expdef:
name:Reproduction of benthic foraminifera
info:~
Genes and parameter values which control reproduction are stored in user1 and user2 fields.

user1:
genes which are not encoded in Ff genotype:
min_repro_energy - Minimum energy necessary for reproduction
hibernation - Defines foram behavior in the case of no nutrients

user2:
Physiological parameters of foraminifera:
max_energy_level - maximum energy level reached so far
gen - generation: 0 haploid, 1 diploid
species - species: 0 not hibernating 1 hibernating
hibernated - 0/1 foram isn't/is hibernated
reproduce - 0/1 foram isn't/is ready for reproduction 
~
code:~

/*
changes 2015-06-24:
- xxx.get(...) changed to xxx[...]
- xxx.set(...,...) changed to xxx[...]=...
- function placeRandomlyNotColliding(cr) explicitly called when adding a new creature, and removed collision checking from onForamsBorn() which is also called when "growing" (since "growing" is implemented as creating a new creature in place of the old one, so onForamsBorn() is also called)
- use creature's center (not the bbox corner) when growing
- added "S" receptor to visualize the difference between diplo and haplo generations
- signal.value is a MechPart (a reference) so it does not have to be updated after changing the object location
*/

global nutrientenergywaiting;
global reprocounter;
global colors;
global chambers;
global o;
global max_chamber_energ;


@include "foraminifera.inc"

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

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

	var pop = Populations[0];
	pop.name = "Forams";
	pop.en_assim = 0;
	pop.nnsim = 0;
	pop.enableperf = 1;
	pop.death = 1;
	pop.energy = 1;
	pop.selfmask = 0x10001;
	pop.othermask = 0x20001;
	//pop.selfmask = 0x20002; pop.othermask = 0x10002;
	pop.perfperiod = 25; 

	pop = Populations.addGroup("Nutrients");
	pop.nnsim = 0;
	pop.enableperf = 0;
	pop.death = 1;
	pop.energy = 1;
	pop.selfmask = 0x20002;
	pop.othermask = 0x10000;
	//pop.othermask = 0x10002;

	//world
	SignalView.mode = 1;
	ExpParams.world_size = 100;
	World.wrldwat = ExpParams.world_size;
	World.wrldsiz = ExpParams.world_size;
	World.wrldbnd = 1;
	ExpParams.stress = 1;
	ExpParams.creath = -0.99; //just above the bottom
	ExpParams.autorestart = 0;

	//ExpParams.logging = 1; //uncomment to enable logging simulation parameters to log files

	//reproduction
	ExpParams.foramPop = 3;
	ExpParams.crossprob = 0.4;
	ExpParams.mutationprob = 0.2;
	ExpParams.repro_time = 20;
	reprocounter = 0;

	//morphology
	init_chambers();
	ExpParams.chamber_proculus_haplo = scale(60);
	ExpParams.chamber_difference_haplo = 0.0;
	ExpParams.chamber_proculus_diplo = scale(20);
	ExpParams.chamber_difference_diplo = 0.2;
	max_chamber_energ = [Vector.new(), Vector.new()];
	for (var j = 0; j < 2; j++)
	{
		for (var i = 0; i < chambers[0].size; i++)
		{
			max_chamber_energ[j].add(((Math.pow(getProperty(j, "chamber_proculus"),3) + Math.pow(getProperty(j, "chamber_proculus") + (i) * getProperty(j, "chamber_difference"),3))*(i+1))/2);

		}                                  
	}
	ExpParams.zone1_range = scale(250);
	ExpParams.zone2_range = scale(5000);

	//energetics
	ExpParams.min_repro_energ_haplo = max_chamber_energ[0][2];
	ExpParams.min_repro_energ_diplo = max_chamber_energ[1][8];
	ExpParams.e_meta = 0.00003 * max_chamber_energ[0][0];
	ExpParams.energy_hib = 0.00003 * max_chamber_energ[0][0];
	ExpParams.energy_move = 0.0003 * max_chamber_energ[0][0];
	ExpParams.energies0_haplo = max_chamber_energ[0][0] - 0.1*max_chamber_energ[0][0];
	ExpParams.energies0_diplo = max_chamber_energ[1][0] - 0.1*max_chamber_energ[1][0];
	ExpParams.feedtrans = 0.05;
	ExpParams.e_repro_cost_haplo = 0.5; 
	ExpParams.e_repro_cost_diplo = 0.3;

