From dbff4414cae32e46a4a1d835af9d68e7c518a836 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Sat, 21 Jan 2023 15:06:40 +0100
Subject: [PATCH] Changed model RNG to StableRNG and enforced its use
---
run.sh | 2 +-
src/Persephone.jl | 3 ++-
src/core/input.jl | 2 +-
src/core/output.jl | 2 +-
src/core/simulation.jl | 11 +++++------
src/nature/ecologicaldata.jl | 15 ++++++++-------
src/nature/nature.jl | 13 ++++++++++++-
src/nature/populations.jl | 10 +++++-----
src/nature/species/wolpertinger.jl | 5 +++--
src/nature/species/wyvern.jl | 10 +++++-----
src/parameters.toml | 4 ++--
11 files changed, 45 insertions(+), 32 deletions(-)
diff --git a/run.sh b/run.sh
index 7cd3d64..fefbafe 100755
--- a/run.sh
+++ b/run.sh
@@ -6,6 +6,6 @@ then
rm -r temp_results
fi
-./run.jl -o temp_results -s 2
+./run.jl -o temp_results
src/analysis/analyse_nature.R temp_results
diff --git a/src/Persephone.jl b/src/Persephone.jl
index 1369288..3d86d2d 100644
--- a/src/Persephone.jl
+++ b/src/Persephone.jl
@@ -21,6 +21,7 @@ using
LoggingExtras,
#MacroTools, #http://fluxml.ai/MacroTools.jl/stable/utilities/
Random,
+ StableRNGs,
TOML
## define exported functions and variables
@@ -56,7 +57,7 @@ export
initialise,
stepsimulation!,
createevent!,
- finalise
+ finalise!
## include all module files (note that the order matters - if file
## b references something from file a, it must be included later)
diff --git a/src/core/input.jl b/src/core/input.jl
index 872486c..814d72d 100644
--- a/src/core/input.jl
+++ b/src/core/input.jl
@@ -33,7 +33,7 @@ Precedence: commandline parameters - user config file - default values
function getsettings(configfile::String, seed::Union{Int64,Nothing}=nothing)
# read in and merge configurations from the commandline, the default config file
# and a user-supplied config file
- defaults = TOML.parsefile(configfile)
+ defaults::Dict{String, Dict{String, Any}} = TOML.parsefile(configfile)
commandline = parsecommandline()
if haskey(commandline, "configfile") && isfile(commandline["configfile"])
configs = TOML.parsefile(commandline["configfile"])
diff --git a/src/core/output.jl b/src/core/output.jl
index dca2801..d0d7626 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -42,7 +42,7 @@ function setupdatadir(model::AgentBasedModel)
simulationlogger = TeeLogger(ConsoleLogger(logfile, loglevel),
ConsoleLogger(stdout, loglevel))
global_logger(simulationlogger)
- @debug "Setting up output directory $(@param(core.outdir))"
+ @debug "Setting up output directory $(@param(core.outdir))."
# Export a copy of the current parameter settings to the output folder.
# This can be used to replicate this exact run in future, and also
# records the current time and git commit.
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index 05a90d9..d47c372 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -20,7 +20,6 @@ configuration file and overriding the `seed` parameter.
function initialise(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
@info "Simulation run started at $(Dates.now())."
settings = getsettings(config, seed)
- Random.seed!(settings["core"]["seed"])
events = Vector{FarmEvent}()
dataoutputs = Vector{DataOutput}()
landscape = initlandscape(settings["core"]["landcovermap"], settings["core"]["farmfieldsmap"])
@@ -32,7 +31,7 @@ function initialise(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing
:events=>events)
@debug "Setting up model."
model = AgentBasedModel(Union{Farmer,Animal,FarmPlot}, space, properties=properties,
- rng=Random.Xoshiro(settings["core"]["seed"]), warn=false)
+ rng=StableRNG(settings["core"]["seed"]), warn=false)
setupdatadir(model)
initfarms!(model)
initfields!(model)
@@ -61,15 +60,15 @@ function stepsimulation!(model::AgentBasedModel)
end
"""
- finalise(model)
+ finalise!(model)
Wrap up the simulation. Currently doesn't do anything except print some information.
"""
-function finalise(model::AgentBasedModel)
+function finalise!(model::AgentBasedModel)
@info "Simulated $(model.date-@param(core.startdate))."
