source: experiments/frams/foraminifera/data/scripts/foraminifera.expdef @ 384

expdef:
name:Foraminifera simulation
info:~
Genes and parameter values which control reproduction are stored in user1 and user2 fields.

user1:
genes which are not encoded in ff genotype:
Vamin - Minimum stored energy necessary for reproduction
amin - minimal age for reproduction

user2:
Physiological parameters of foraminifera:
Va - amount of the stored energy
gen - generation: 0 haploid, 1 diploid
~
code:~

global foodenergywaiting;
global reprocounter;

// -------------------------------- experiment begin --------------------------------

function onExpDefLoad()
{
        // define genotype and creature groups
        GenePools.clear();
        Populations.clear();
        GenePools[0].name = "Unused";

        var pop = Populations[0];
        pop.name = "Creatures";
        pop.en_assim = 0;
        pop.nnsim = 1;
        pop.enableperf = 1;
        pop.death = 1;
        pop.energy = 1;
        pop.selfmask = 0x10001;
        pop.othermask = 0x30000;
        pop.perfperiod = 25;

        pop = Populations.addGroup("Food");
        pop.nnsim = 0;
        pop.enableperf = 0;
        pop.death = 1;
        pop.energy = 1;
        pop.selfmask = 0x20002;
        pop.othermask = 0x30002;

        ExpParams.genh = "/*F*/1,1.1,1.1,1.1,1,1,1";
        ExpParams.gend = "/*F*/1,1,1,1,1,1,1";
        ExpParams.p_mut = 50;
        ExpParams.e_meta = 0.1;
        ExpParams.feedrate = 0.7;
        ExpParams.feede0 = 100;
        ExpParams.feedtrans = 3;
        ExpParams.creath = -0.99; //just above the bottom
        ExpParams.foodgen = "//0\np:sh=1,sx=0.1,sy=0.1,sz=0.1";
        ExpParams.autorestart = 0;
        ExpParams.psize = 10;
        ExpParams.ofnumh = 14;
        ExpParams.ofnumd = 4;
        ExpParams.v_min_d = 200;
        ExpParams.v_min_h = 500;
        ExpParams.age_min_d = 150;
        ExpParams.age_min_h = 300;
        ExpParams.crossprob = 0.3;
        ExpParams.repro_time = 200;
        ExpParams.repro_thr = 1;

        ExpState.totaltestedcr = 0;
        ExpState.food = "";
        foodenergywaiting = ExpParams.feede0;
        reprocounter = 0;

        ExpParams.wsize = 30;

        World.wrldwat = 50;
        World.wrldsiz = ExpParams.wsize;
        World.wrldbnd = 1;
}

@include "standard_placement.inc"

function onExpInit()
{
        Populations[0].clear();
        Populations[1].clear();

        for (var i = 0; i < ExpParams.psize; i++)
        {
                var cr = Populations[0].add(ExpParams.genh);
                cr.name = "Initial creature" + i;
                placeCreatureRandomly(cr, 0, 0);
                cr.energ0 = ExpParams.v_min_h - ExpParams.repro_thr;
                cr.energy = cr.energ0;
                cr.user1 = {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h};
                cr.user2 = {"Va" : ExpParams.v_min_h - ExpParams.repro_thr, "gen" : 0 };
        }
        ExpState.totaltestedcr = 0;
        foodenergywaiting = ExpParams.feede0;
}

function onExpLoad()
{
        for (var pop in Populations)
                pop.clear();

        Loader.addClass(sim_params.*);
        Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
        Loader.run();

