expdef:
name:Reproduction of benthic foraminifera
info:~
Basic information about this simulation:
www.framsticks.com/foraminifera

Technical information:
Genes and parameter values which control reproduction are stored in data->genes and data->lifeparams fields.

genes:
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

lifeparams:
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 is/isn't hibernated
reproduce - 0/1 foram isn't/is ready for reproduction 
~
code:~

global colors;
global curColor;
global max_chamber_volume;
global movePerStep;
global reprocounter;
global changePeriod;
global phase;
global nutrientSqrCm;
global species_genes;
global max_chambers_def;
global foram_uid; //introduced because each replacement of a creature (while growing) would generate a new Creature.uid
global chamber_vis_denominator;
global curRadius;
global nutrient_num_counter;
global wrldsizSquareMeters;

@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 = 0;
	pop.othermask = 0;
	//pop.selfmask = 0x20002; pop.othermask = 0x10002;
	pop.perfperiod = 25; 
	pop.bodysim = 0;

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

	pop = Populations.addGroup("ReticulopodiaNutrients");
	pop.nnsim = 0;
	pop.enableperf = 0;
	pop.death = 0;
	pop.energy = 0;
	pop.selfmask = 0;
	pop.othermask = 0;
	pop.bodysim = 0;

	//world
	SignalView.mode = 1;
	World.wrldwat = 200;
	World.wrldsiz = micronsToFrams(100000);
	wrldsizSquareMeters = Math.pow(framsToMicrons(World.wrldsiz)*0.000001,2);
	World.wrldbnd = 1;

	//ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions

	//ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files	
	ExpProperties.logPref = "";

	//morphology
	ExpProperties.zone1_range = micronsToFrams(1000);
	ExpProperties.zone2_range = micronsToFrams(3000);
	ExpProperties.chamber_proculus_haplo = micronsToFrams(20);
	ExpProperties.chamber_proculus_diplo = micronsToFrams(10);
	colors = ["1.0,1.0,0.3","1.0,0.7,0.0"]; //yellow and orange
	curColor = colors[0];
	curRadius = ExpProperties.zone1_range;

	//nutrients
	ExpProperties.nutrientradius = micronsToFrams(10);
	ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
	nutrientSqrCm = 10;
	ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;

	ExpState.totaltestedcr = 0;
	ExpState.nutrient = "";

	max_chambers_def = 35;
	chamber_vis_denominator = 12;
	//addSpecies({"min_repro_energies" : [4,6]});
	//addSpecies({"min_repro_energies" : [4,8]});
	
	//Simulator.print(create_genotype(0.2, 30, "1.0,1.0,0.0", 0.6)); //sample call
	//Simulator.print(create_genotype(0.1, 40, "1.0,0.5,0.0", 0.1)); //sample call
}

@include "standard_placement.inc"

function onExpInit()
{
	species_genes = [];
	foram_uid = 0;
	movePerStep = getMovePerStep();

	Populations[0].clear();
	Populations[1].clear();
	Populations[2].clear(); //reticulopodia and nutrients

	if (ExpProperties.max_chamber_num_haplo == max_chambers_def && ExpProperties.max_chamber_num_diplo == max_chambers_def)
	{
		max_chamber_volume = [[30403.5869594578,52812.2546633948,79578.5148482541,113588.815134453,154620.677376218,205094.322220826,262572.712174265,326078.453295303,402342.518962956,498133.985678766,615066.864740109,759500.497626816,937064.025544282,1155915.25563075,1429139.14079748,1762487.92940157,2176286.62046069,2685795.63187845,3316190.12127043,4096436.04462706,5051343.25226193,6231980.1061213,7687880.79524734,9485307.02904958,11716968.9852569,14459866.4934433,17836388.9853663,22004935.7247348,27138607.2546045,33482425.1582986,41336775.1280297,50997910.7842793,62888631.7871037,77563060.9243464,95659468.591964]
, [3430.07716920763,6159.93090353532,9322.94192815286,13462.9896597283,18399.8550832969,24558.9218126892,31468.8148639192,39189.4977865513,48404.4292075836,60185.8639086061,74490.6048472854,92117.8178412275,113852.779747083,140714.366929552,174450.937643841,215250.242147183,266323.295274072,328858.042352538,406552.379957238,503526.321155323,621060.781025019,767240.824049468,947210.683224091,1169506.19906112,1447211.61255879,1787155.29073739,2205627.64766244,2723413.2837305,3360233.53738709,4147771.02835393,5126445.06973928,6328060.3331703,7805693.278958,9631924.72156452,11884287.1596814]];
	}