@info "Simulation run completed at $(Dates.now()),\nwrote output to $(@param(core.outdir))."
#XXX is there anything to do here?
- #genocide!(model)
+ model
end
"""
@@ -82,5 +81,5 @@ function simulate(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
model = initialise(config, seed)
runtime = Dates.value(@param(core.enddate)-@param(core.startdate))+1
step!(model, dummystep, stepsimulation!, runtime)
- finalise(model)
+ finalise!(model)
end
diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl
index 564097a..aa21296 100644
--- a/src/nature/ecologicaldata.jl
+++ b/src/nature/ecologicaldata.jl
@@ -21,9 +21,10 @@ end
"""
savepopulationdata(model)
-Print a comma-separated set of lines to `populations.csv`, giving the current date
-and population size for each animal species. May be called never, daily, monthly,
-yearly, or at the end of a simulation, depending on the parameter `nature.popoutfreq`.
+Return a comma-separated set of lines (to be printed to `populations.csv`), giving
+the current date and population size for each animal species. May be called never,
+daily, monthly, yearly, or at the end of a simulation, depending on the parameter
+`nature.popoutfreq`.
"""
function savepopulationdata(model::AgentBasedModel)
pops = Dict{String,Int}(s=>0 for s = @param(nature.targetspecies))
@@ -41,10 +42,10 @@ end
"""
saveindividualdata(model)
-Print a comma-separated set of lines to `individuals.csv`, listing all properties
-of all animal individuals in the model. May be called never, daily, monthly, yearly, or
-at the end of a simulation, depending on the parameter `nature.indoutfreq`.
-WARNING: Produces very big files!
+Return a comma-separated set of lines (to be printed to `individuals.csv`), listing
+all properties of all animal individuals in the model. May be called never, daily,
+monthly, yearly, or at the end of a simulation, depending on the parameter
+`nature.indoutfreq`. WARNING: Produces very big files!
"""
function saveindividualdata(model::AgentBasedModel)
data = ""
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 3606cd1..8010f13 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -156,7 +156,7 @@ variables:
Several utility macros can be used within the body of `@phase` as a short-hand for
common expressions: `@trait`, `@setphase`, `@respond`, `@here`, `@kill`,
-`@reproduce`, `@neighbours`.
+`@reproduce`, `@neighbours`, `@rand`.
Note that the first phase that is defined in a species definition block will be
the phase that animals are assigned at birth, unless the variable `phase` is
@@ -197,6 +197,7 @@ end
Switch this animal over to a different phase. This can only be used nested within `@phase`.
"""
macro setphase(newphase)
+ #XXX make this usable in the top part of a species definition?
:($(esc(:animal)).traits["phase"] = $(String(newphase)))
end
@@ -364,4 +365,14 @@ macro countanimals(args...)
:(countanimals($(esc(:pos)), $(esc(:model)); $(map(esc, args)...)))
end
+"""
+ @rand(args...)
+
+Return a random number or element from the sample, using the model RNG.
+This is a utility wrapper that can only be used nested within `@phase` or `@habitat`.
+"""
+macro rand(args...)
+ :(rand($(esc(:model)).rng, $(map(esc, args)...)))
+end
+
##TODO add movement macros
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index dbe6924..a760088 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -40,15 +40,15 @@ function initpopulation(habitatdescriptor::Function; phase::Union{String,Nothing
(!isnothing(phase)) && (species["phase"] = phase)
width, height = size(model.landscape)
while n == 0 || n < popsize
- for x in shuffle!(Vector(1:width))
- for y in shuffle!(Vector(1:height))
+ for x in shuffle!(model.rng, Vector(1:width))
+ for y in shuffle!(model.rng, Vector(1:height))
if habitatdescriptor((x,y), model)
if pairs
add_agent!((x,y), Animal, model, deepcopy(species), female, 0)
add_agent!((x,y), Animal, model, deepcopy(species), male, 0)
n += 2
else
- sex = asexual ? hermaphrodite : rand([male, female])
+ sex = asexual ? hermaphrodite : rand(model.rng, [male, female])
add_agent!((x,y), Animal, model, deepcopy(species), sex, 0)
n += 1
end
@@ -88,7 +88,7 @@ Produce one or more offspring for the given animal at its current location.
