[Avida-SVN] r1511 - in development: Avida.xcodeproj source/main source/tools tests tests/demes_hex_repl tests/demes_hex_repl/config tests/demes_hex_repl/expected tests/demes_hex_repl/expected/data tests/demes_hex_repl/expected/data/archive
dknoester at myxo.css.msu.edu
dknoester at myxo.css.msu.edu
Tue May 1 06:31:29 PDT 2007
Author: dknoester
Date: 2007-05-01 09:31:29 -0400 (Tue, 01 May 2007)
New Revision: 1511
Added:
development/tests/demes_hex_repl/
development/tests/demes_hex_repl/config/
development/tests/demes_hex_repl/config/avida.cfg
development/tests/demes_hex_repl/config/default-classic.org
development/tests/demes_hex_repl/config/environment.cfg
development/tests/demes_hex_repl/config/events.cfg
development/tests/demes_hex_repl/config/instset-classic.cfg
development/tests/demes_hex_repl/expected/
development/tests/demes_hex_repl/expected/data/
development/tests/demes_hex_repl/expected/data/archive/
development/tests/demes_hex_repl/expected/data/archive/100-aaaaa.org
development/tests/demes_hex_repl/expected/data/average.dat
development/tests/demes_hex_repl/expected/data/count.dat
development/tests/demes_hex_repl/expected/data/detail-100.pop
development/tests/demes_hex_repl/expected/data/dominant.dat
development/tests/demes_hex_repl/expected/data/historic-100.pop
development/tests/demes_hex_repl/expected/data/resource.dat
development/tests/demes_hex_repl/expected/data/stats.dat
development/tests/demes_hex_repl/expected/data/tasks.dat
development/tests/demes_hex_repl/expected/data/tasks_exe.dat
development/tests/demes_hex_repl/expected/data/tasks_quality.dat
development/tests/demes_hex_repl/expected/data/time.dat
development/tests/demes_hex_repl/test_list
Modified:
development/Avida.xcodeproj/project.pbxproj
development/source/main/cPopulation.cc
development/source/main/nGeometry.h
development/source/tools/cTopology.h
Log:
Added a hexagonal (6-neighbor) grid topology, and deme-based test for same.
Modified: development/Avida.xcodeproj/project.pbxproj
===================================================================
--- development/Avida.xcodeproj/project.pbxproj 2007-05-01 12:49:29 UTC (rev 1510)
+++ development/Avida.xcodeproj/project.pbxproj 2007-05-01 13:31:29 UTC (rev 1511)
@@ -10,10 +10,13 @@
1097463F0AE9606E00929ED6 /* cDeme.cc in Sources */ = {isa = PBXBuildFile; fileRef = 1097463D0AE9606E00929ED6 /* cDeme.cc */; };
109746410AE9606E00929ED6 /* cDeme.cc in Sources */ = {isa = PBXBuildFile; fileRef = 1097463D0AE9606E00929ED6 /* cDeme.cc */; };
109746430AE9606E00929ED6 /* cDeme.cc in Sources */ = {isa = PBXBuildFile; fileRef = 1097463D0AE9606E00929ED6 /* cDeme.cc */; };
- 4201F39B0BE187F6006279B9 /* cTopology.h in CopyFiles */ = {isa = PBXBuildFile; fileRef = 4201F39A0BE187F6006279B9 /* cTopology.h */; };
4233358A0BC067E3000DF681 /* cHardwareGX.cc in Sources */ = {isa = PBXBuildFile; fileRef = 423335880BC067E3000DF681 /* cHardwareGX.cc */; };
- 4233358B0BC067E3000DF681 /* cHardwareGX.h in CopyFiles */ = {isa = PBXBuildFile; fileRef = 423335890BC067E3000DF681 /* cHardwareGX.h */; };
- 42490F000BE2472800318058 /* cGermline.h in CopyFiles */ = {isa = PBXBuildFile; fileRef = 42490EFE0BE2472800318058 /* cGermline.h */; };
+ 427E798D0BE6A2E80083B133 /* cCliqueTopology.cc in Sources */ = {isa = PBXBuildFile; fileRef = 42829ADB0BE631A500F6BF8F /* cCliqueTopology.cc */; };
+ 427E798E0BE6A2EB0083B133 /* cGridTopology.cc in Sources */ = {isa = PBXBuildFile; fileRef = 42829AE00BE631A500F6BF8F /* cGridTopology.cc */; };
+ 427E798F0BE6A2EC0083B133 /* cHexTopology.cc in Sources */ = {isa = PBXBuildFile; fileRef = 42829AE20BE631A500F6BF8F /* cHexTopology.cc */; };
+ 427E79900BE6A2EE0083B133 /* cTorusTopology.cc in Sources */ = {isa = PBXBuildFile; fileRef = 42829AE40BE631A500F6BF8F /* cTorusTopology.cc */; };
+ 427E79910BE6A2EF0083B133 /* iTopology.cc in Sources */ = {isa = PBXBuildFile; fileRef = 42829AE60BE631A500F6BF8F /* iTopology.cc */; };
+ 427E79C40BE6A7D40083B133 /* CMakeLists.txt in CopyFiles */ = {isa = PBXBuildFile; fileRef = 427E79C30BE6A7D40083B133 /* CMakeLists.txt */; };
7005A70409BA0FA90007E16E /* cTestCPUInterface.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */; };
7005A70609BA0FA90007E16E /* cTestCPUInterface.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */; };
7005A70809BA0FA90007E16E /* cTestCPUInterface.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */; };
@@ -427,9 +430,7 @@
7049F3730A66AD7E00640512 /* default-transsmt.org in CopyFiles */,
70B1A7430B7E3FFD00067486 /* instset-experimental.cfg in CopyFiles */,
70B1A75A0B7E431F00067486 /* experimental.org in CopyFiles */,
- 4233358B0BC067E3000DF681 /* cHardwareGX.h in CopyFiles */,
- 4201F39B0BE187F6006279B9 /* cTopology.h in CopyFiles */,
- 42490F000BE2472800318058 /* cGermline.h in CopyFiles */,
+ 427E79C40BE6A7D40083B133 /* CMakeLists.txt in CopyFiles */,
);
runOnlyForDeploymentPostprocessing = 0;
};
@@ -452,6 +453,18 @@
423335880BC067E3000DF681 /* cHardwareGX.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cHardwareGX.cc; sourceTree = "<group>"; };
423335890BC067E3000DF681 /* cHardwareGX.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cHardwareGX.h; sourceTree = "<group>"; };
42490EFE0BE2472800318058 /* cGermline.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cGermline.h; sourceTree = "<group>"; };
+ 427E79C30BE6A7D40083B133 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
+ 42829ADB0BE631A500F6BF8F /* cCliqueTopology.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cCliqueTopology.cc; sourceTree = "<group>"; };
+ 42829ADC0BE631A500F6BF8F /* cCliqueTopology.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cCliqueTopology.h; sourceTree = "<group>"; };
+ 42829ADF0BE631A500F6BF8F /* cDiscreteTopology.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cDiscreteTopology.h; sourceTree = "<group>"; };
+ 42829AE00BE631A500F6BF8F /* cGridTopology.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cGridTopology.cc; sourceTree = "<group>"; };
+ 42829AE10BE631A500F6BF8F /* cGridTopology.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cGridTopology.h; sourceTree = "<group>"; };
+ 42829AE20BE631A500F6BF8F /* cHexTopology.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cHexTopology.cc; sourceTree = "<group>"; };
+ 42829AE30BE631A500F6BF8F /* cHexTopology.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cHexTopology.h; sourceTree = "<group>"; };
+ 42829AE40BE631A500F6BF8F /* cTorusTopology.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cTorusTopology.cc; sourceTree = "<group>"; };
