # Locate the end of the organism
-nop-C #
-nop-A #
-nop-B #
-mov-head # Place write-head at beginning of offspring.
-nop-C #
-
-# --- Not-so-Quick Tasks ---
-h-search # Mark beginning of task loop
-push # Push AX onto the stack to save it.
-nop-A
-swap-stk
-
-IO # Random stuff that might help in doing tasks...
-pop
-nop-C
-nand
-swap
-push
-IO
-swap
-nop-A
-pop
-nand
-push
-nop-C
-
-swap-stk # Restore AX and set BX to 0
-pop
-nop-A
-pop
-
-dec # Decriment BX. If it becomes zero, stop!
-nop-A
-if-n-equ
-nop-A
-mov-head
-
-# --- Copy Loop ---
-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 #
-nop-B #
-
-h-search # Set the next move to jump to the divide module...
-nop-C #
-nop-C #
-nop-C #
-
-mov-head # Jump to our "proper" destination.
-
-# --- Divide Module ---
-nop-A # Beginning marker
-nop-A #
-nop-A #
-
-#---- Infection --------------------------------------------------------
-
-nop-C # Extend template so other infections can't get in here
-h-search # Mark the beginning of the infection
-
-## Save the positions of the read/write heads so divide works later ##
-h-push # Back up the read head
-nop-B
-h-push # Back up the write head twice
-nop-C
-h-push # (second one for putting read head here later...)
-nop-C
-
-## Move the read head to the beginning of the infection... ##
-mov-head # Move the read head to the h-search above...
-nop-B
-dec # Decrement BX to -1
-dec # Decrement BX to -2
-swap # Put the -2 into CX
-jmp-head # Move read head back to "correct" begining of infection
-nop-B
-
-## Infection copy loop... ##
-h-search # Mark the beginning of the copy loop
-h-copy # Do the copy
-if-label # If we're done copying....
-nop-C #
-nop-C #
-h-search # ... reset the jump point to after the loop
-nop-C
-nop-B
-nop-B
-mov-head # Jump! (either back, or past...)
-nop-A # Copy loop end label
-nop-C #
-nop-C #
-
-## Setup and perform injection ##
-h-pop # Move read head to beginning of copy...
-nop-B
-rotate-r # Find a good host
-nop-C
-nop-C
-nop-C
-inject # Inject!!!
-nop-C
-nop-C
-nop-C
-
-## Restore state for host ##
-h-pop # Restore the write head...
-nop-C
-h-pop # Restore the read head...
-nop-B
-IO # Template divider...
-nop-A # End template of infection
-nop-A
-#---- End Infection ----------------------------------------------------
-
-
-# --- Real Divide
-h-divide # ...divide!
-
-nop-A # End label.
-nop-B #
-nop-C #
Deleted: development/support/config/misc/organism.infected2
===================================================================
--- development/support/config/misc/organism.infected2 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.infected2 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,72 +0,0 @@
-# --- Setup ---
-h-alloc # 1: Allocate space for child
-h-search # 2: Locate the end of the organism
-nop-C # 3:
-nop-A # 4:
-
-# --- Infection ---
-
-nop-C # I 1: ???Extend the template we targeted...
-mov-head # I 2: Place the write-head at the beginning of new infection
-nop-C # I 3:
-h-search # I 4: Find the beginning of the infection...
-nop-B # I 5: ...match the C:A before infection
-nop-C # I 6:
-mov-head # I 7: Place read-head at beginning of infection
-nop-B # I 8:
-h-search # I 9: Find the beginning of the copy loop
-nop-A # I10:
-nop-A # I11:
-h-push # I12: Save location of the current IP; move it to copy loop.
-
-h-search # I13: Fix placement of read head
-nop-C # I14:
-nop-A # I15:
-nop-C # I16:
-mov-head # I17:
-nop-B # I18:
-
-#inject-r # I19: We're done! Inject...
-rotate-r
-nop-B
-nop-C
-inject
-
-nop-B # I20: ... lock onto C:A template at beginning of host.
-nop-C # I21:
-h-pop # I22: Jump back to the beginning of the host.