	else
	{
		max_chamber_volume = [Vector.new(), Vector.new()];
		var density = 100;
		for (var ploid = 0; ploid < 2; ploid++) 
		{
			var rad = getPloidRadius(ploid);
			for (var cham_num = 0; cham_num < getProperty(ploid,"max_chamber_num"); cham_num++)
			{
				max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num+1, density));
			}                                  
		}
	}

	if (species_genes.size == 0)
	{
		addSpecies({}); //default
	}

	for (var spec = 0; spec < species_genes.size; spec++)
	{
		for (var i = 0; i < ExpProperties.foramPop; i++)
		{
			addInitialForam(spec, i);	
		}
	}
	ExpState.totaltestedcr = 0;

	reprocounter = 0;
	nutrient_num_counter = 0;
	changePeriod = 0;
	phase = "low";
}

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.data->genes) == "Vector") && (g.data->genes.size >= 3))
			{
				// [x,y,energy]
				cr.move(g.data->genes[0] - cr.bboxCenter.x, g.data->genes[1] - cr.bboxCenter.y, 0);
				cr.energy = g.data->genes[2];
			}
			else
			{
				cr.move(Math.rnd01 * World.wrldsiz - cr.bboxCenter.x, Math.rnd01 * World.wrldsiz - cr.bboxCenter.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.bboxCenter.x, cr.bboxCenter.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 --------------------------------

function volumeFromGeno(morphotype, rad, chamber_num, density)
{
	var geno = create_genotype(rad, chamber_num, colors[morphotype], 1);
	var m=Model.newFromString(geno);
	var mg=ModelGeometry.forModel(m);
	mg.geom_density=density; 
	var volumeInFrams = mg.volume();

	return volumeInFrams/Math.pow(ExpProperties.scalingFactor,3);
}

function secToSimSteps(value_in_sec){
	return value_in_sec/ExpProperties.secPerStep;
}

function volumeInMicrons(radiusInFrams)
{
	return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
}

function energyFromVolume(base, isRadiusInFrams)
{
	if (isRadiusInFrams == 1) //radius in frams
	{
		return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
	}
	else //volume in microns
	{
		return ExpProperties.picoCarbonPerMikro * base;
	}
}

function getMovePerStep()
{
	return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
}

function micronsToFrams(micrometers)
{
	return micrometers*ExpProperties.scalingFactor;
}

function framsToMicrons(framsworldunits)
{
	return framsworldunits/ExpProperties.scalingFactor;
}

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

function getGene(cr, gen_id, gen_set)
{
	if (cr.data->lifeparams->gen == 0) 
		return cr.data->genes[gen_id];
	else 
		return cr.data->genes[gen_set][gen_id];
}

function getPloidRadius(ploid)
{
	var radius = ExpProperties.chamber_proculus_haplo;
		if (ploid == 1)
		{
			radius = ExpProperties.chamber_proculus_diplo;
		}
	return radius;
}

function chamberNumFromEnergy(energy, ploid)
{
	var chamber_num = max_chamber_volume[ploid].size;
	for (var i = 0; i < chamber_num; i++)
	{
		if (energy < energyFromVolume(max_chamber_volume[ploid][i],0))
		{
			chamber_num = i+1;
			break;
		}	
	}                                  
	
	return chamber_num;
}

function createAndRotate(geno, rotate_min, rotate_max, pop_num)
{
	var cr = Populations[pop_num].add(geno);
	cr.rotate(0,0,Math.rndUni(rotate_min, rotate_max));
	return cr;	
}

//TODO unifiy addForam, foramGrow and createOffspring
function addForam(species, iter, start_energy, ploid)
{
	var chambernum =  chamberNumFromEnergy(start_energy, ploid);
	var radius = getPloidRadius(ploid);
	var geno = create_genotype(radius, chambernum, colors[ploid], 1);
	curColor = colors[ploid];
	var cr = createAndRotate(geno, 0, 2*Math.pi, 0);
	cr.name = "Initial creature" + species + "_" + iter;
	placeRandomlyNotColliding(cr);
	cr.energy = start_energy;
	setGenotype({"opt" : "birth", "cr" : cr, "gen" : ploid, "species" : species, "energy0" : cr.energy, "genes" : species_genes[species], "parentsuids" : ["c0"]});
	if (ploid == 1)
	{
		cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
	}
	moveReticulopodia(cr);
}

function addInitialForam(species, iter)
{
	var ploid = 0;
	if (Math.rnd01 > 0.5)
	{
		ploid = 1;
	}	
	//add new foram with random energy bewtween starting energy and reproduction threshold
	var repro_thr = species_genes[species]->min_repro_energies[ploid];
	var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid),1),repro_thr-0.25*repro_thr);
	addForam(species, iter, start_energy,ploid);
}