+ 42829AE50BE631A500F6BF8F /* cTorusTopology.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cTorusTopology.h; sourceTree = "<group>"; };
+ 42829AE60BE631A500F6BF8F /* iTopology.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = iTopology.cc; sourceTree = "<group>"; };
+ 42829AE70BE631A500F6BF8F /* iTopology.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = iTopology.h; sourceTree = "<group>"; };
7005A70109BA0FA90007E16E /* cTestCPUInterface.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cTestCPUInterface.h; sourceTree = "<group>"; };
7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cTestCPUInterface.cc; sourceTree = "<group>"; };
7005A70909BA0FBE0007E16E /* cOrgInterface.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cOrgInterface.h; sourceTree = "<group>"; };
@@ -935,7 +948,7 @@
DCC315CF076253A5008F7A48 /* Makefile */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.make; path = Makefile; sourceTree = "<group>"; };
DCC315D0076253A5008F7A48 /* task_event_gen.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.cc; sourceTree = "<group>"; };
DCC315D1076253A5008F7A48 /* task_event_gen.old.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.old.cc; sourceTree = "<group>"; };
- DCC3164D07626CF3008F7A48 /* avida */ = {isa = PBXFileReference; includeInIndex = 0; lastKnownFileType = "compiled.mach-o.executable"; path = avida; sourceTree = BUILT_PRODUCTS_DIR; };
+ DCC3164D07626CF3008F7A48 /* avida */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = avida; sourceTree = BUILT_PRODUCTS_DIR; };
/* End PBXFileReference section */
/* Begin PBXFrameworksBuildPhase section */
@@ -972,6 +985,25 @@
/* End PBXFrameworksBuildPhase section */
/* Begin PBXGroup section */
+ 42829ADA0BE631A500F6BF8F /* topology */ = {
+ isa = PBXGroup;
+ children = (
+ 42829ADB0BE631A500F6BF8F /* cCliqueTopology.cc */,
+ 42829ADC0BE631A500F6BF8F /* cCliqueTopology.h */,
+ 42829ADF0BE631A500F6BF8F /* cDiscreteTopology.h */,
+ 42829AE00BE631A500F6BF8F /* cGridTopology.cc */,
+ 42829AE10BE631A500F6BF8F /* cGridTopology.h */,
+ 42829AE20BE631A500F6BF8F /* cHexTopology.cc */,
+ 42829AE30BE631A500F6BF8F /* cHexTopology.h */,
+ 42829AE40BE631A500F6BF8F /* cTorusTopology.cc */,
+ 42829AE50BE631A500F6BF8F /* cTorusTopology.h */,
+ 42829AE60BE631A500F6BF8F /* iTopology.cc */,
+ 42829AE70BE631A500F6BF8F /* iTopology.h */,
+ 427E79C30BE6A7D40083B133 /* CMakeLists.txt */,
+ );
+ path = topology;
+ sourceTree = "<group>";
+ };
701D9115094B770B008B845F /* drivers */ = {
isa = PBXGroup;
children = (
@@ -1336,6 +1368,7 @@
DCC30C670762539A008F7A48 /* Main Source */ = {
isa = PBXGroup;
children = (
+ 42829ADA0BE631A500F6BF8F /* topology */,
707AEEEE09E80699001AEA89 /* actions */,
70422A1B091B141000A5E67F /* analyze */,
70F7D8C8092546DC009E311D /* classification */,
@@ -2194,6 +2227,11 @@
70B1A6500B7E237F00067486 /* cHardwareExperimental.cc in Sources */,
706C6FFF0B83F265003174C1 /* cInstSet.cc in Sources */,
4233358A0BC067E3000DF681 /* cHardwareGX.cc in Sources */,
+ 427E798D0BE6A2E80083B133 /* cCliqueTopology.cc in Sources */,
+ 427E798E0BE6A2EB0083B133 /* cGridTopology.cc in Sources */,
+ 427E798F0BE6A2EC0083B133 /* cHexTopology.cc in Sources */,
+ 427E79900BE6A2EE0083B133 /* cTorusTopology.cc in Sources */,
+ 427E79910BE6A2EF0083B133 /* iTopology.cc in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
@@ -2241,6 +2279,7 @@
isa = XCBuildConfiguration;
buildSettings = {
GCC_MODEL_CPU = G4;
+ HEADER_SEARCH_PATHS = /usr/local/boost;
OTHER_LDFLAGS = (
"-multiply_defined",
suppress,
Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc 2007-05-01 12:49:29 UTC (rev 1510)
+++ development/source/main/cPopulation.cc 2007-05-01 13:31:29 UTC (rev 1511)
@@ -91,6 +91,7 @@
case nGeometry::GRID: { cout << "Geometry: Bounded grid" << endl; break; }
case nGeometry::TORUS: { cout << "Geometry: Torus" << endl; break; }
case nGeometry::CLIQUE: { cout << "Geometry: Clique" << endl; break; }
+ case nGeometry::HEX: { cout << "Geometry: Hex" << endl; break; }
default: {
cout << "Unknown geometry!" << endl;
assert(false);
@@ -111,7 +112,7 @@
cell_array.Resize(num_cells);
resource_count.ResizeSpatialGrids(world_x, world_y);
market.Resize(MARKET_SIZE);
-
+
// Setup the cells. Do things that are not dependent upon topology here.
for(int i=0; i<num_cells; ++i) {
cell_array[i].Setup(world, i, environment.GetMutRates());
@@ -161,6 +162,11 @@
deme_size_x, deme_size_y);
break;
}
+ case nGeometry::HEX: {
+ build_hex(&cell_array.begin()[i], &cell_array.begin()[i+deme_size],
+ deme_size_x, deme_size_y);
+ break;
+ }
default: {
assert(false);
}
Modified: development/source/main/nGeometry.h
===================================================================
--- development/source/main/nGeometry.h 2007-05-01 12:49:29 UTC (rev 1510)
+++ development/source/main/nGeometry.h 2007-05-01 13:31:29 UTC (rev 1511)
@@ -30,7 +30,8 @@
GLOBAL = 0,
GRID,
TORUS,
- CLIQUE
+ CLIQUE,
+ HEX
};
}
Modified: development/source/tools/cTopology.h
===================================================================
--- development/source/tools/cTopology.h 2007-05-01 12:49:29 UTC (rev 1510)
+++ development/source/tools/cTopology.h 2007-05-01 13:31:29 UTC (rev 1511)
@@ -10,6 +10,8 @@
#ifndef _C_TOPOLOGY_H_
#define _C_TOPOLOGY_H_
+#include "functions.h"
+
/*! Builds a torus topology out of the cells betwen the iterators.
In a torus, each cell is connected to up to 8 neighbors (including diagonals),
and connections DO wrap around the logical edges of the torus.
@@ -88,4 +90,21 @@
}
}
+
+/*! Builds a hexagonal grid topology out of the cells between the iterators. In
+a hex grid, each cell has at most 6 neighbors, and connections do not wrap around
+edges.
+*/
+template< typename InputIterator >
+void build_hex(InputIterator begin, InputIterator end, unsigned int rowSize, unsigned int colSize) {
+ // Start with a grid:
+ build_grid(begin, end, rowSize, colSize);
+ int offset = begin->GetID();
+ // ... and remove connections to the NE,SW:
+ for(InputIterator i=begin; i!=end; ++i) {
+ i->ConnectionList().Remove(&begin[GridNeighbor(i->GetID()-offset, colSize, rowSize, 1, -1)]);
+ i->ConnectionList().Remove(&begin[GridNeighbor(i->GetID()-offset, colSize, rowSize, -1, 1)]);
+ }
+}
+
#endif
Added: development/tests/demes_hex_repl/config/avida.cfg
===================================================================
--- development/tests/demes_hex_repl/config/avida.cfg (rev 0)
+++ development/tests/demes_hex_repl/config/avida.cfg 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,258 @@
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.7.0 # Do not change this value.