"""
function reproduce!(animal::Animal, model::AgentBasedModel, n::Int64=1)
for i in 1:n
- sex = (animal.sex == hermaphrodite) ? hermaphrodite : rand([male, female])
+ sex = (animal.sex == hermaphrodite) ? hermaphrodite : rand(model.rng, [male, female])
# We need to generate a fresh species dict here
species = @eval $(Symbol(animal.traits["name"]))($model)
add_agent!(animal.pos, Animal, model, species, sex, 0)
@@ -103,7 +103,7 @@ Kill this animal, optionally with a given percentage probability.
Returns true if the animal dies, false if not.
"""
function kill!(animal::Animal, model::AgentBasedModel, probability::Float64=1.0, cause::String="")
- if rand() < probability
+ if rand(model.rng) < probability
postfix = isempty(cause) ? "." : " from $cause."
@debug "$(animalid(animal)) has died$(postfix)"
kill_agent!(animal, model)
diff --git a/src/nature/species/wolpertinger.jl b/src/nature/species/wolpertinger.jl
index a4bc779..af1f1b6 100644
--- a/src/nature/species/wolpertinger.jl
+++ b/src/nature/species/wolpertinger.jl
@@ -25,11 +25,12 @@ of a deer.
"""
@phase lifephase begin
direction = Tuple(rand([-1,1], 2))
- for i in 1:rand(1:@trait(maxspeed))
+ for i in 1:@rand(1:@trait(maxspeed))
walk!(animal, direction, model; ifempty=false)
end
- if rand() < @trait(fecundity) && @countanimals(species="Wolpertinger") < @trait(crowding)
+ if @rand() < @trait(fecundity) &&
+ @countanimals(species="Wolpertinger") < @trait(crowding)
@reproduce
end
diff --git a/src/nature/species/wyvern.jl b/src/nature/species/wyvern.jl
index dc6be0b..f5a8fde 100644
--- a/src/nature/species/wyvern.jl
+++ b/src/nature/species/wyvern.jl
@@ -30,15 +30,15 @@ legs, but that doesn't make it any less dangerous...
# check if a wolpertinger is in pouncing distance
if a.traits["name"] == "Wolpertinger"
move_agent!(animal, a.pos, model)
- if rand() < @trait(huntsuccess)
+ if @rand() < @trait(huntsuccess)
@debug "$(animalid(animal)) killed $(animalid(a))."
kill_agent!(a, model)
@goto reproduce
end
- elseif a.traits["name"] == "Wyvern" && rand() < @trait(aggression)
+ elseif a.traits["name"] == "Wyvern" && @rand() < @trait(aggression)
# wyverns also fight against each other if they get too close
move_agent!(animal, a.pos, model)
- outcome = rand()
+ outcome = @rand()
if outcome < 0.4
@debug "$(animalid(animal)) killed $(animalid(a)) in a fight."
kill_agent!(a, model)
@@ -49,7 +49,7 @@ legs, but that doesn't make it any less dangerous...
end
end
# check if a wolpertinger is in seeing distance, or walk in a random direction
- direction = Tuple(rand([-1,1], 2))
+ direction = Tuple(@rand([-1,1], 2))
for a in @neighbours(@trait(vision))
if a.traits["name"] == "Wolpertinger"
direction = get_direction(animal.pos, a.pos, model)
@@ -61,7 +61,7 @@ legs, but that doesn't make it any less dangerous...
end
# reproduce every once in a blue moon
@label reproduce
- (rand() < @trait(fecundity)) && @reproduce
+ (@rand() < @trait(fecundity)) && @reproduce
# hibernate from November to March
if monthday(model.date) == (11,1)
@trait(phase) = "winter"
diff --git a/src/parameters.toml b/src/parameters.toml
index d028184..9f8f8e0 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -13,10 +13,10 @@ farmfieldsmap = "data/fields_jena.tif" # location of the field geometry map
outdir = "results" # location and name of the output folder
overwrite = "ask" # overwrite the output directory? (true/false/"ask")
loglevel = "debug" # verbosity level: "debug", "info", "quiet"
-seed = 0 # seed value for the RNG (0 -> random value)
+seed = 2 # seed value for the RNG (0 -> random value)
# dates to start and end the simulation
startdate = 2022-01-01
-#enddate = 2022-01-02
+#enddate = 2022-03-31
enddate = 2022-12-31
[farm]
--
GitLab