//new species can be added as a dictionary with parameter values that are different than default values
function addSpecies(new_genes)
{
	species_genes.add({"min_repro_energies" : [ExpProperties.min_repro_energ_haplo,ExpProperties.min_repro_energ_diplo], "energies0" : [ExpProperties.energies0_haplo, ExpProperties.energies0_diplo], "hibernation" : 0, "morphotype" : 0});
	for (var i = 0; i < new_genes.size; i++)
	{
		var key = new_genes.getKey(i);
		species_genes[species_genes.size-1][key] = new_genes[key];
	} 
}

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

function setForamMeta(cr)
{
	//percent of current energy
	cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
}

function lastChamberNum(cr)
{
	return cr.numparts;
}

function getZoneRange(cr, zone_num)
{
	return ExpProperties.["zone"+zone_num+"_range"];
}

function addReticulopodia(cr, radius)
{
		if (reticulopodiaExists(cr))
		{
			Populations[2].delete(cr.data->reticulopodiacreature);
		}
		var ret = Populations[2].add("//0\nm:Vstyle=reticulopodia\np:sh=1,sx=0.001,sy=0.001,sz=0.001\np:sh=3,sx=0.01,sy="+radius+",sz="+radius+",ry=1.57079633,vr="+curColor+"\nj:0, 1, sh=1");
		cr.data->reticulopodiacreature = ret;
		ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
		ret.locationSetBboxLow(cr.bboxCenter.x-radius, cr.bboxCenter.y-radius, cr.bboxCenter.z-radius);
}

function onForamsBorn(cr)
{
	setForamMeta(cr);
	if (ExpProperties.visualize == 1)
	{
		addReticulopodia(cr, curRadius);
		moveReticulopodia(cr);
	}
}

function placeRandomlyNotColliding(cr)
{
	var retry = 100; //try 100 times
	while (retry--)
	{
		placeCreatureRandomly(cr, 0, 0);
		if (!cr.boundingBoxCollisions(0))
		{
			cr.locationSetBboxLow(cr.bboxLow.x, cr.bboxLow.y, -cr.getPart(cr.numparts-1).sx); //place slightly under the bottom surface ("z" value depends on the size of the last=largest chamber)
			return cr;
		}
	}

	Populations[0].delete(cr);
}

function reticulopodiaExists(cr)
{
	var has_ret = 0;

	if (cr.data->reticulopodiacreature != null)
	{
		if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
		{
			has_ret = 1;
		}
	}

	return has_ret;
}

function visualization(cr)
{
	return reticulopodiaExists(cr);
}

function foramGrow(cr, chamber_num, lastchambergrowth)
{
	if ((chamber_num+1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
	{
		curColor = colors[cr.data->lifeparams->gen];
		var ploid = cr.data->lifeparams->gen;
		var geno = create_genotype(getPloidRadius(ploid), chamber_num+1, colors[ploid], lastchambergrowth);
		var cr2 = createAndRotate(geno, 0, 0, 0);

		cr2.orient.set(cr.orient);
		cr2.energy0 = cr.energy;
		cr2.energy = cr2.energy0;

		setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
		cr2.locationSetBboxLow(cr.bboxLow.x, cr.bboxLow.y,cr.bboxLow.z);
		setForamMeta(cr2);

		if (reticulopodiaExists(cr))
		{
			Populations[2].delete(cr.data->reticulopodiacreature);
		}
		Populations[0].delete(cr);
		return cr2;
	}
	return cr;
}

function visualizeChamberGrowth(cr, chamber_time)
{
	var total_time = secToSimSteps(ExpProperties.chamberGrowthSec);
	var ret_unit = total_time/chamber_vis_denominator;
	var chamber_unit = total_time-ret_unit;

	if (chamber_time < ret_unit || chamber_time >= chamber_unit)
	{
		var new_rad = Math.min(Math.max((chamber_time%ret_unit)/ret_unit*getZoneRange(cr,1),0.01),getZoneRange(cr,1));

		if(chamber_time < ret_unit)
		{
			new_rad = getZoneRange(cr,1)-new_rad;
		}

		curColor = colors[cr.data->lifeparams->gen];
		addReticulopodia(cr,new_rad);