+
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 0 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 1 # Initial viewer screen
+CLONE_FILE - # Clone file to load
+VERBOSITY 1 # Control output verbosity
+
+### ARCH_GROUP ###
+# Architecture Variables
+WORLD_X 10 # Width of the Avida world
+WORLD_Y 1000 # Height of the Avida world
+WORLD_GEOMETRY 4 # 1 = Bounded Grid
+ # 2 = Torus
+ # 3 = Clique
+ # 4 = Hex
+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
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET - # File containing instruction set
+EVENT_FILE events.cfg # File containing list of events during run
+ANALYZE_FILE analyze.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment.cfg # File that describes the environment
+START_CREATURE default-classic.org # Organism to seed the soup
+
+### DEME_GROUP ###
+# Demes and Germlines
+NUM_DEMES 100 # Number of independent groups in the population.
+DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline; 0=off
+DEMES_HAVE_MERIT 0 # Whether demes have merit; 0=no
+GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
+ # germline replication.
+GERMLINE_REPLACES_SOURCE 0 # Whether the source germline is updated
+ # on replication; 0=no.
+GERMLINE_RANDOM_PLACEMENT 0 # Whether the seed for a germline is placed
+ # randomly within the deme; 0=no.
+MAX_DEME_AGE 40 # The maximum age of a deme (in updates) to be
+ # used for age-based replication (default=500).
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 0 # Which organism should be replaced on birth?
+ # 0 = Random organism in neighborhood
+ # 1 = Oldest in neighborhood
+ # 2 = Largest Age/Merit in neighborhood
+ # 3 = None (use only empty cells in neighborhood)
+ # 4 = Random from population (Mass Action)
+ # 5 = Oldest in entire population
+ # 6 = Random within deme
+ # 7 = Organism faced by parent
+ # 8 = Next grid cell (id+1)
+ # 9 = Largest energy used in entire population
+ # 10 = Largest energy used in neighborhood
+PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
+ALLOW_PARENT 1 # Allow births to replace the parent organism?
+DEATH_METHOD 2 # 0 = Never die of old age.
+ # 1 = Die when inst executed = AGE_LIMIT (+deviation)
+ # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
+AGE_LIMIT 20 # Modifies DEATH_METHOD
+AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
+ALLOC_METHOD 0 # (Orignal CPU Only)
+ # 0 = Allocated space is set to default instruction.
+ # 1 = Set to section of dead genome (Necrophilia)
+ # 2 = Allocated space is set to random instruction.
+DIVIDE_METHOD 1 # 0 = Divide leaves state of mother untouched.
+ # 1 = Divide resets state of mother
+ # (after the divide, we have 2 children)
+ # 2 = Divide resets state of current thread only
+ # (does not touch possible parasite threads)
+GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
+ # increased on divide.
+ # 1 = Both the generation of the mother and child are
+ # increased on divide (good with DIVIDE_METHOD 1).
+
+### RECOMBINATION_GROUP ###
+# Sexual Recombination and Modularity
+RECOMBINATION_PROB 1.0 # probability of recombination in div-sex
+MAX_BIRTH_WAIT_TIME -1 # Updates incipiant orgs can wait for crossover
+MODULE_NUM 0 # number of modules in the genome
+CONT_REC_REGS 1 # are (modular) recombination regions continuous
+CORESPOND_REC_REGS 1 # are (modular) recombination regions swapped randomly
+ # or with corresponding positions?
+TWO_FOLD_COST_SEX 0 # 1 = only one recombined offspring is born.
+ # 2 = both offspring are born
+SAME_LENGTH_SEX 0 # 0 = recombine with any genome
+ # 1 = only recombine w/ same length
+
+### DIVIDE_GROUP ###
+# Divide Restrictions
+CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
+MIN_COPIED_LINES 0.5 # Code fraction which must be copied before divide.
+MIN_EXE_LINES 0.5 # Code fraction which must be executed before divide.
+REQUIRE_ALLOCATE 1 # (Original CPU Only) Require allocate before divide?
+REQUIRED_TASK -1 # Task ID required for successful divide.
+IMMUNITY_TASK -1 # Task providing immunity from the required task.
+REQUIRED_REACTION -1 # Reaction ID required for successful divide.
+REQUIRED_BONUS 0 # The bonus that an organism must accumulate to divide.
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
+INS_MUT_PROB 0.0 # Insertion rate (per site, applied on divide)
+DEL_MUT_PROB 0.0 # Deletion rate (per site, applied on divide)
+DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
+DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
+DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
+DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
+PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+INJECT_INS_PROB 0.0 # Insertion rate (per site, applied on inject)
+INJECT_DEL_PROB 0.0 # Deletion rate (per site, applied on inject)
+INJECT_MUT_PROB 0.0 # Mutation rate (per site, applied on inject)
+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.
+
+### REVERSION_GROUP ###
+# Mutation Reversion
+# These slow down avida a lot, and should be set to 0.0 normally.
+REVERT_FATAL 0.0 # Should any mutations be reverted on birth?
+REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
+REVERT_NEUTRAL 0.0 #
+REVERT_BENEFICIAL 0.0 #
+STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
+STERILIZE_DETRIMENTAL 0.0 #
+STERILIZE_NEUTRAL 0.0 #
+STERILIZE_BENEFICIAL 0.0 #
+FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
+ # be eliminated?
+NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness to be considered neutral.
+NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness to be considered neutral.
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
+ # 1 = Merit proportional to copied size
+ # 2 = Merit prop. to executed size
+ # 3 = Merit prop. to full size
+ # 4 = Merit prop. to min of executed or copied size
+ # 5 = Merit prop. to sqrt of the minimum size
+ # 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 the default bonus
+ # rather than the accumulated bonus of the parent?
+MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts (-1=none, 0= 1st in INST_SET.)
+MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned per INST (-1=penalty, 0= no effect.)
+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.
+MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
+DONATE_SIZE 5.0 # Amount of merit donated with 'donate' command
+DONATE_MULT 10.0 # Multiple of merit given that the target receives.
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on edit distance for donate; -1=no max
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+
+### PROMOTER_GROUP ###
+# Promoters
+PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
+ # Certain instructions must also be included.
+PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating after each cpu cycle.
+PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after each instruction.
+PROMOTER_BG_STRENGTH 0 # Probability of positions that are not promoter
+ # instructions initiating execution (promoters are 1).
+REGULATION_STRENGTH 1 # Strength added or subtracted to a promoter by regulation.
+REGULATION_DECAY_FRAC 0.1 # Fraction of regulation that decays away.
+ # Max regulation = 2^(REGULATION_STRENGTH/REGULATION_DECAY_FRAC)
+
+### GENEOLOGY_GROUP ###
+# Geneology
+TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
+ # 0=no, 1=yes, 2=yes,w/sexual population
+THRESHOLD 3 # Number of organisms in a genotype needed for it
+ # to be considered viable.
+GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
+GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
+ # this many updates. (0 = off)
+SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
+SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
+SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
+TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
+
+### LOG_GROUP ###
+# Log Files
+LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
+LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
+LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
+LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
+
+### LINEAGE_GROUP ###
+# Lineage
+# NOTE: This should probably be called "Clade"
+# This one can slow down avida a lot. It is used to get an idea of how
+# often an advantageous mutation arises, and where it goes afterwards.
+# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
+# 0 = manual creation (on inject, use successive integers as lineage labels).
+# 1 = when a child's (potential) fitness is higher than that of its parent.
+# 2 = when a child's (potential) fitness is higher than max in population.
+# 3 = when a child's (potential) fitness is higher than max in dom. lineage
+# *and* the child is in the dominant lineage, or (2)
+# 4 = when a child's (potential) fitness is higher than max in dom. lineage
+# (and that of its own lineage)
+# 5 = same as child's (potential) fitness is higher than that of the
+# currently dominant organism, and also than that of any organism
+# currently in the same lineage.
+# 6 = when a child's (potential) fitness is higher than any organism
+# currently in the same lineage.