	//nutrients
	ExpParams.nutrientsize = scale(10);
	ExpParams.energy_nut = 100 * Math.pow(ExpParams.nutrientsize, 3);
	ExpParams.nutrientPop = 10;
	ExpParams.feedrate = 0.0025;
	nutrientenergywaiting = ExpParams.energy_nut;
	ExpState.totaltestedcr = 0;
	ExpState.nutrient = "";
}

@include "standard_placement.inc"

function scale(x)
{
	return x*0.025;
}

function getProperty(gen, prop_id)
{
	var ploid = "haplo";
	if (gen == 1) ploid = "diplo";
	return ExpParams.[prop_id + "_" + ploid];
}

function addInitialForam(species, i)
{
	var geno = createForamGenotype(0, species, 0);
	var cr = Populations[0].add(geno);
	cr.name = "Initial creature" + species + "_" + i;
	placeCreatureRandomly(cr, 0, 0);
	cr.energy0 = getProperty(0, "energies0");
	cr.energy = cr.energy0;
	setGenotype({"opt" : 0, "cr" : cr, "species" : species});
}

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

	for (var i = 0; i < ExpParams.foramPop; i++)
	{
		addInitialForam(0, i);	
		addInitialForam(1, i);
	}
	o = Populations[0][0].getMechPart(0).orient.clone();
	ExpState.totaltestedcr = 0;
	nutrientenergywaiting = ExpParams.energy_nut;
}

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 + " Forams and " + Populations[1].size + " nutrient 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 tmpvec = [], i;

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

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

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

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

// -------------------------------- foram begin -----------------------------------

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

function placeRandomlyNotColliding(cr)
{
	var retry = 100; //try 100 times
	while (retry--)
	{
		placeCreatureRandomly(cr, 0, 0);
		if (!cr.boundingBoxCollisions(0))
			return cr;
	}

	Populations[0].delete(cr);
}

function foramGrow(cr, chamber_num)
{
	var geno = createForamGenotype(cr.user2["gen"], cr.user2["species"], chamber_num);
	var cr2 = Populations[0].add(geno);

	cr2.energy0 = cr.energy;
	cr2.energy = cr2.energy0;

	setGenotype({"cr" : cr2, "parent_user1" : cr.user1, "parent_user2" : cr.user2, "opt" : 2});
	cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);

	Populations[0].delete(cr);
}

function stepToNearest(cr, range)
{
	var p = cr.getMechPart(0);
	var n = cr.signals.receiveSet("nutrient", ExpParams.zone2_range);

	//if signals are received find the source of the nearest
	if (n.size > 0)
	{
		var i;
		var mp;
		var distvec = XYZ.new(0, 0, 0);
		var dist;
		var mindist = 100000000000;
		var mindistvec = null;

		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();
			}
		}

		mindistvec.normalize();
		mindistvec.scale(-0.08);
		cr.localDrive = mindistvec;
		return 1;
	}
	
	else
		return 0;
}

function moveEnergyDec(cr)
{
	if (cr.user2["hibernated"] == 1)
	{
		cr.energy_m += ExpParams.energy_hib;
	}
	else
	{
		cr.energy_m += ExpParams.energy_move;
	}
}

function foramMove(cr)
{
	//TODO moving inside sediment?

	//adjustment in z axis
	cr.moveAbs(cr.pos_x, cr.pos_y, 0.5);

	//are there any nutrients in zone 1?
	if (cr.boundingBoxCollisions() == 2)
	{
		if (cr.user2["hibernated"] == 1)
			cr.user2["hibernated"] = 0;
		return;	
	}

	else if (cr.user2["hibernated"] == 1)
	{ 
		moveEnergyDec(cr);
		return;
	}

	//are there any nutrients in zone 2?
	else
	{
		var moved = stepToNearest(ExpParams.zone2_range); //TODO weighted sum of distance and energy
		if (moved==1)
		{
			moveEnergyDec(cr); 
			return;
		}
	}