-
-nop-A # I23: Infection end template
-nop-B # I24:
-
-# --- Host Setup Continued...
-mov-head # 5: Place write-head at beginning of offspring.
-nop-C # 6:
-h-search # 7: Find the beginning of the copy loop.
-nop-A # 8:
-nop-A # 9:
-h-push # 10: Save the location of the current IP; move it to the flow head.
-
-# --- Post Copy ---
-IO # 11: Pull an input into BX
-IO # 12: Pull an input into CX
-nop-C # 13:
-nand # 14: Nand the two inputs together...
-IO # 15: ...and output the result.
-h-divide # 16: Finally divide!
-h-pop # 17: Jump back to the beginning of genome (pop 0 off stack...)
-
-# --- Copy Loop ---
-nop-B # 18: Mark the beginning of the copy loop.
-nop-B # 19:
-h-copy # 20: Do the copy
-if-label # 21: If we're done copying....
-nop-C # 22:
-nop-A # 23:
-h-pop # 24: ...jump out of the copy loop.
-mov-head # 25: Otherwise, loop back to the beginning of the copy loop.
-
-nop-A # 26: End label.
-nop-B # 27: End label.
-
-
Deleted: development/support/config/misc/organism.multi-birth
===================================================================
--- development/support/config/misc/organism.multi-birth 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.multi-birth 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,103 +0,0 @@
-# This organism will function under a DIVIDE_METHOD of 0 where it does not
-# get reset to initial conditions on divide.
-
-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 #
-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-search # Move flow head to divide routine...
-nop-A # Divide represented by single nop-B
-mov-head # Otherwise, loop back to the beginning of the copy loop.
-nop-A #
-nop-C #
-nop-B # Start of divide routine
-h-divide # ...divide!
-nop-A # End label.
-nop-B #
Deleted: development/support/config/misc/organism.noheads
===================================================================
--- development/support/config/misc/organism.noheads 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/organism.noheads 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,20 +0,0 @@
-search-f # calc Size
-nop-A
-nop-A
-add
-inc
-allocate
-push # Move size into CX and clear BX
-nop-B
-pop
-nop-C
-sub
-nop-B # Copy Loop
-copy
-inc
-if-n-equ
-jump-b
-nop-A
-divide # And divide...
-nop-B
-nop-B
Deleted: development/support/config/misc/template-classic.org
===================================================================
--- development/support/config/misc/template-classic.org 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/support/config/misc/template-classic.org 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,18 +0,0 @@
-# --- Setup ---
-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 #
-
-# --- Copy Loop ---
-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 # End label.
Deleted: development/tests/analyze_dumplandscape/config/instset-classic.cfg
===================================================================
--- development/tests/analyze_dumplandscape/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/analyze_dumplandscape/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/tests/analyze_dumplandscape/config/instset-heads.cfg (from rev 3432, development/tests/analyze_dumplandscape/config/instset-classic.cfg)
===================================================================
--- development/tests/analyze_dumplandscape/config/instset-heads.cfg (rev 0)
+++ development/tests/analyze_dumplandscape/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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
Deleted: development/tests/analyze_fulllandscape_1step/config/instset-classic.cfg
===================================================================
--- development/tests/analyze_fulllandscape_1step/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/analyze_fulllandscape_1step/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/tests/analyze_fulllandscape_1step/config/instset-heads.cfg (from rev 3432, development/tests/analyze_fulllandscape_1step/config/instset-classic.cfg)
===================================================================
--- development/tests/analyze_fulllandscape_1step/config/instset-heads.cfg (rev 0)
+++ development/tests/analyze_fulllandscape_1step/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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
Deleted: development/tests/analyze_fulllandscape_2step/config/instset-classic.cfg
===================================================================
--- development/tests/analyze_fulllandscape_2step/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/analyze_fulllandscape_2step/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/tests/analyze_fulllandscape_2step/config/instset-heads.cfg (from rev 3432, development/tests/analyze_fulllandscape_2step/config/instset-classic.cfg)
===================================================================
--- development/tests/analyze_fulllandscape_2step/config/instset-heads.cfg (rev 0)
+++ development/tests/analyze_fulllandscape_2step/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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
Deleted: development/tests/analyze_truncate_lineage/config/instset-classic.cfg
===================================================================