        Simulator.print("Loaded " + Populations[0].size + " creatures and " + Populations[1].size + " food objects");
}

function onExpLoad_Unknown()
{
        if (Loader.objectName == "org") // saved by the old expdef
        {
                var g = Genotype.newFromString("");
                Loader.currentObject = g;
                Interface.makeFrom(g).setAllDefault();
                Loader.loadObject();
                var cr = Populations[0].add(g);
                if (cr != null)
                {
                        cr.rotate(0, 0, Math.rnd01*Math.twopi);
                        if ((typeof(g.user1) == "Vector") && (g.user1.size >= 3))
                        { // [x,y,energy]
                                cr.move(g.user1[0] - cr.center_x, g.user1[1] - cr.center_y, 0);
                                cr.energy = g.user1[2];
                        }
                        else
                        {
                                cr.move(Math.rnd01*World.wrldsiz - cr.center_x, Math.rnd01*World.wrldsiz - cr.center_y, 0);
                        }
                }
        }
        else if (Loader.objectName == "Creature")
        {
                Loader.currentObject = CreatureSnapshot.new();
                Loader.loadObject();
                Populations[0].add(Loader.currentObject);
        }
}

function onExpSave()
{
        File.writeComment("saved by '%s.expdef'" % Simulator.expdef);

        var i, tmpvec = [];

        for (var cr in Populations[1])
                tmpvec.add([cr.center_x, cr.center_y, cr.energy]);

        ExpState.food = tmpvec;
        File.writeObject(sim_params.*);
        ExpState.food = null; //vectors are only created for saving and then discarded

        for (var cr in Populations[0])
                File.writeObject(cr);
}

// -------------------------------- experiment end --------------------------------

// -------------------------------- creature begin --------------------------------

function onCreaturesBorn(cr)
{
        cr.idleen = ExpParams.e_meta;
}

function readyToRepro(cr)
{
        cr.signals.add("repro");
        cr.signals.get(0).power = 1;
}

function onCreaturesStep(cr)
{
        cr.moveAbs(cr.pos_x, cr.pos_y, 0);
        var p = cr.getMechPart(0);
        var n = cr.signals.receiveSet("food", ExpParams.food_range);

        if (n.size > 0)
        {
                var i;
                var mp;
                var distvec = XYZ.new(0, 0, 0);
                var dist;
                var mindist = 100000000000;
                var mindistvec = null;

                if (Math.rnd01 < 0.8)
                {
                        for (i = 0;i < n.size;i++)
                        {
                                mp = n[i].value;
                                distvec.set(mp.pos);
                                distvec.sub(p.pos);
                                dist = distvec.length;
                                if (dist < mindist)
                                {
                                        mindist = dist;
                                        mindistvec = distvec.clone();
                                }
                        }
                }
                else
                {
                        mp = n[Math.random(n.size)].value;
                        distvec.set(mp.pos);
                        distvec.sub(p.pos);
                        mindistvec = distvec.clone();
                }

                mindistvec.normalize();
                mindistvec.scale( -0.1);
                cr.localDrive = mindistvec;
        }
        else
        {
                cr.localDrive = (0.1, 0, 0);
        }

        var properAge = cr.user2["Va"] >= cr.user1["vamin"];
        var properSize = cr.user1["amin"] <= cr.lifespan;

        //if creature has proper age and cytoplasm amount
        if ( properAge && properSize )
        {
                //reproduce with probability repro_prob
                if (Math.rnd01 <= ExpParams.repro_prob)
                {
                        readyToRepro(cr);
                }
        }
        if ( properAge && properSize && (cr.signals.receive("repro") > 0))
        {
                readyToRepro(cr);
        }
}

function onCreaturesDied(cr)
{
        //fossilization
        var geno = GenePools[0].add(cr.genotype);
        geno.user1 = cr.user1;
        geno.user2 = cr.user2;
        Simulator.print("\"" + cr.name + "\" died...");
        ExpState.totaltestedcr++;
}

// -------------------------------- creature end --------------------------------