+# 7 = when a child's (potential) fitness is higher than that of any
+# organism in its line of descent
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
+
+### ORGANISM_NETWORK_GROUP ###
+# Organism Network Communication
+NET_ENABLED 0 # Enable Network Communication Support
+NET_DROP_PROB 0.0 # Message drop rate
+NET_MUT_PROB 0.0 # Message corruption probability
+NET_MUT_TYPE 0 # Type of message corruption. 0 = Random Single Bit, 1 = Always Flip Last
+NET_STYLE 0 # Communication Style. 0 = Random Next, 1 = Receiver Facing
+
+### BUY_SELL_GROUP ###
+# Buying and Selling Parameters
+SAVE_RECEIVED 0 # Enable storage of all inputs bought from other orgs
+BUY_PRICE 0 # price offered by organisms attempting to buy
+SELL_PRICE 0 # price offered by organisms attempting to sell
+
+### ANALYZE_GROUP ###
+# Analysis Settings
+MT_CONCURRENCY 1 # Number of concurrent analyze threads
+ANALYZE_OPTION_1 # String variable accessible from analysis scripts
+ANALYZE_OPTION_2 # String variable accessible from analysis scripts
Added: development/tests/demes_hex_repl/config/default-classic.org
===================================================================
--- development/tests/demes_hex_repl/config/default-classic.org (rev 0)
+++ development/tests/demes_hex_repl/config/default-classic.org 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,100 @@
+h-alloc # Allocate space for child
+h-search # Locate the end of the organism
+nop-C #
+nop-A #
+mov-head # Place write-head at beginning of offspring.
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+nop-C #
+h-search # Mark the beginning of the copy loop
+h-copy # Do the copy
+if-label # If we're done copying....
+nop-C #
+nop-A #
+h-divide # ...divide!
+mov-head # Otherwise, loop back to the beginning of the copy loop.
+nop-A # End label.
+nop-B #
Added: development/tests/demes_hex_repl/config/environment.cfg
===================================================================
--- development/tests/demes_hex_repl/config/environment.cfg (rev 0)
+++ development/tests/demes_hex_repl/config/environment.cfg 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,9 @@
+REACTION NOT not process:value=1.0:type=pow requisite:max_count=1
+REACTION NAND nand process:value=1.0:type=pow requisite:max_count=1
+REACTION AND and process:value=2.0:type=pow requisite:max_count=1
+REACTION ORN orn process:value=2.0:type=pow requisite:max_count=1
+REACTION OR or process:value=3.0:type=pow requisite:max_count=1
+REACTION ANDN andn process:value=3.0:type=pow requisite:max_count=1
+REACTION NOR nor process:value=4.0:type=pow requisite:max_count=1
+REACTION XOR xor process:value=4.0:type=pow requisite:max_count=1
+REACTION EQU equ process:value=5.0:type=pow requisite:max_count=1
Added: development/tests/demes_hex_repl/config/events.cfg
===================================================================
--- development/tests/demes_hex_repl/config/events.cfg (rev 0)
+++ development/tests/demes_hex_repl/config/events.cfg 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,19 @@
+# Print all of the standard data files...
+u 0 InjectDemes
+u 0:10:end PrintAverageData # Save info about they average genotypes
+u 0:10:end PrintDominantData # Save info about most abundant genotypes
+u 0:10:end PrintStatsData # Collect satistics about entire pop.
+u 0:10:end PrintCountData # Count organisms, genotypes, species, etc.
+u 0:10:end PrintTasksData # Save organisms counts for each task.
+u 0:10:end PrintTimeData # Track time conversion (generations, etc.)
+u 0:10:end PrintResourceData # Track resource abundance.
+u 0:10:end PrintDominantGenotype # Save the most abundant genotypes
+u 0:10:end PrintTasksExeData # Num. times tasks have been executed.
+u 0:10:end PrintTasksQualData # Task quality information
+
+u 1:1:end ReplicateDemes deme-age
+
+# Setup the exit time and full population data collection.
+u 100 SavePopulation # Save current state of population.
+u 100 SaveHistoricPopulation # Save ancestors of current population.
+u 100 exit # exit
Added: development/tests/demes_hex_repl/config/instset-classic.cfg
===================================================================
--- development/tests/demes_hex_repl/config/instset-classic.cfg (rev 0)
+++ development/tests/demes_hex_repl/config/instset-classic.cfg 2007-05-01 13:31:29 UTC (rev 1511)
@@ -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?
+
Added: development/tests/demes_hex_repl/expected/data/archive/100-aaaaa.org
===================================================================
--- development/tests/demes_hex_repl/expected/data/archive/100-aaaaa.org (rev 0)
+++ development/tests/demes_hex_repl/expected/data/archive/100-aaaaa.org 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,134 @@
+# Tue May 1 09:13:52 2007
+# Filename........: archive/100-aaaaa.org
+# Update Output...: 100
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+# Update Created..: -1
+# Genotype ID.....: 1
+# Parent Gen ID...: -1
+# Tree Depth......: 0
+# Parent Distance.: -1
+#
+# Generation: 0
+# Merit...........: 97.000000
+# Gestation Time..: 389
+# Fitness.........: 0.249357
+# Errors..........: 0
+# Genome Size.....: 100
+# Copied Size.....: 100
+# Executed Size...: 97
+# Offspring.......: SELF
+#
+# Tasks Performed:
+# not 0 (0.000000)
+# nand 0 (0.000000)
+# and 0 (0.000000)
+# orn 0 (0.000000)
+# or 0 (0.000000)
+# andn 0 (0.000000)
+# nor 0 (0.000000)
+# xor 0 (0.000000)
+# equ 0 (0.000000)
+
+
+h-alloc
+h-search
+nop-C
+nop-A
+mov-head
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+nop-C
+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
+h-copy
+if-label
+nop-C
+nop-A
+h-divide
+mov-head
+nop-A
+nop-B
Added: development/tests/demes_hex_repl/expected/data/average.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/average.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/average.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,30 @@
+# Avida Average Data
+# Tue May 1 09:13:50 2007
+# 1: Update
+# 2: Merit
+# 3: Gestation Time
+# 4: Fitness
+# 5: Repro Rate?
+# 6: Size
+# 7: Copied Size
+# 8: Executed Size
+# 9: Abundance
+# 10: Proportion of organisms that gave birth in this update
+# 11: Proportion of Breed True Organisms
+# 12: Genotype Depth
+# 13: Generation
+# 14: Neutral Metric
+# 15: Lineage Label
+# 16: True Replication Rate (based on births/update, time-averaged)
+
+0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 101.000000 101.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+10 97 389 0 0 100 100 97 0 0 0 0 0 0 0 0
+20 97 389 0.249357 0 100.015 100 97 3.57143 0 0 0.285 1 0.128671 0 0
+30 95.7848 387.223 0.247028 0 100.02 99.4987 95.7848 2.2191 0 0 0.58481 1.98734 0.153769 0 0
+40 96.43 389.72 0.247491 0 100.01 99.98 96.43 2.5641 0 0 0.62 2.37 0.324309 -1 0
+50 96.43 389.72 0.247491 0 100.01 99.98 96.43 2.5641 0 0 0.62 2.37 0.324309 -1 0
+60 96.4074 389.608 0.247507 0 100.063 99.7302 96.4074 2.25 0 0 0.825397 3.31746 0.202733 -1 0
+70 95.915 388.272 0.246901 0 100.365 99.5949 95.915 2.04046 0 0 1.04533 4.27479 0.0911235 -1 0
+80 94.2 389.04 0.241872 0 102.1 99.03 94.2 1.88679 0 0 1.29 4.77 -0.115848 -1 0
+90 94.2 389.04 0.241872 0 102.1 99.03 94.2 1.88679 0 0 1.29 4.77 -0.115848 -1 0
+100 94.4637 389.503 0.242441 0 101.324 98.9609 94.4637 1.72115 0.00558659 0 1.55866 5.82123 -0.255469 -1 0
Added: development/tests/demes_hex_repl/expected/data/count.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/count.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/count.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,30 @@
+# Avida count data
+# Tue May 1 09:13:50 2007
+# 1: update
+# 2: number of insts executed this update
+# 3: number of organisms
+# 4: number of different genotypes
+# 5: number of different threshold genotypes
+# 6: number of different species
+# 7: number of different threshold species
+# 8: number of different lineages
+# 9: number of births in this update
+# 10: number of deaths in this update
+# 11: number of breed true
+# 12: number of breed true organisms?