--- development/tests/analyze_truncate_lineage/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/analyze_truncate_lineage/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/tests/analyze_truncate_lineage/config/instset-heads.cfg (from rev 3432, development/tests/analyze_truncate_lineage/config/instset-classic.cfg)
===================================================================
--- development/tests/analyze_truncate_lineage/config/instset-heads.cfg (rev 0)
+++ development/tests/analyze_truncate_lineage/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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
Deleted: development/tests/analyze_truncate_lineage_fulllandscape/config/instset-classic.cfg
===================================================================
--- development/tests/analyze_truncate_lineage_fulllandscape/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/analyze_truncate_lineage_fulllandscape/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/tests/analyze_truncate_lineage_fulllandscape/config/instset-heads.cfg (from rev 3432, development/tests/analyze_truncate_lineage_fulllandscape/config/instset-classic.cfg)
===================================================================
--- development/tests/analyze_truncate_lineage_fulllandscape/config/instset-heads.cfg (rev 0)
+++ development/tests/analyze_truncate_lineage_fulllandscape/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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
Deleted: development/tests/avida_GA_lim_res/config/instset-classic.cfg
===================================================================
--- development/tests/avida_GA_lim_res/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/avida_GA_lim_res/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,3 +0,0 @@
-IObuf-add0 1 #a
-IObuf-add1 1 #b
-repro 0 #c
Copied: development/tests/avida_GA_lim_res/config/instset-heads.cfg (from rev 3432, development/tests/avida_GA_lim_res/config/instset-classic.cfg)
===================================================================
--- development/tests/avida_GA_lim_res/config/instset-heads.cfg (rev 0)
+++ development/tests/avida_GA_lim_res/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,3 @@
+IObuf-add0 1 #a
+IObuf-add1 1 #b
+repro 0 #c
Deleted: development/tests/avida_GA_sex/config/instset-classic.cfg
===================================================================
--- development/tests/avida_GA_sex/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/avida_GA_sex/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,4 +0,0 @@
-IObuf-add0 1 #a
-IObuf-add1 1 #b
-repro-sex 0 #c
-repro 0 #d
\ No newline at end of file
Copied: development/tests/avida_GA_sex/config/instset-heads.cfg (from rev 3432, development/tests/avida_GA_sex/config/instset-classic.cfg)
===================================================================
--- development/tests/avida_GA_sex/config/instset-heads.cfg (rev 0)
+++ development/tests/avida_GA_sex/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,4 @@
+IObuf-add0 1 #a
+IObuf-add1 1 #b
+repro-sex 0 #c
+repro 0 #d
\ No newline at end of file
Deleted: development/tests/default_classic_500u/config/instset-classic.cfg
===================================================================
--- development/tests/default_classic_500u/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/default_classic_500u/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,28 +0,0 @@
-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?
-
Copied: development/tests/default_classic_500u/config/instset-heads.cfg (from rev 3432, development/tests/default_classic_500u/config/instset-classic.cfg)
===================================================================
--- development/tests/default_classic_500u/config/instset-heads.cfg (rev 0)
+++ development/tests/default_classic_500u/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,28 @@
+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?
+
Deleted: development/tests/demes_germline/config/instset-classic.cfg
===================================================================
--- development/tests/demes_germline/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/demes_germline/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,28 +0,0 @@
-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?
-
Copied: development/tests/demes_germline/config/instset-heads.cfg (from rev 3432, development/tests/demes_germline/config/instset-classic.cfg)
===================================================================
--- development/tests/demes_germline/config/instset-heads.cfg (rev 0)
+++ development/tests/demes_germline/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,28 @@
+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?
+
Deleted: development/tests/demes_grid_repl/config/instset-classic.cfg
===================================================================
--- development/tests/demes_grid_repl/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/demes_grid_repl/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,28 +0,0 @@
-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?
-
Copied: development/tests/demes_grid_repl/config/instset-heads.cfg (from rev 3432, development/tests/demes_grid_repl/config/instset-classic.cfg)
===================================================================
--- development/tests/demes_grid_repl/config/instset-heads.cfg (rev 0)
+++ development/tests/demes_grid_repl/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,28 @@
+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?
