[Avida-cvs] [Avida2-svn] r388 - in development: Avida.xcodeproj source source/main source/support
brysonda@myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Thu Nov 10 13:47:16 PST 2005
Author: brysonda
Date: 2005-11-10 16:47:15 -0500 (Thu, 10 Nov 2005)
New Revision: 388
Removed:
development/source/support/genesis
Modified:
development/Avida.xcodeproj/project.pbxproj
development/source/defs.h
development/source/main/cAvidaConfig.h
development/source/main/cEnvironment.cc
development/source/main/cPopulation.cc
development/source/main/cWorld.cc
development/source/support/avida.cfg
Log:
Fix 'genebank' MkDir handling.
Modified: development/Avida.xcodeproj/project.pbxproj
===================================================================
--- development/Avida.xcodeproj/project.pbxproj 2005-11-10 21:12:24 UTC (rev 387)
+++ development/Avida.xcodeproj/project.pbxproj 2005-11-10 21:47:15 UTC (rev 388)
@@ -69,7 +69,6 @@
70486BA00826722F009328F0 /* analyze.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC3114B0762539E008F7A48 /* analyze.cfg */; };
70486BA10826722F009328F0 /* environment.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311800762539F008F7A48 /* environment.cfg */; };
70486BA20826722F009328F0 /* events.cfg in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311810762539F008F7A48 /* events.cfg */; };
- 70486BA30826722F009328F0 /* genesis in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311820762539F008F7A48 /* genesis */; };
70486BA40826722F009328F0 /* genesis.4stack in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311830762539F008F7A48 /* genesis.4stack */; };
70486BA50826722F009328F0 /* inst_set.4stack in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311840762539F008F7A48 /* inst_set.4stack */; };
70486BA60826722F009328F0 /* inst_set.default in CopyFiles */ = {isa = PBXBuildFile; fileRef = DCC311850762539F008F7A48 /* inst_set.default */; };
@@ -342,7 +341,6 @@
70486BA00826722F009328F0 /* analyze.cfg in CopyFiles */,
70486BA10826722F009328F0 /* environment.cfg in CopyFiles */,
70486BA20826722F009328F0 /* events.cfg in CopyFiles */,
- 70486BA30826722F009328F0 /* genesis in CopyFiles */,
70486BA40826722F009328F0 /* genesis.4stack in CopyFiles */,
70486BA50826722F009328F0 /* inst_set.4stack in CopyFiles */,
70486BA60826722F009328F0 /* inst_set.default in CopyFiles */,
Modified: development/source/defs.h
===================================================================
--- development/source/defs.h 2005-11-10 21:12:24 UTC (rev 387)
+++ development/source/defs.h 2005-11-10 21:47:15 UTC (rev 388)
@@ -30,13 +30,12 @@
// #define VIEW_ANSI
-// -= Speedups =- (define these to allow features to be turned on)
-
// #define BREAKPOINTS
// #define QUICK_BASE_TEST_CPU
// #define QUICK_HEAD_TEST_CPU
#define INSTRUCTION_COSTS
#define INSTRUCTION_COUNT
+// #define SMT_FULLY_ASSOCIATIVE
// -= Toggles =- (define these to actually turn features on)
Modified: development/source/main/cAvidaConfig.h
===================================================================
--- development/source/main/cAvidaConfig.h 2005-11-10 21:12:24 UTC (rev 387)
+++ development/source/main/cAvidaConfig.h 2005-11-10 21:47:15 UTC (rev 388)
@@ -167,7 +167,7 @@
CONFIG_ADD_VAR(HARDWARE_TYPE, int, 0, "0 = Original CPUs\n1 = New, Stack-based CPUs\n2 = Newer -- Stacks, Memory, Threading");
CONFIG_ADD_GROUP(CONFIG_FILE_GROUP, "Configuration Files");
- CONFIG_ADD_VAR(DATA_DIR, cString, ".", "Directory in which config files are found");
+ CONFIG_ADD_VAR(DATA_DIR, cString, "data", "Directory in which config files are found");
CONFIG_ADD_VAR(INST_SET, cString, "inst_set.default", "File containing instruction set");
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");
Modified: development/source/main/cEnvironment.cc
===================================================================
--- development/source/main/cEnvironment.cc 2005-11-10 21:12:24 UTC (rev 387)