	//no nutrients in zone 2

	var hibernation = 0;
	if (cr.user2["gen"] == 0) hibernation =  cr.user1["hibernation"];
	else hibernation =  cr.user1[0]["hibernation"];
	//hibernation
	if (hibernation == 1)
	{
		moveEnergyDec(cr);
		cr.user2["hibernated"] = 1;
		cr.localDrive = XYZ.new(0,0,0);
	}
	//random move
	else
	{
		cr.localDrive = (0.1 * Math.rnd01, 0.1 * Math.rnd01, 0);
		moveEnergyDec(cr);
	}
}

function onForamsCollision()
{
	if (Collision.Creature1.user2 != null)
	{
		Collision.Creature1.localDrive = XYZ.new(0,0,0);
		var e = Collision.Part2.ing * ExpParams.feedtrans; //TODO efficiency dependent on age
		//Simulator.print("transferring "+e+" to "+Collision.Creature1.name+" from "+Collision.Creature2.name+" ("+Collision.Creature2.energy+")");
		Collision.Creature2.energy_m = Collision.Creature2.energy_m + e;
		Collision.Creature1.energy_p = Collision.Creature1.energy_p + e;
		Collision.Creature1.user2["hibernated"] = 0;
	}
}

function onForamsStep(cr)
{
	cr.getMechPart(0).orient.set(o);

	if (deathConditions(cr) == 1)
	{
		Populations[0].kill(cr);
		return;
	}

	foramMove(cr);

	cr.user2["max_energy_level"] = Math.max(cr.energy, cr.user2["max_energy_level"]);
	if  (cr.numparts <= chambers[0].size)
	{
		if ((cr.user2["max_energy_level"] >= max_chamber_energ[cr.user2["gen"]][cr.numparts-1])) 	
		{
			foramGrow(cr, cr.numparts); 
			return;
		}	
	}

	foramReproduce(cr);	
}

function deathConditions(cr)
{
	if ((cr.energy <= ExpParams.e_death_level) || (Math.rnd01 < ExpParams.hunted_prob))
		return 1;
	else
		return 0;
}

function onForamsDied(cr)
{
	//fossilization
	var geno = GenePools[0].add(cr.genotype);
	geno.user1 = cr.user1;
	geno.user2 = cr.user2;
	if (ExpParams.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
	ExpState.totaltestedcr++;
}

// --------------------------------foram end -------------------------------------

// -------------------------------- nutrient begin --------------------------------

function createNutrientGenotype(nutrientsize, zone1_range)
{
	return "//0\np:sh=3,sx="+nutrientsize+",sy="+(zone1_range + nutrientsize)+",sz="+(zone1_range+nutrientsize)+",ry=1.5,vr=0.0,1.0,0.0"; 
}

function onNutrientsStep(cr)
{
	cr.moveAbs(cr.pos_x % ExpParams.world_size, cr.pos_y % ExpParams.world_size, -ExpParams.zone1_range+0.5);
}

function addNutrient()
{
	var cr = Populations[1].add(createNutrientGenotype(ExpParams.nutrientsize, ExpParams.zone1_range));

	cr.name = "Nutrients";
	cr.idleen = 0;
	cr.energy0 = ExpParams.energy_nut;
	cr.energy = cr.energy0;
	cr.signals.add("nutrient");

	cr.signals[0].value = cr.getMechPart(0);

	placeCreatureRandomly(cr, 0, 0);
}

function nutrientGrowth()
{
	nutrientenergywaiting = nutrientenergywaiting + ExpParams.feedrate;
	if (nutrientenergywaiting > ExpParams.energy_nut)
	{
		for (var i = 0; i < ExpParams.nutrientPop; i++)
		{
			addNutrient();
		}

		nutrientenergywaiting = 0.0;
		Simulator.checkpoint();
	}
}

// -------------------------------- nutrient end --------------------------------

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

function onStep()
{
	if (ExpParams.logging == 1)
	{
		createStatistics();
	}

	nutrientGrowth();

	//reproduction --------------------------------------------
	reprocounter += 1;
	if (reprocounter > ExpParams.repro_time)
	{
		reprocounter = 0;
		reproduce_parents(0);
		reproduce_parents(1);
	}