+
Deleted: development/tests/demes_torus_repl/config/instset-classic.cfg
===================================================================
--- development/tests/demes_torus_repl/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/demes_torus_repl/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,28 +0,0 @@
-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?
-
Copied: development/tests/demes_torus_repl/config/instset-heads.cfg (from rev 3432, development/tests/demes_torus_repl/config/instset-classic.cfg)
===================================================================
--- development/tests/demes_torus_repl/config/instset-heads.cfg (rev 0)
+++ development/tests/demes_torus_repl/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,28 @@
+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?
+
Deleted: development/tests/midrun_classic_30u/config/instset-classic.cfg
===================================================================
--- development/tests/midrun_classic_30u/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/midrun_classic_30u/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,28 +0,0 @@
-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?
-
Copied: development/tests/midrun_classic_30u/config/instset-heads.cfg (from rev 3432, development/tests/midrun_classic_30u/config/instset-classic.cfg)
===================================================================
--- development/tests/midrun_classic_30u/config/instset-heads.cfg (rev 0)
+++ development/tests/midrun_classic_30u/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,28 @@
+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?
+
Deleted: development/tests/optimize_multivar_lim_res/config/instset-classic.cfg
===================================================================
--- development/tests/optimize_multivar_lim_res/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/optimize_multivar_lim_res/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,3 +0,0 @@
-IObuf-add0 1 #a
-IObuf-add1 1 #b
-repro 0 #c
Copied: development/tests/optimize_multivar_lim_res/config/instset-heads.cfg (from rev 3432, development/tests/optimize_multivar_lim_res/config/instset-classic.cfg)
===================================================================
--- development/tests/optimize_multivar_lim_res/config/instset-heads.cfg (rev 0)
+++ development/tests/optimize_multivar_lim_res/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,3 @@
+IObuf-add0 1 #a
+IObuf-add1 1 #b
+repro 0 #c
Deleted: development/tests/reaction_ordering/config/instset-classic.cfg
===================================================================
--- development/tests/reaction_ordering/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/reaction_ordering/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/tests/reaction_ordering/config/instset-heads.cfg (from rev 3432, development/tests/reaction_ordering/config/instset-classic.cfg)
===================================================================
--- development/tests/reaction_ordering/config/instset-heads.cfg (rev 0)
+++ development/tests/reaction_ordering/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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
Deleted: development/tests/resources_9r/config/instset-classic.cfg
===================================================================
--- development/tests/resources_9r/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/resources_9r/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/tests/resources_9r/config/instset-heads.cfg (from rev 3432, development/tests/resources_9r/config/instset-classic.cfg)
===================================================================
--- development/tests/resources_9r/config/instset-heads.cfg (rev 0)
+++ development/tests/resources_9r/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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
Deleted: development/tests/spatial_res_100u/config/instset-classic.cfg
===================================================================
--- development/tests/spatial_res_100u/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/spatial_res_100u/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,28 +0,0 @@
-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?
-
Copied: development/tests/spatial_res_100u/config/instset-heads.cfg (from rev 3432, development/tests/spatial_res_100u/config/instset-classic.cfg)
===================================================================
--- development/tests/spatial_res_100u/config/instset-heads.cfg (rev 0)
+++ development/tests/spatial_res_100u/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -0,0 +1,28 @@
+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?
+
Deleted: development/tests/task_sort_analyze/config/instset-classic.cfg
===================================================================
--- development/tests/task_sort_analyze/config/instset-classic.cfg 2009-09-30 14:37:46 UTC (rev 3432)
+++ development/tests/task_sort_analyze/config/instset-classic.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -1,52 +0,0 @@
-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
Copied: development/tests/task_sort_analyze/config/instset-heads.cfg (from rev 3432, development/tests/task_sort_analyze/config/instset-classic.cfg)
===================================================================
--- development/tests/task_sort_analyze/config/instset-heads.cfg (rev 0)
+++ development/tests/task_sort_analyze/config/instset-heads.cfg 2009-09-30 15:34:39 UTC (rev 3433)
@@ -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
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