+++ development/source/main/cEnvironment.cc 2005-11-10 21:47:15 UTC (rev 388)
@@ -563,8 +563,7 @@
} else if (item_type == "") {
cerr << "Format: SET_ACTIVE <type> <name> <new_status=true>" << endl;
} else {
- cerr << "Error: Cannot deactivate items of type "
- << item_type << endl;
+ cerr << "Error: Cannot deactivate items of type " << item_type << endl;
return false;
}
@@ -616,14 +615,11 @@
for (int i = 0; i < reaction_lib.GetSize(); i++) {
if (reaction_lib.GetReaction(i)->GetTask() == NULL) {
cerr << "Error: Pre-declared reaction '"
- << reaction_lib.GetReaction(i)->GetName()
- << "' never defined." << endl;
+ << reaction_lib.GetReaction(i)->GetName() << "' never defined." << endl;
return false;
}
}
- cerr << "--- FINISHED ENVIRONMENT SETUP---" << endl;
-
return true;
}
Modified: development/source/main/cPopulation.cc
===================================================================
--- development/source/main/cPopulation.cc 2005-11-10 21:12:24 UTC (rev 387)
+++ development/source/main/cPopulation.cc 2005-11-10 21:47:15 UTC (rev 388)
@@ -206,8 +206,8 @@
// Load a saved population if one is provided.
cString fname(m_world->GetConfig().POPULATION_FILE.Get());
- if (fname != "-" || fname != "") {
- cout << "Loading Population from " << fname() << endl;
+ if (fname != "-" && fname != "") {
+ cout << "Loading Population: " << fname << endl;
// If last three chars of filename are ".gz" , gunzip it first
if (fname.Find(".gz") == fname.GetSize() - 3) {
Modified: development/source/main/cWorld.cc
===================================================================
--- development/source/main/cWorld.cc 2005-11-10 21:12:24 UTC (rev 387)
+++ development/source/main/cWorld.cc 2005-11-10 21:47:15 UTC (rev 388)
@@ -53,6 +53,7 @@
m_conf->DATA_DIR.Set(dir);
}
m_data_mgr = new cDataFileManager(dir);
+ cTools::MkDir(dir + "genebank", true);
m_env = new cEnvironment(this);
m_hw_mgr = new cHardwareManager(this);
@@ -72,10 +73,7 @@
m_event_list = new cEventList(m_event_mgr, new cAvidaTriggers(*m_stats) );
ReadEventListFile(m_conf->EVENT_FILE.Get());
-
- // Make sure the directory 'genebank' exits!
- cTools::MkDir("genebank", true);
-
+
const bool revert_fatal = m_conf->REVERT_FATAL.Get() > 0.0;
const bool revert_neg = m_conf->REVERT_DETRIMENTAL.Get() > 0.0;
const bool revert_neut = m_conf->REVERT_NEUTRAL.Get() > 0.0;
Modified: development/source/support/avida.cfg
===================================================================
--- development/source/support/avida.cfg 2005-11-10 21:12:24 UTC (rev 387)
+++ development/source/support/avida.cfg 2005-11-10 21:47:15 UTC (rev 388)
@@ -3,7 +3,7 @@
# For more information, see doc/config.html
#############################################################################
-VERSION_ID 2.3.1 # Do not change this value.
+VERSION_ID 2.5.0 # Do not change this value.
### GENERAL_GROUP ###
# General Settings
@@ -183,5 +183,5 @@
# 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 1 #
-LINEAGE_CREATION_METHOD 1 #
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
Deleted: development/source/support/genesis
===================================================================
--- development/source/support/genesis 2005-11-10 21:12:24 UTC (rev 387)
+++ development/source/support/genesis 2005-11-10 21:47:15 UTC (rev 388)
@@ -1,165 +0,0 @@
-#############################################################################
-# This file includes all the basic run-time defines for avida.
-# For more information, see doc/genesis.html
-#############################################################################
-
-VERSION_ID 2.3.1 # Do not change this value!
-
-### Architecture Variables ###
-MAX_UPDATES -1 # Maximum updates to run simulation (-1 = no limit)
-MAX_GENERATIONS -1 # Maximum generations to run simulation (-1 = no limit)
-END_CONDITION_MODE 0 # End run when ...