		if (chamber_time == 0)//checking for end of chamber growth process
		{
			cr.data->lifeparams->chamber_growth = -1;	
		}
	}
	else
	{
		var new_rad = 1 - Math.min(Math.max((chamber_time-ret_unit)/chamber_unit,0.01),1);
		curRadius = cr.data->reticulopodiacreature.getPart(1).sy;
				
		if (chamber_time == ret_unit)
		{
			new_rad = 1;
		}

		var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen)-1, new_rad);
		curRadius = getZoneRange(new_cr,1);
	}
}

function stepToNearest(cr)
{
	var p = XYZ.new(cr.bboxCenter.x, cr.bboxCenter.y, cr.bboxCenter.z);
	var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));

	//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 = 100000000000.0;
		var mindistvec = null;
		var eating = 0;

		for (i = 0; i < n.size; i++)
		{
			mp = XYZ.new(n[i].value.bboxCenter.x, n[i].value.bboxCenter.y, n[i].value.bboxCenter.z);
			distvec.set(mp);
			distvec.sub(p);
			dist = distvec.length;
			if (dist < getZoneRange(cr,1))
			{
				if (n[i].value != null)
				{
					energyTransfer(cr, n[i].value);
					eating = 1;
				}
			}
			else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
			{
				mindist = dist;
				mindistvec = distvec.clone();
			}
		}

		if (!eating && cr.data->lifeparams->hibernated == 0)
		{
			mindistvec.z = 0;
			mindistvec.normalize();
			mindistvec.scale(movePerStep);
			cr.drive = mindistvec;
			moveEnergyDec(cr);
		}

		return 1;
	}
	
	else
	{
		return 0;
	}
}

function moveEnergyDec(cr)
{
	if (cr.data->lifeparams->hibernated == 0)
	{
		//percent of maximal energy
		cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
	}
}

function fence(center, zone)
{
	return Math.min(Math.max(0+zone,center),World.wrldsiz-zone); //add and subtract zone from the world size to prevent reticulopodia from crossing the fence
}

function foramMove(cr)
{
	//are there any nutrients in zone 1 or 2?
	{
		var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
		if (moved==1)
		{ 
			moveReticulopodia(cr);
			return;
		}
	}

	//Prevents forams from crossing the world border. In the case of touching the border with the reticulopodia direction of the movement should be changed. 
	var change_direction = 0;
	var new_x = fence(cr.bboxCenter.x, getZoneRange(cr, 1));
	var new_y = fence(cr.bboxCenter.y, getZoneRange(cr, 1));

	if ((new_x != cr.bboxCenter.x) || (new_y != cr.bboxCenter.y) || (cr.data->lifeparams->dir_counter >= int(secToSimSteps(ExpProperties.dir_change_sec))))
	{
		change_direction = 1;
		cr.locationSetBboxLow(new_x-cr.bboxSize.x/2, new_y-cr.bboxSize.y/2, -cr.getPart(cr.numparts-1).sx);//place slightly under the bottom surface ("z" value depends on the size of the last=largest chamber)
	}

	//no nutrients in zone 2
	if (getGene(cr, "hibernation",0) == 1)
	{
		reverseHib(cr);
		cr.drive = XYZ.new(0,0,0);
	}
	//random move
	else if (change_direction == 1)
	{
		cr.data->lifeparams->dir = randomDir();
		cr.data->lifeparams->dir_counter = 0;
		cr.drive = cr.data->lifeparams->dir;
		moveEnergyDec(cr);
	}
	else
	{
		cr.drive = cr.data->lifeparams->dir;
	}
	moveReticulopodia(cr);
}

function moveReticulopodia(cr)
{
	if (visualization(cr))
	{
		cr.data->reticulopodiacreature.locationSetBboxLow(cr.bboxCenter.x-getZoneRange(cr,1), cr.bboxCenter.y-getZoneRange(cr,1), cr.bboxCenter.z-getZoneRange(cr,1));
		cr.data->reticulopodiacreature.drive = cr.drive;
	}
}

function randomDir()
{
	var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0);	
	dir.normalize();
	dir.scale(-1*movePerStep);
	return dir;
}

function energyTransfer(cr1, cr2)
{
	cr1.drive = XYZ.new(0,0,0);
	var e =  ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
	//Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
	var transferred = cr2.transferEnergyTo(cr1, e);
	cr1.energy -= transferred*(1-ExpProperties.ingestion);
	if (cr1.data->lifeparams->hibernated == 1)
	{
		reverseHib(cr1);
	}
}