+# 13: number of no-birth organisms
+# 14: number of single-threaded organisms
+# 15: number of multi-threaded organisms
+# 16: number of modified organisms
+
+0 30 1 1 1 0 0 0 101 1 101 1 1 1 0 0
+10 3000 100 1 1 0 0 0 0 0 0 100 100 100 0 0
+20 6000 200 56 2 0 0 0 0 0 0 143 100 200 0 0
+30 11850 395 178 2 0 0 0 0 0 0 216 200 395 0 0
+40 3000 100 39 6 0 0 0 0 0 0 11 100 100 0 0
+50 3000 100 39 6 0 0 0 0 0 0 11 100 100 0 0
+60 5670 189 84 15 0 0 0 0 0 0 54 100 189 0 0
+70 10590 353 173 22 0 0 0 0 0 0 126 186 353 0 0
+80 3000 100 53 28 0 0 0 0 0 0 6 100 100 0 0
+90 3000 100 53 28 0 0 0 0 0 0 6 100 100 0 0
+100 5340 179 104 31 0 0 0 1 0 0 33 100 179 0 0
Added: development/tests/demes_hex_repl/expected/data/detail-100.pop
===================================================================
--- development/tests/demes_hex_repl/expected/data/detail-100.pop (rev 0)
+++ development/tests/demes_hex_repl/expected/data/detail-100.pop 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,121 @@
+#filetype genotype_data
+#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
+
+# 1: ID
+# 2: parent ID
+# 3: parent distance
+# 4: number of orgranisms currently alive
+# 5: total number of organisms that ever existed
+# 6: length of genome
+# 7: merit
+# 8: gestation time
+# 9: fitness
+# 10: update born
+# 11: update deactivated
+# 12: depth in phylogentic tree
+# 13: genome of organism
+
+1 -1 -1 22 389 100 97 389 0.249357 -1 -1 0 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+171 1 2 5 14 99 96 384 0.25 28 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccfcutycasvab
+142 1 1 5 12 100 97 388 0.25 27 -1 1 rucavccccccccccccccccccxcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+278 110 1 4 7 100 97 387 0.250646 52 -1 2 rucavccccccccccccccccccccccccccccccccccccccccqccccccccccccccccccmccccccccccccccccccccccccccutycasvab
+339 1 1 4 6 100 97 389 0.249357 65 -1 1 rucavchccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+331 140 1 3 5 100 97 387 0.250646 65 -1 2 rucavcccccccccccccccccccccccccccccmcccccccccccccccccccccccccccccccqccccccccccccccccccccccccutycasvab
+96 1 1 3 8 100 97 388 0.25 26 -1 1 rucavccxcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+313 1 1 3 5 100 97 388 0.25 64 -1 1 rucavccccccccccccccccccccccccccncccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+378 1 2 3 5 99 96 384 0.25 67 -1 1 rucavccccccccccccccccdccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+389 154 1 3 5 99 96 384 0.25 67 -1 2 rucavcccccccccccccccccccccccccccccccccccccccccceccccccccccccccccccccccccccccccccccccccccccutycasvab
+533 345 3 3 4 100 87 375 0.232 79 -1 3 rucavccccxccccccccccccccccccccccczcccccgcccccccccccccccccchcccccccccccccccyccccccccccccccccutycasvab
+273 1 3 3 6 101 98 392 0.25 52 -1 1 rucavcccccccccccccccccsccccsccccccccccccccccccccccccccccccccccccvcccccccccccccccccccccccccccutycasvab
+406 326 2 3 4 100 91 379 0.240106 77 -1 3 rucavccccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccpcccccucccccccutycasvab
+34 1 1 3 12 100 97 389 0.249357 14 -1 1 rucavccccccccccccccccccccccccccccbcccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+10 1 1 3 9 101 98 493 0.198783 13 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccuqtycasvab
+358 296 3 2 3 102 99 395 0.250633 66 -1 2 aarucavccccccccccckcccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccccccccccccccutycasvab
+486 370 101 2 3 200 0 0 0 79 -1 3 aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaarucavccccccccccccccccccccccccccccdcccccccccccccciccccccccccccccccccccccccccccccccccccwcccccutycasvab
+90 1 2 2 5 100 0 0 0 26 -1 1 rucwavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+364 45 1 2 3 100 49 336 0.145833 66 -1 2 rucavcccccccclccccccccccccccccccccccccccccccccccccccccclcccccccccccccccccccccccccccccccccccutlcasvab
+43 1 1 2 5 100 0 0 0 14 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasnab
+128 1 2 2 5 99 0 0 0 27 -1 1 rucavcccccccccccccccccccccccccccccccccccccctcccccccccccccccccccccccccccccccccccccccccccccccutyasvab
+422 1 1 2 3 100 0 0 0 77 -1 1 rucivccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+483 1 1 2 3 100 97 388 0.25 79 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccicccccccccccccccccccccccccccccccccutycasvab
+304 10 2 2 4 101 98 492 0.199187 55 -1 2 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccpccccccccccccccccccccuktycasvab
+472 140 2 2 3 100 0 0 0 78 -1 2 rucyvcccccccccccccccccccccccccccccmccccccccccccccccccccfcccccccccccccccccccccccccccccccccccutycasvab
+254 1 2 2 5 100 0 0 0 39 -1 1 rucavccccccccccccccccccccccccccccccccccccczccccccccccccccccccccccccccccccccccccccccccccccccxtycasvab
+316 184 4 2 3 103 100 399 0.250627 64 -1 2 aarucavcccccccccccccccccccccccacccccccccccccccccccccccccccccwccccwccccccccccccccccccccccccccccutycasvab
+319 301 26 2 3 100 0 0 0 65 -1 2 cccccbcccccccccccccccccccccccccccccccccccutxcasvabrucavccccccccccccccccccccccccccccccccccccccccccccc
+350 271 1 2 3 99 96 383 0.250653 66 -1 2 rucavccccccccccccccccckcccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+435 1 3 2 4 100 0 0 0 77 -1 1 rucavccccccccccccccccccccccccccccccccccccvccccccccccccccccccccfccccccccccccctccccccccccccccutycasvab
+2 1 1 2 31 99 96 385 0.249351 12 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+489 1 1 2 4 100 0 0 0 79 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccccccccccccccccccccccutycasvab
+352 2 2 2 4 99 96 383 0.250653 66 -1 2 rucavccccccccccccccccccccccccccceccccccccccccccccccccccccccccccccccccccxccccccccccccccccccutycasvab
+225 1 1 2 9 100 97 388 0.25 39 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccceccccccccccccccccccccccccccccccccutycasvab
+321 270 2 2 5 100 87 375 0.232 65 -1 3 rucavccccccccycccccccccccccccccccccccccccccccccccccccccccgecdccccccccccccccczccccccccccccccutycasvab
+160 1 2 1 5 100 0 0 0 28 -1 1 uucavcccccccccccccccccccccccccccxccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+363 264 1 1 3 100 78 367 0.212534 66 -1 3 rucavccccccccccccccccccyccccccccccccccccccccccpccccccccccccucccccccccccccccccccccccccccccccutycasvab
+421 2 3 1 3 100 0 0 0 77 -1 2 rucavcccccccccccccccccccccccccccccccccxcccccccccccccccccccccccccccccccccoccccccccccccciccccutycasvab
+15 1 1 1 7 100 88 379 0.23219 13 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccuccccccccccccccccutycasvab
+534 300 1 1 3 100 0 0 0 79 -1 2 rucavcccccccccccccccqccccccccccccccccccccccccccccccccccccccccccccccdcccccccccccccccccccccccutycasvab
+328 1 1 1 4 100 97 388 0.25 65 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccfccccccccccccccccccccccccccccccutycasvab
+458 1 2 1 3 100 0 0 0 78 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccvccccccccccccccccccccccccccccccocccccccccccutycasvab