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

function createStatistics()
{	
	var number_ploidy = [0, 0];
	var number_species = [0, 0];
	var e_inc = [0.0, 0.0];
	var e_nut = 0.0;

	for (var i = 0; i < Populations[0].size; i++)
	{
		var cr = Populations[0].get(i);
		var gen = cr.user2["gen"];
		number_ploidy[gen] = number_ploidy[gen] + 1;
		var species = cr.user2["species"];
		number_species[species] = number_species[species] + 1; 
		e_inc[gen] = e_inc[gen] + cr.energy;
	}

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

	var log_numbers = [number_ploidy[0], number_ploidy[1], Populations[1].size];
	var log_species = [number_species[0], number_species[1]];
	var log_energy = [e_inc[0], e_inc[1], e_nut];

	log(log_numbers, "log_sizes.txt");
	log(log_species, "log_species.txt");
	log(log_energy, "log_energy.txt");
}

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

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

@include "standard_events.inc"

~

prop:
id:e_repro_cost_haplo
name:Cost of reproduction
type:f 0.1 0.9 0.5
group:Foraminifera

prop:
id:e_repro_cost_diplo
name:Cost of reproduction
type:f 0.1 0.9 0.3
group:Foraminifera

prop:
id:chamber_proculus_haplo
name:Size of proculus
type:f
group:Foraminifera

prop:
id:chamber_proculus_diplo
name:Size of proculus
type:f
group:Foraminifera

prop:
id:chamber_difference_haplo
name:Difference in size between subsequent chambers
type:f
group:Foraminifera

prop:
id:chamber_difference_diplo
name:Difference in size between subsequent chambers
type:f
group:Foraminifera

prop:
id:hunted_prob
name:Probability of being hunted
type:f 0 1 0
group:Forminifera

prop:
id:zone1_range
name:Zone 1 range 
type:f 0 200
group:Foraminifera

prop:
id:zone2_range
name:Zone 2 range
type:f 0 3000
group:Foraminifera

prop:
id:colors
name:Haploid and diploid colors
type:x
group:Foraminifera

prop:
id:min_repro_energ_haplo
name:Min reproduction energy of forams
type:f
group:Foraminifera

prop:
id:min_repro_energ_diplo
name:Min reproduction energy of forams
type:f
group:Foraminifera

prop:
id:repro_prob
name:Probability of reproduction
type:f 0 1 0.8
group:Foraminifera

prop:
id:energies0_haplo
name:Energy of offspring from diploid forams
type:f
group:Foraminifera

prop:
id:energies0_diplo
name:Energy of offspring from diploid forams
type:f
group:Foraminifera

prop:
id:energy_hib
name:Energy used for hibernation during one step
type:f 0 1 0.001
group:Foraminifera

prop:
id:energy_move
name:Energy used for movement during one step
type:f 0 20 0.001
group:Foraminifera

prop:
id:min_vol
name:Minimal volume for reproduction
type:f 100 900 100
group:Foraminifera

prop:
id:max_size
name:Maximal size
type:d 1 10 5 
group:Foraminifera

prop:
id:foramPop
name:Initial forams population size
type:d 1 1000 100
group:Foraminifera

prop:
id:crossprob
name:Crossover probability
type:f 0 1 0
group:Foraminifera

prop:
id:mutationprob
name:Mutation probability
type:f 0 1 0
group:Foraminifera

prop:
id:e_death_level
name:Minimal level of energy to sustain life
type:f 0 20 0
group:Foraminifera


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:energy_nut
name:Nutrients's energy
type:f 0 1000
group:Energy

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

prop:
id:nutrientsize
name:Nutrients's size
type:f 0.1 0.9 0.1
group:Energy

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

prop:
id:nutrientsize
name:Nutrients's size
group:Energy
type:f 0.1

prop:
id:nutrientPop
name:Nutrients population size
group:Energy
type:d 1 1000 10


prop:
id:world_size
name:World size
type:d 10 1000 20
group:World

prop:
id:stress
name:Environmental stress
type:d 0 1 1
group:World

prop:
id:repro_trigger
name:Reproduction trigger
type:d 0 1 1
group:World


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

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

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

prop:
id:autorestart
name:Restart after extinction
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 Forams
help:Total number of the Forams evaluated in the experiment
type:d
flags:16

prop:
id:logging
name:Log statistics to file
type:d 0 1 0