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