+428 346 2 1 3 104 0 0 0 77 -1 3 aaaarucavcccccccccccccccccccrccccvccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccutycasvab
+158 1 1 1 8 101 98 392 0.25 28 -1 1 rucavccccccccccccccccccccccccccccccccccccnccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+336 96 1 1 4 100 97 387 0.250646 65 -1 2 rucavccxcccccccccccccccccccccccccccccmcccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+281 1 1 1 3 101 98 393 0.249364 52 -1 1 rucavccccccccccccccccccccccaccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+512 351 2 1 3 101 0 0 0 79 -1 3 rucavccccccccccccnccccccrccccccccccccccccccccccccccccccccccccqcccvccccccccccccccccccccccccccutycasvab
+112 1 1 1 9 100 97 388 0.25 27 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccutycasvab
+154 1 1 1 8 100 97 388 0.25 28 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccceccccccccccccccccccccccccccccccccccccccccccutycasvab
+125 11 1 1 5 101 0 0 0 27 -1 2 ruqcavccccccccccccccccccccccccccccccccccccccccccccccccccccccmcccccccccccccccccccccccccccccccutycasvab
+147 1 2 1 5 100 49 287 0.170732 27 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccoccccccccccccccccccccccccccccutycosvab
+162 1 1 1 5 100 0 0 0 28 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycashab
+204 1 2 1 5 100 0 0 0 39 -1 1 ruclvcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccyccccccccccccutycasvab
+536 483 2 1 1 100 0 0 0 91 -1 2 rucavcccccccccccccccccccccccccccoccccccccccccccccccccccccicccccccccccccccccccccccccccccccccutyzasvab
+537 389 1 1 1 99 0 0 0 91 -1 3 rucavcccccccccccccccccccccccccvcccccccccccccccceccccccccccccccccccccccccccccccccccccccccccutycasvab
+538 1 1 1 1 100 0 0 0 91 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccytycasvab
+539 313 2 1 1 100 0 0 0 91 -1 2 rucavccccccccccccccccccccccccccncccccccccccccccccccccccccccccccccccccccccccccccccccccccctccutycanvab
+540 512 3 1 1 100 0 0 0 91 -1 4 rucavccccccccccccnccccccrccccccccccccccccccccqcccccccccccccrqcccvccccccccccccccccccccccccccutycasvab
+541 1 1 1 1 100 0 0 0 91 -1 1 rucavcccccccccccccccccccpccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+542 112 1 1 1 100 0 0 0 92 -1 2 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccwcccccccccccccccccciccccccccccccutycasvab
+543 428 2 1 1 106 0 0 0 92 -1 4 aaaaaarucavcccccccccccccccccccrccccvccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccutycasvab
+544 273 1 1 1 101 0 0 0 92 -1 2 rucavcccccccccccccccccsccccsccccccccccccccccccccccccccccccccccccvcccccccccccccccccccccpcccccutycasvab
+545 34 2 1 1 100 0 0 0 92 -1 2 uucavccccccccccccccccccccccccccccbccccccccckcccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+546 1 1 1 1 100 0 0 0 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccwcccccccccccccccccccccccccccccccccutycasvab
+547 154 2 1 1 100 0 0 0 92 -1 2 rucavcccccpcccccccccccccccccccccccccccccccccccccecccccoccccccccccccccccccccccccccccccccccccutycasvab
+548 1 1 1 1 100 0 0 0 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasjab
+549 336 2 1 1 99 0 0 0 92 -1 3 rucavccxcccccccccccccccccccccccccccccmccccccccccccccccczccccccccccccccccccccccccccccccccccutycasvab
+550 406 2 1 1 100 0 0 0 92 -1 4 rucavcccdccccgcccccccccccccccccccccccccccccccccccccccccccccycccccciccccccccccpcccccucccccccutycasvab
+551 316 5 1 1 107 0 0 0 92 -1 3 aaaaaarucavcccccccccccccccccccccccacccccccccccccccccncccccccccccwccccwccccccccccccccccccccccccccccutycasvab
+552 142 1 1 1 100 0 0 0 92 -1 2 rucavccccccccccccccccccxcccccccccccccccccccccvcccccccccccccccccccccccccccccccccccccccccccccutycasvab
+553 142 1 1 1 100 0 0 0 92 -1 2 rucavccccccccccccccccccxccccccccccccccccccccccccccccccccccccccccccccccccxccccccccccccccccccutycasvab
+554 358 4 1 1 106 0 0 0 92 -1 3 aaaaaarucavccccccccccckcccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccccccccccccccutycasvab
+555 158 1 1 1 101 0 0 0 92 -1 2 rucavccccccccccccccccccccccccccccccccccocnccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+556 142 2 1 1 100 0 0 0 92 -1 2 rucavcccccccsccccccccccxccccccccccccccccccccccccccccccccccccccccccccccccccccccccuccccccccccutycasvab
+557 1 1 1 1 100 0 0 0 92 -1 1 rucavcccccccccccccccccccccccccccccccuccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+558 2 2 1 1 99 0 0 0 92 -1 2 rucavcccccccccccccccccccccxccccccccccccclcccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+559 421 3 1 1 100 0 0 0 92 -1 3 recavcccccccccccccccccccccccccccccccccxcccccccccccccccccacccccccccccccccoccccccccccocciccccutycasvab
+560 171 1 1 1 99 0 0 0 92 -1 2 rucavcccccccccccccccccccccccccccccccccccccccccccccclccccccccccccccccccccccccccccccccccccfcutycasvab
+561 96 1 1 1 100 0 0 0 92 -1 2 rucavccxcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccpcccccccccccccccccccccccutycasvab
+562 171 1 1 1 99 0 0 0 92 -1 2 rucavcccccccccccccccccccccccccccccccccccmcccccccccccccccccccccccccccccccccccccccccccccccfcutycasvab
+563 1 1 1 1 100 0 0 0 92 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccwcccccutycasvab
+564 350 1 1 1 99 0 0 0 92 -1 3 rucavccccccccccccccccckcccccgccccccccccwccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+565 1 1 1 1 100 0 0 0 92 -1 1 rucavcccccccccccccccccccccckcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+566 281 2 1 1 101 0 0 0 92 -1 2 rucavccccxcccccccccccccccccaccccccccccccccccccccccccccccccccccccccccccccccccccccccccscccccccutycasvab
+567 483 1 1 1 100 0 0 0 92 -1 2 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccicccccccecccccccccccccccccccccccccutycasvab
+568 358 5 1 1 106 0 0 0 92 -1 3 aaaaaarucavccccccccqcckcccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccccccccccccccutycasvab
+569 534 2 1 1 100 0 0 0 92 -1 3 rucavcccccccccccjcccqccccccccccccccccccccccccccccccccccccccccccccccdcccccccccccccccccccccccutyfasvab
+570 1 1 1 1 101 0 0 0 93 -1 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccscccccccccccccutycasvab
+571 458 1 1 1 100 0 0 0 93 -1 2 rucavcccccccccccccccccccccccccccccccccccccccccccvccccccccycccccccccccccccccccccocccccccccccutycasvab
+572 328 2 1 1 100 0 0 0 93 -1 2 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccfcccccccccccccccclcecccccccccccutycasvab
+573 15 2 1 1 100 0 0 0 93 -1 2 rucavccccccccccccccccccccccccccccyccccccccccccccccccccccccccccccccccccccccuccccccccccceccccutycasvab
+574 350 1 1 1 99 0 0 0 93 -1 3 rucavccccccccccccccccckcccccgccccccccccccccccccccccccccccccccccccccccjccccccccccccccccccccutycasvab
+575 316 5 1 1 107 0 0 0 93 -1 3 aaaaaarucavcccccccccccccccccccccccaccccccccccccccccccccccccjccccwccccwccccccccccccccccccccccccccccutycasvab
+576 533 1 1 1 100 0 0 0 93 -1 4 rucavccccxccccccccccccccccccccccczcccccgcccccccccccccccccchcccccccccccccccycccccccccctcccccutycasvab
+577 171 2 1 1 99 0 0 0 93 -1 2 rucavcceccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccmcccccccfcutycasvab
