Merge branch 'master' into multicell-parasite

avida-core/tests/loadpopulation_divdupbug_regression/config/avida.cfg

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+# Let's output a bit about the threads and parasites to stdout
+VERBOSITY 3
+# We use a bigger world than default
+WORLD_X 25
+WORLD_Y 1000
+NUM_DEMES 40
+RANDOM_SEED 353548561
+
+
+
+# DEME CONFIGURATION
+#------------------------------------------------------------------------------
+
+# Deme seeding method.
+# 0 = Maintain old consistency
+# 1 = New method using genotypes
+DEMES_SEED_METHOD 0  # this doesn't matter for DEMES_USE_GERMLINE 1
+
+# Number of organisms in a deme to trigger its replication (0 = OFF).
+DEMES_REPLICATE_ORGS 625
+
+# Deme divide method.
+# Only works with DEMES_SEED_METHOD 1
+# 0 = Replace source and target demes
+# 1 = Replace target deme, reset source deme to founders
+# 2 = Replace target deme, leave source deme unchanged
+# 3 = Replace the target deme, and reset the number of resources consumed by the source deme.
+# 4 = Replace the target deme,  reset the number of resources consumed by the source deme, and kill the germ line organisms of the source deme
+DEMES_DIVIDE_METHOD 0
+
+# divide hosts into separate subpopulations of five deme slots
+DEMES_PARTITION_INTERVAL 10
+
+# Should demes use a distinct germline?
+# 0: No
+# 1: Traditional germ lines
+# 2: Genotype tracking
+# 3: Organism flagging germline
+DEMES_USE_GERMLINE 1
+
+# Give empty demes preference as targets of deme replication?
+DEMES_PREFER_EMPTY 1
+
+# Reset resources in demes on replication?
+# 0 = reset both demes
+# 1 = reset target deme
+# 2 = deme resources remain unchanged
+DEMES_RESET_RESOURCES 2
+
+# Number of offspring produced by a deme to trigger its replication.
+# 0 = OFF
+DEMES_REPLICATE_BIRTHS 0
+
+# Max number of births that can occur within a deme;
+# used with birth-count replication
+DEMES_MAX_BIRTHS 0
+
+# Give empty demes preference as targets of deme replication?
+DEMES_PREFER_EMPTY 1
+
+# Which demes can an offspring land in when it migrates?
+# 0 = Any other deme
+# 1 = Eight neighboring demes
+# 2 = Two adjacent demes in list
+# 3 = Proportional based on the number of points
+# 4 = Use the weight matrix specified in MIGRATION_FILE
+DEMES_MIGRATION_METHOD 4  # necessary for parasite migration
+
+# Probability of a parasite migrating to a different deme
+# NOTE: only works with DEMES_MIGRATION_METHOD 4
+DEMES_PARASITE_MIGRATION_RATE 0.002
+
+# Probability of an offspring being born in a different deme.
+DEMES_MIGRATION_RATE 0.0
+
+MIGRATION_FILE migration.mat
+
+# Log deme replications?
+LOG_DEMES_REPLICATE 1
+# Log injection of organisms.  0/1 (off/on)
+LOG_INJECT 1
+
+
+# Cell Configuration
+#------------------------------------------------------------------------------
+
+# Make birth non-spatial
+# Which organism should be replaced when a birth occurs?
+# 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
+# 11 = Local neighborhood dispersal
+# 12 = Kill offpsring after recording birth stats (for behavioral trials)
+# 13 = Kill parent and offpsring (for behavioral trials)
+BIRTH_METHOD 6 # random within deme
+# Overide BIRTH_METHOD to preferentially choose empty cells for offsping?
+PREFER_EMPTY 0
+
+# Hosts get to live a bit longer than usual
+# When should death by old age occur?
+# When executed genome_length * AGE_LIMIT (+dev) instructions
+AGE_LIMIT 30
+
+
+
+# MUTATION CONFIGURATION
+#------------------------------------------------------------------------------
+
+# should be redundant with disabling indel mutations, but
+# parasites are somehow figuring out how to shrink anyways
+# (likely due to bug in Avida :/)
+# note: hosts have a larger genome size of 240 :)
+MIN_GENOME_SIZE 80
+
+# Substitution rate (per copy)
+# We assign mtuation rates independently for hosts/parasites
+COPY_MUT_PROB 0
+# Insertion rate (per copy)
+COPY_INS_PROB 0
+# Deletion rate (per copy)
+COPY_DEL_PROB 0
+# Uniform mutation probability (per copy)
+# Randomly apply insertion, deletion or substition mutation
+COPY_UNIFORM_PROB 0
+# Slip rate (per copy)
+COPY_SLIP_PROB 0
+
+# Substitution rate (per site, applied on divide)
+DIV_MUT_PROB 0.001000
+# Insertion rate (per site, applied on divide)
+DIV_INS_PROB 0.0
+# Deletion rate (per site, applied on divide)
+DIV_DEL_PROB 0.0
+# Uniform mutation probability (per site, applied on divide)\n- Randomly apply insertion, deletion or point mutation
+DIV_UNIFORM_PROB 0.0
+# Slip rate (per site, applied on divide)
+DIV_SLIP_PROB 0.0
+
+# Substitution rate (max one, per divide
+DIVIDE_MUT_PROB 0
+# Insertion rate (max one, per divide)
+DIVIDE_INS_PROB 0
+# Deletion rate (max one, per divide)
+DIVIDE_DEL_PROB 0
+
+# Substitution rate (per site, applied on inject)
+INJECT_MUT_PROB 0.005625
+# Insertion rate (per site, applied on inject)
+INJECT_INS_PROB 0.0
+# Deletion rate (per site, applied on inject)
+INJECT_DEL_PROB 0.0
+
+# Prob. of copy mutations during germline replication
+GERMLINE_COPY_MUT 0.0075
+# Prob. of insertion mutations during germline replication
+GERMLINE_INS_MUT 0.0
+# Prob. of deletion mutations during germline replication
+GERMLINE_DEL_MUT 0.0
+
+# Keep genomes from programatically creating their own variation
+# ...because it's complicated enough as is
+# Should genotypes that cannot replicate perfectly not be allowed to replicate?
+STERILIZE_UNSTABLE 1
+
+GENOME_SIZE_RECOVERY 3  # sterilize too-small or too-large genomes
+
+
+# PARASITE CONFIGURATION
+#------------------------------------------------------------------------------
+
+# Don't reset host thread upon infection
+# What should happen to a parasite when it gives birth?
+# 0 = Leave the parasite thread state untouched.
+# 1 = Resets the state of the calling thread (for SMT parasites, this must be 1)
+INJECT_METHOD 1
+
+# 0: Infection always succeeds.
+# 1: Infection succeeds if parasite matches at least one host task
+# 2: Infection succeeds if parasite does NOT match at least one task
+# 3: Parasite tasks must match host tasks exactly (Matching Alleles)
+INFECTION_MECHANISM 1
+
+# If set to 1, at least one reaction is required for a successful divide
+REQUIRE_SINGLE_REACTION 1
+
+# Infection causes host steralization and takes all cpu cycles
+# (setting this to 1 will override inject_virulence)
+INJECT_IS_VIRULENT 0
+
+# The probabalistic percentage of cpu cycles allocated to the parasite instead of the host.
+# Ensure INJECT_IS_VIRULENT is set to 0.
+# This only works for single infection at the moment.
+# Note that this should be set to a default even if virulence is evolving.
+PARASITE_VIRULENCE 0.85
+
+# Maximum number of Threads a CPU can spawn
+MAX_CPU_THREADS 2
+
+# Should inject instruction be a no-op for non-parasites?
+# Prevents host-generated pseudo-parasites. 0 for no, 1 for yes.
+TRANSSMT_DISABLE_NONPARASITE_INJECT 1
+
+#Parasites use the TransSMT simulated hardware, which is setup in this weird way
+#include INST_SET=instset-transsmt.cfg