// -------------------------------- food begin --------------------------------

function onFoodStep(cr)
{
        cr.moveAbs(cr.pos_x % ExpParams.wsize, cr.pos_y % ExpParams.wsize, 0.5);
}

function addfood()
{
        var cr = Populations[1].add(ExpParams.foodgen);

        cr.name = "Food";
        cr.idleen = 0;
        cr.energ0 = ExpParams.feede0;
        cr.energy = cr.energ0;
        cr.signals.add("food");

        cr.signals.get(0).value = cr.getMechPart(0);

        var retry = 50; //try 50 times
        while (retry--)
        {
                placeCreatureRandomly(cr, 0, 0);
                cr.signals.get(0).value = cr.getMechPart(0);
                if (!cr.boundingBoxCollisions(0))
                        return cr;
        }

        return cr;
}

function onFoodCollision()
{
        if (Collision.Creature2.user2 != null)
        {
                var e = Collision.Part2.ing * ExpParams.feedtrans;
                //Simulator.print("transferring "+e+" from "+Collision.Creature1.name+" to "+Collision.Creature2.name+" ("+Collision.Creature2.energy+")");
                Collision.Creature1.energy_m = Collision.Creature1.energy_m + e;
                Collision.Creature2.energy_p = Collision.Creature2.energy_p + e;
                var ener = float(Collision.Creature2.user2.get("Va"));
                var sum = float(float(ener) + float(e));
                Collision.Creature2.user2.set("Va", float(sum));
        }
}

// -------------------------------- food end --------------------------------

// -------------------------------- step begin --------------------------------

function reproduce(repro_list, number)
{
        for (var i = 0; i < repro_list.size; i++)
        {
                var parent = Populations[0].get(repro_list[i]);

                var energ = parent.user2["Va"] / number;
                for (var j = 0; j < number; j++)
                {
                        var cr = Populations[0].add(ExpParams.gend);
                        cr.energ0 = energ;
                        cr.energy = cr.energ0;
                        if (parent.user2["gen"] == 0)
                        {
                                cr.user1 = {"vamin" : ExpParams.v_min_d, "amin": ExpParams.age_min_d};
                        }
                        else
                        {
                                cr.user1 = {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h};
                        }
                        cr.user2 = { "Va" : cr.energ0, "gen" : 1 - parent.user2["gen"] };
                        placeCreatureRandomly(cr, 0, 0);
                }
        }
        for (var j = 0; j < repro_list.size; j++)
        {
                Populations[0].kill(repro_list[j]);
        }
}

function log(tolog, fname)
{
        var f = File.appendDirect(fname, "description");
        f.writeString("" + Simulator.stepNumber);
        for (var i = 0; i < tolog.size; i++)
        {
                f.writeString(";" + tolog[i]);
        }
        f.writeString("\n");
        f.close();
}



function onStep()
{
        var haploids = 0;
        var diploids = 0;
        var e_inc_h = 0.0;
        var e_inc_d = 0.0;
        var e_nut = 0.0;

        for (var i = 0; i < Populations[0].size; i++)
        {
                var cr = Populations[0].get(i);
                if (cr.user2["gen"] == 0)
                {
                        haploids += 1;
                        e_inc_h += cr.energy;
                }
                else
                {
                        diploids += 1;
                        e_inc_d += cr.energy;
                }
        }

        for (var i = 0; i < Populations[1].size; i++)
        {
                var cr = Populations[1].get(i);
                e_nut += cr.energy;
        }

        if (haploids < 2 && diploids == 0)
        {
                Simulator.print("no more creatures, stopped.");
                Simulator.stop();
        }

        var l1 = Vector.new();
        l1 = [haploids, diploids, Populations[1].size];
        var l2 = Vector.new();
        l2 = [e_inc_h, e_inc_d, e_nut];

        log(l1, "log.txt");
        log(l2, "log2.txt");
        //food growth ---------------------------------------------
        foodenergywaiting = foodenergywaiting + ExpParams.feedrate;
        if (foodenergywaiting > ExpParams.feede0)
        {
                for (var i = 0; i < ExpParams.foodPop; i++)
                {
                        addfood();
                }