+578 378 1 1 1 99 0 0 0 93 -1 2 rucavccccccccccccccccdccccccccccccccccccccccccccccccccccccccccccccccccccccccecccccccccccccutycasvab
+579 331 1 1 1 100 0 0 0 93 -1 3 rucavcccccccceccccccccccccccccccccmcccccccccccccccccccccccccccccccqccccccccccccccccccccccccutycasvab
+580 1 1 1 1 100 0 0 0 93 -1 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutynasvab
+581 363 2 1 1 100 0 0 0 93 -1 4 rucavccccccsccccccyccccyccccccccccccccccccccccpccccccccccccucccccccccccccccccccccccccccccccutycasvab
+582 10 2 1 1 101 0 0 0 95 -1 2 rucavcccctcccccccceccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccuqtycasvab
+583 304 2 1 1 101 0 0 0 96 -1 3 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccacccccccmcccpccccccccccccccccccccuktycasvab
+584 304 1 1 1 101 0 0 0 96 -1 3 rucavcccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccpccccccccccccccccccccuktycasvab
+585 147 27 1 1 100 0 0 0 98 -1 2 ccccccccccccoccccccccccccccccccccccccccccutycosvabrucavcccccqccccccccccccccccccccccccccccccccccccccc
+586 364 28 1 1 100 0 0 0 100 -1 3 ccccclcccccccccccccccccccccccccccccccccccutlcasvabrucavcccccccclcccccccccccccyccccccccccccccwccccccc
Added: development/tests/demes_hex_repl/expected/data/dominant.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/dominant.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/dominant.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,30 @@
+# Avida Dominant Data
+# Tue May 1 09:13:50 2007
+# 1: Update
+# 2: Average Merit of the Dominant Genotype
+# 3: Average Gestation Time of the Dominant Genotype
+# 4: Average Fitness of the Dominant Genotype
+# 5: Repro Rate?
+# 6: Size of Dominant Genotype
+# 7: Copied Size of Dominant Genotype
+# 8: Executed Size of Dominant Genotype
+# 9: Abundance of Dominant Genotype
+# 10: Number of Births
+# 11: Number of Dominant Breed True?
+# 12: Dominant Gene Depth
+# 13: Dominant Breed In
+# 14: Max Fitness?
+# 15: Genotype ID of Dominant Genotype
+# 16: Name of the Dominant Genotype
+
+0 0.000000 0.000000 0.000000 0.000000 100 0.000000 0.000000 1 0 0 0 0 0.000000 1 100-aaaaa
+10 0 0 0 0 100 0 0 100 0 0 0 0 0 1 100-aaaaa
+20 97 389 0.249357 0.00257069 100 100 97 143 0 0 0 0 0.249357 1 100-aaaaa
+30 97 389 0.249357 0.00257069 100 100 97 196 0 0 0 0 0.251295 1 100-aaaaa
+40 97 389 0.249357 0.00257069 100 100 97 45 0 0 0 0 0.251948 1 100-aaaaa
+50 97 389 0.249357 0.00257069 100 100 97 45 0 0 0 0 0.251948 1 100-aaaaa
+60 97 389 0.249357 0.00257069 100 100 97 67 0 0 0 0 0.251908 1 100-aaaaa
+70 97 389 0.249357 0.00257069 100 100 97 98 0 0 0 0 0.251908 1 100-aaaaa
+80 97 389 0.249357 0.00257069 100 100 97 16 0 0 0 0 0.250653 1 100-aaaaa
+90 97 389 0.249357 0.00257069 100 100 97 16 0 0 0 0 0.250653 1 100-aaaaa
+100 97 389 0.249357 0.00257069 100 100 97 22 0 0 0 0 0.252604 1 100-aaaaa
Added: development/tests/demes_hex_repl/expected/data/historic-100.pop
===================================================================
--- development/tests/demes_hex_repl/expected/data/historic-100.pop (rev 0)
+++ development/tests/demes_hex_repl/expected/data/historic-100.pop 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,38 @@
+#filetype genotype_data
+#format id parent_id parent_dist num_cpus total_cpus length merit gest_time fitness update_born update_dead depth sequence
+
+# 1: ID
+# 2: parent ID
+# 3: parent distance
+# 4: number of orgranisms currently alive
+# 5: total number of organisms that ever existed
+# 6: length of genome
+# 7: merit
+# 8: gestation time
+# 9: fitness
+# 10: update born
+# 11: update deactivated
+# 12: depth in phylogentic tree
+# 13: genome of organism
+
+271 1 2 0 2 100 97 387 0.250646 52 79 1 rucavccccccccccccccccckccccccgcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+301 1 2 0 1 100 0 0 0 54 79 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccbcccccccccccccccccccccccccccccccccccutxcasvab
+184 1 1 0 4 100 97 388 0.25 38 79 1 rucavcccccccccccccccccccccccccccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccutycasvab
+110 1 1 0 4 100 97 388 0.25 27 79 1 rucavccccccccccccccccccccccccccccccccccccccccqcccccccccccccccccccccccccccccccccccccccccccccutycasvab
+264 2 2 0 1 100 0 0 0 52 79 2 rucavccccccccccccccccccyccccccccccccccccccccccpccccccccccccccccccccccccccccccccccccccccccccutycasvab
+168 1 1 0 4 100 97 389 0.249357 28 79 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccchccccccccccccccccccccccccccccccccutycasvab
+345 168 1 0 1 100 0 0 0 65 79 2 rucavccccxcccccccccccccccccccccccccccccccccccccccccccccccchccccccccccccccccccccccccccccccccutycasvab
+140 1 1 0 7 100 97 388 0.25 27 79 1 rucavcccccccccccccccccccccccccccccmccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+48 1 1 0 6 101 98 393 0.249364 14 79 1 rucavcccccccccccccccccccrcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+351 48 1 0 1 101 0 0 0 66 79 2 rucavcccccccccccccccccccrccccccccccccccccccccccccccccccccccccqccccccccccccccccccccccccccccccutycasvab
+346 184 4 0 1 102 0 0 0 65 79 2 aarucavcccccccccccccccccccrccccvccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccutycasvab
+45 1 2 0 6 100 97 387 0.250646 14 79 1 rucavcccccccclccccccccccccccccccccccccccccccccccccccccclcccccccccccccccccccccccccccccccccccutycasvab
+135 1 1 0 7 100 97 388 0.25 27 79 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccczccccccccccccccutycasvab
+270 135 2 0 1 100 87 376 0.231383 52 79 2 rucavccccccccycccccccccccccccccccccccccccccccccccccccccccceccccccccccccccccczccccccccccccccutycasvab
+300 1 1 0 1 100 97 388 0.25 54 79 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccdcccccccccccccccccccccccutycasvab
+148 1 1 0 4 100 97 388 0.25 28 79 1 rucavccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccccccccccccccccccccccccccccutycasvab
+370 148 1 0 1 100 0 0 0 66 79 2 rucavccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccccccccccccccccccccccwcccccutycasvab
+326 52 2 0 1 100 0 0 0 65 79 2 rucavccccccccmcccccccccccccccccccccccccccccccccccccccccccccccccccciccccccccccccccccucccccccutycasvab
+52 1 1 0 5 100 97 388 0.25 14 79 1 rucavccccccccmcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccutycasvab
+296 1 1 0 1 100 97 388 0.25 53 79 1 rucavcccccccccccccccccccccccccccccccccccccccccccccwccccccccccccccccccccccccccccccccccccccccutycasvab
+11 1 1 0 1 100 0 0 0 13 39 1 rucavccccccccccccccccccccccccccccccccccccccccccccccccccccccmcccccccccccccccccccccccccccccccutycasvab
Added: development/tests/demes_hex_repl/expected/data/resource.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/resource.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/resource.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,17 @@
+# Avida resource data
+# Tue May 1 09:13:50 2007
+# First column gives the current update, all further columns give the quantity
+# of the particular resource at that update.