avida-core/tests/loadpopulation_divdupbug_regression/config/environment.cfg

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+RESOURCE resECHO:inflow=125:outflow=0.10
+# disable host task rewards to avoid weirdness due to having "fast" and
+# "slow" hosts at the same time
+
+REACTION NAND nand process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION NOT not process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION ORN orn process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3BO logic_3BO process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION AND and process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3CI logic_3CI process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION ANDN andn process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3BZ logic_3BZ process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3AG logic_3AG process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION OR or process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3CP logic_3CP process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3BY logic_3BY process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION NOR nor process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3BS logic_3BS process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3BA logic_3BA process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3CJ logic_3CJ process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3AH logic_3AH process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3AQ logic_3AQ process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3CN logic_3CN process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3CB logic_3CB process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3AX logic_3AX process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3AR logic_3AR process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3AO logic_3AO process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3CH logic_3CH process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1
+REACTION LOG3CC logic_3CC process:resource=resECHO:value=0.0:type=add:frac=1.0:min=0:max=1:  requisite:reaction_max_count=1

avida-core/tests/loadpopulation_divdupbug_regression/config/events.cfg

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+##############################################################################
+#
+# This is the setup file for the events system.  From here, you can
+# configure any actions that you want to have happen during the course of
+# an experiment, including setting the times for data collection.
+#
+# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
+#
+# This file is currently setup to record key information every 100 updates.
+#
+# For information on how to use this file, see:  doc/events.html
+# For other sample event configurations, see:  support/config/
+#
+##############################################################################
+
+# need to prevent extinction abort on startup
+i LoadPopulation host-parasite-smt.spop
+i LoadGermlines host-smt.sgerm 1
+
+u 5 Exit