- # 0 = MAX_UPDATES _OR_ MAX_GENERATIONS is reached
- # 1 = MAX_UPDATES _AND_ MAX_GENERATIONS is reached
-WORLD-X 60 # Width of the world in Avida mode.
-WORLD-Y 60 # Height of the world in Avida mode.
-WORLD_GEOMETRY 2 # 1 = Bounded Grid
- # 2 = Torus (Default)
-RANDOM_SEED 0 # Random number seed. (0 for based on time)
-HARDWARE_TYPE 0 # 0 = Original CPUs
- # 1 = New, Stack-based CPUs
-MAX_CPU_THREADS 1 # Number of Threads CPUs can spawn
-
-### Configuration Files ###
-DEFAULT_DIR ../work/ # Directory in which config files are found
-INST_SET inst_set.default # File containing instruction set
-EVENT_FILE events.cfg # File containing list of events during run
-ANALYZE_FILE analyze.cfg # File used for analysis mode
-ENVIRONMENT_FILE environment.cfg # File that describes the environment
-START_CREATURE organism.default # Organism to seed the soup
-
-### Reproduction ###
-BIRTH_METHOD 4 # 0 = Replace random organism in neighborhood
- # 1 = Replace oldest organism in neighborhood
- # 2 = Replace largest Age/Merit in neighborhood
- # 3 = Place only in empty cells in neighborhood
- # 4 = Replace random from entire population (Mass Action)
- # 5 = Replace oldest in entire population (like Tierra)
-PREFER_EMPTY 1 # Are empty cells given preference in offspring placement?
-DEATH_METHOD 2 # 0 = Never die of old age.
- # 1 = Die when inst executed = AGE_LIMIT (with deviation)
- # 2 = Die when inst executed = length * AGE_LIMIT (+ dev.)
-AGE_LIMIT 20 # Modifies DEATH_METHOD
-AGE_DEVIATION 0 # Modified DEATH_METHOD
-ALLOC_METHOD 0 # 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)
-
-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).
-
-### 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 # Is a an allocate required before a divide? (0/1)
-REQUIRED_TASK -1 # Number of task required for successful divide.
-
-### Mutations ###
-
-# mutations that occur during execution..
-POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
-COPY_MUT_PROB 0.0075 # Mutation rate (per copy).
-
-# mutations that occur on divide...
-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
-
-# heads based mutations
-# READ_SHIFT_PROB 0.0
-# READ INS_PROB 0.0
-# READ_DEL_PROB 0.0
-# WRITE_SHIFT_PROB 0.0
-# WRITE_INS_PROB 0.0
-# WRITE_DEL_PROB 0.0
-
-
-### Mutation reversions ###
-# these slow down avida a lot, and should be set to 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 # 0.0 to 1.0; Probability of reset.
-STERILIZE_NEUTRAL 0.0
-STERILIZE_BENEFICIAL 0.0
-
-FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
- # be eliminated?
-
-### Time Slicing ###
-AVE_TIME_SLICE 30
-SLICING_METHOD 2 # 0 = CONSTANT: all organisms get default...
- # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
- # 2 = INTEGRATED: Perfectly integrated deterministic.
-SIZE_MERIT_METHOD 4 # 0 = off (merit is independent of size)
- # 1 = Merit proportional to copied size
- # 2 = Merit prop. to executed size
- # 3 = Merit prop. to full size
- # 4 = Merit prop. to min of executed or copied size
- # 5 = Merit prop. to sqrt of the minimum size
-TASK_MERIT_METHOD 1 # 0 = No task bonuses
- # 1 = Bonus just equals the task bonus
-THREAD_SLICING_METHOD 0 # 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
-MERIT_TIME 1 # 0 = Merit Calculated when task completed
- # 1 = Merit Calculated on Divide
-MAX_NUM_TASKS_REWARDED -1 # -1 = Unlimited
-
-### Genotype Info ###
-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)
-TRACK_MAIN_LINEAGE 1 # Track primary lineage leading to final population?
-
-### 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.
-
-LOG_LINEAGES 0 # 0/1 (off/on) to log advantageous mutations
-# 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.
-# See also LINEAGE_CREATION_METHOD.
-
-LINEAGE_CREATION_METHOD 0
-# 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
-
-### END ###
-
-
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