+# 1: Update
+
+0
+10
+20
+30
+40
+50
+60
+70
+80
+90
+100
Added: development/tests/demes_hex_repl/expected/data/stats.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/stats.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/stats.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,26 @@
+# Generic Statistics Data
+# Tue May 1 09:13:50 2007
+# 1: update
+# 2: average inferiority (energy)
+# 3: ave probability of any mutations in genome
+# 4: probability of any mutations in dom genome
+# 5: log(average fidelity)
+# 6: log(dominant fidelity)
+# 7: change in number of genotypes
+# 8: genotypic entropy
+# 9: species entropy
+# 10: depth of most reacent coalescence
+# 11: Total number of resamplings this generation
+# 12: Total number of organisms that failed to resample this generation
+
+0 0.000000 0.097500 0.562358 0.102587 0.826353 1 0.000000 0.000000 0 0 0
+10 0 0.562358 0.562358 0.826353 0.826353 0 0 0 0 0 0
+20 2.44249e-15 0.562405 0.562358 0.826462 0.826353 0 1.7334 0 0 0 0
+30 0.0093872 0.562422 0.562358 0.8265 0.826353 0 3.27633 0 0 0 0
+40 0.00751309 0.562389 0.562358 0.826426 0.826353 -217 2.64264 0 0 0 0
+50 0.00751309 0.562389 0.562358 0.826426 0.826353 0 2.64264 0 0 0 0
+60 0.00744606 0.562559 0.562358 0.826813 0.826353 0 3.39441 0 0 0 0
+70 0.00990077 0.563514 0.562358 0.828998 0.826353 0 4.13243 0 0 0 0
+80 0.0304772 0.568959 0.562358 0.841552 0.826353 -261 3.69022 0 0 0 0
+90 0.0304772 0.568959 0.562358 0.841552 0.826353 0 3.69022 0 0 0 0
+100 0.0281291 0.566532 0.562358 0.835936 0.826353 1 4.31659 0 0 0 0
Added: development/tests/demes_hex_repl/expected/data/tasks.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/tasks.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/tasks.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,26 @@
+# Avida tasks data
+# Tue May 1 09:13:50 2007
+# First column gives the current update, next columns give the number
+# of organisms that have the particular task as a component of their merit
+# 1: Update
+# 2: Not
+# 3: Nand
+# 4: And
+# 5: OrNot
+# 6: Or
+# 7: AndNot
+# 8: Nor
+# 9: Xor
+# 10: Equals
+
+0 0 0 0 0 0 0 0 0 0
+10 0 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0
+30 0 0 0 0 0 0 0 0 0
+40 0 0 0 0 0 0 0 0 0
+50 0 0 0 0 0 0 0 0 0
+60 0 0 0 0 0 0 0 0 0
+70 0 0 0 0 0 0 0 0 0
+80 0 0 0 0 0 0 0 0 0
+90 0 0 0 0 0 0 0 0 0
+100 0 0 0 0 0 0 0 0 0
Added: development/tests/demes_hex_repl/expected/data/tasks_exe.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/tasks_exe.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/tasks_exe.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,26 @@
+# Avida tasks execution data
+# Tue May 1 09:13:50 2007
+# First column gives the current update, all further columns give the number
+# of times the particular task has been executed this update.
+# 1: Update
+# 2: Not
+# 3: Nand
+# 4: And
+# 5: OrNot
+# 6: Or
+# 7: AndNot
+# 8: Nor
+# 9: Xor
+# 10: Equals
+
+0 0 0 0 0 0 0 0 0 0
+10 0 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0
+30 0 0 0 0 0 0 0 0 0
+40 0 0 0 0 0 0 0 0 0
+50 0 0 0 0 0 0 0 0 0
+60 0 0 0 0 0 0 0 0 0
+70 0 0 0 0 0 0 0 0 0
+80 0 0 0 0 0 0 0 0 0
+90 0 0 0 0 0 0 0 0 0
+100 0 0 0 0 0 0 0 0 0
Added: development/tests/demes_hex_repl/expected/data/tasks_quality.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/tasks_quality.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/tasks_quality.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,34 @@
+# Avida tasks quality data
+# Tue May 1 09:13:50 2007
+# First column gives the current update, rest give average and max task quality
+# 1: Update
+# 2: Not Average
+# 3: Not Max
+# 4: Nand Average
+# 5: Nand Max
+# 6: And Average
+# 7: And Max
+# 8: OrNot Average
+# 9: OrNot Max
+# 10: Or Average
+# 11: Or Max
+# 12: AndNot Average
+# 13: AndNot Max
+# 14: Nor Average
+# 15: Nor Max
+# 16: Xor Average
+# 17: Xor Max
+# 18: Equals Average
+# 19: Equals Max
+
+0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Added: development/tests/demes_hex_repl/expected/data/time.dat
===================================================================
--- development/tests/demes_hex_repl/expected/data/time.dat (rev 0)
+++ development/tests/demes_hex_repl/expected/data/time.dat 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,18 @@
+# Avida time data
+# Tue May 1 09:13:50 2007
+# 1: update
+# 2: avida time
+# 3: average generation
+# 4: num_executed?
+
+0 0.000000 0.000000 30
+10 0.0927835 0 3000
+20 0.195876 1 6000
+30 0.299976 1.98734 11850
+40 0.404392 2.37 3000
+50 0.508094 2.37 3000
+60 0.611667 3.31746 5670
+70 0.715719 4.27479 10590
+80 0.8203 4.77 3000
+90 0.926457 4.77 3000
+100 1.03195 5.82123 5340
Added: development/tests/demes_hex_repl/test_list
===================================================================
--- development/tests/demes_hex_repl/test_list (rev 0)
+++ development/tests/demes_hex_repl/test_list 2007-05-01 13:31:29 UTC (rev 1511)
@@ -0,0 +1,35 @@
+;--- Begin Test Configuration File (test_list) ---
+[main]
+args = -s 100 ; Command line arguments to pass to the application
+app = %(app)s ; Application path to test
+nonzeroexit = disallow ; Exit code handling (disallow, allow, or require)
+ ; disallow - treat non-zero exit codes as failures
+ ; allow - all exit codes are acceptable
+ ; require - treat zero exit codes as failures, useful
+ ; for creating tests for app error checking
+createdby = Dave Knoester ; Who created the test
+email = dk at cse.msu.edu ; Email address for the test's creator
+
+[consistency]
+enabled = yes ; Is this test a consistency test?
+long = no ; Is this test a long test?
+
+[performance]
+enabled = no ; Is this test a performance test?
+long = no ; Is this test a long test?
+
+; The following variables can be used in constructing setting values by calling
+; them with %(variable_name)s. For example see 'app' above.
+;
+; app
+; builddir
+; cpus
+; mode
+; perf_repeat
+; perf_user_margin
+; perf_wall_margin
+; svn
+; svnmetadir
+; svnversion
+; testdir
+;--- End Test Configuration File ---
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