                foodenergywaiting = 0.0;
                Simulator.checkpoint();
        }

        //reproduction --------------------------------------------
        reprocounter += 1;
        if (reprocounter > ExpParams.repro_time)
        {
                reprocounter = 0;
                var to_repro_h = Vector.new();
                var to_repro_d = Vector.new();
                for (var i = 0; i < Populations[0].size; i++)
                {
                        var cr = Populations[0].get(i);
                        if (cr.signals.size > 0)
                        {
                                if (cr.user2["gen"] == 0)
                                {
                                        to_repro_h.add(i);
                                }
                                else
                                {
                                        to_repro_d.add(i);
                                }
                        }
                }
                if (to_repro_h.size > 0)
                {
                        reproduce(to_repro_h, ExpParams.ofnumh);
                }
                if (to_repro_d.size > 1)
                {
                        reproduce(to_repro_d, ExpParams.ofnumd);
                }
        }

        //check for death -----------------------------------------------
        if (Populations[0].size == 0)
        {
                if (ExpParams.autorestart)
                {
                        Simulator.print("no more creatures, restarting...");
                        onExpInit();
                }
                else
                {
                        Simulator.print("no more creatures, stopped.");
                        Simulator.stop();
                }
        }
}

// -------------------------------- step end --------------------------------


@include "standard_events.inc"

~

prop:
id:wsize
name:world size
type:d 10 1000 20

prop:
id:foodPop
name:food size
type:d 1 1000 10

prop:
id:age_min
name:minimal age for reproduction
type:d 100 10000 200

prop:
id:age_min_h
name:Min reproduction age of haploid forams
type:d 100 10000 300
group:Foraminifera

prop:
id:age_min_d
name:Min reproduction age of diploid forams
type:d 100 10000 200
group:Foraminifera

prop:
id:v_min_h
name:Min reproduction energy of haploid forams
type:d 100 10000 300
group:Foraminifera

prop:
id:v_min_d
name:Min reproduction energy of diploid forams
type:d 100 10000 150
group:Foraminifera

prop:
id:repro_thr
name:treshold for reproduction
type:d 1 1000 1

prop:
id:food_range
name:range of food smell
type:d 0 10000 10000

prop:
id:repro_time
name:time before reproduction
type:d 0 1000

prop:
id:psize
name:initial population size
type:d 1 1000 100

prop:
id:ofnumh
name:Number of offspring from haploid forams
type:d
group:Foraminifera

prop:
id:ofnumd
name:Number of offspring from diploid forams
type:d
group:Foraminifera

prop:
id:repro_prob
name:probability of reproduction
type:f 0 1 0.9

prop:
id:crossprob
name:crossover probability
type:f 0 1

prop:
id:genh
name:Initial genotype of haploid forams
type:s 1
group:Foraminifera

prop:
id:gend
name:Initial genotype of diploid forams
type:s 1
group:Foraminifera

prop:
id:creath
name:Creation height
type:f -1 50
help:~
Vertical position (above the surface) where new creatures are revived.
Negative values are only used in the water area:
  0   = at the surface
-0.5 = half depth
-1   = just above the bottom~

prop:
id:p_mut
name:Mutations
type:f 0 100

prop:
id:e_meta
name:Idle metabolism
type:f 0 1
group:Energy
help:Each stick consumes this amount of energy in one time step

prop:
id:feedrate
name:Feeding rate
type:f 0 100
group:Energy
help:How fast energy is created in the world

prop:
id:feede0
name:Food's energy
group:Energy
type:f 0 1000

prop:
id:feedtrans
name:Ingestion multiplier
group:Energy
type:f 0 100

prop:
id:foodgen
name:Food's genotype
group:Energy
type:s 1

prop:
id:autorestart
name:Restart after extinction
group:
help:Restart automatically this experiment after the last creature has died?
type:d 0 1

state:
id:notes
name:Notes
type:s 1
help:~
You can write anything here
(it will be saved to the experiment file)~

state:
id:totaltestedcr
name:Evaluated creatures
help:Total number of the creatures evaluated in the experiment
type:d
flags:16

state:
id:food
name:Food locations
help:vector of vectors [x,y,energy]
type:x
flags:32