function reverseHib(cr)
{
	if (cr.data->lifeparams->hibernated == 1)
	{
		setForamMeta(cr); //unhibernate
	} 
	else
	{
		cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
	}
	cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
}

function onForamsStep(cr)
{
	//checking for gametogenesis process
	if (cr.data->lifeparams->division_time > 0)
	{
		cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
	}
	//checking for end of gametogenesis
	else if (cr.data->lifeparams->division_time == 0)
	{
		//waiting for gamets fusion
	}
	//checking for chamber growth process
	else if (cr.data->lifeparams->chamber_growth > 0)
	{
		var chamber_time = Math.max(cr.data->lifeparams->chamber_growth-1,0);
		cr.data->lifeparams->chamber_growth = chamber_time;
		cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;

		if (visualization(cr))
		{
			visualizeChamberGrowth(cr, chamber_time);
		}
	}
	//checking for end of the chamber growth process
	else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr)==0)
	{	
		foramGrow(cr, lastChamberNum(cr), 1); 
		cr.data->lifeparams->chamber_growth = -1;
		//Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
	}
	else
	{
		//update of metabolism rate
		if (cr.data->lifeparams->hibernated == 0)
		{
			setForamMeta(cr);
		}

		if (deathConditions(cr) == 1)
		{
			if (ExpProperties.logging == 1)
			{
				log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
				log(createLogVector(cr, cr.lifespan),ExpProperties.logPref+"lifespan_log.txt");
			}			
			Populations[0].kill(cr);
			return;
		}

		//update direction change counter
		cr.data->lifeparams->dir_counter += 1;

		foramMove(cr);

		var repro = foramReproduce(cr);
		if (repro == 1)
		{
			return;
		}

		cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);

		//cheking conditions of chamber growth process start
		if  (lastChamberNum(cr) < max_chamber_volume[cr.data->lifeparams->gen].size)
		{
			if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)-1],0))) 	
			{
				cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
			}	
		}
	}	
}

function deathConditions(cr)
{
	if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
	{
		return 1;
	}
	else
		return 0;
}

function onForamsDied(cr)
{
	if (visualization(cr))
	{
		Populations[2].delete(cr.data->reticulopodiacreature);
	}
	//fossilization
	var geno = GenePools[0].add(cr.genotype);
	geno.data->genes = cr.data->genes;
	geno.data->lifeparams = cr.data->lifeparams;
	if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
	ExpState.totaltestedcr++;
}

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

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

function createNutrientGenotype(nutrientradius)
{
	return "//0\nm:Vstyle=nutrient\np:sh=3,sx="+nutrientradius+",sy="+nutrientradius+",sz="+nutrientradius+",ry=1.57,vr=0.0,1.0,0.0";
}

function onNutrientsStep(cr)
{
	cr.locationSetBboxLow(cr.bboxLow.x % World.wrldsiz, cr.bboxLow.y % World.wrldsiz, 0.5);
}

function addNutrient()
{
	var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));

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

	cr.signals[0].value = cr;

	placeCreatureRandomly(cr, 0, 0);
	if (ExpProperties.visualize == 1)
	{
		var nutsize = ExpProperties.nutrientradius*10;
		var nut = Populations[2].add("//0\nm:Vstyle=nutrient_visual\np:sh=2,sx="+nutsize+",sy="+nutsize+",sz="+nutsize+",ry=1.5,vr=0.0,1.0,0.0");
		cr.data->reticulopodiacreature = nut;
		nut.locationSetBboxLow( cr.bboxLow.x+cr.bboxSize.x/2-nut.bboxSize.x/2,  cr.bboxLow.y+cr.bboxSize.y/2-nut.bboxSize.y/2, -nutsize); 
	}
}

function onNutrientsDied(cr)
{
	if (visualization(cr))
	{
		Populations[2].delete(cr.data->reticulopodiacreature);
	}
}

function getNumberCounter(counter, increase, unitsize) //increase counter and then deduct and return an integer (=discrete) number of "full" units
{
	counter += increase;
	var unitcount = int(counter/unitsize);
	counter -= unitcount*unitsize;
	return {"counter" : counter, "number" : unitcount};
}

function nutrientGrowth()
{
	if (ExpProperties.foodfluxChange > 0)
	{
			changePeriod += 1;
			if (phase=="low" && changePeriod >= secToSimSteps(23328000)) //9 months
			{
				ExpProperties.foodflux = ExpProperties.foodflux/ExpProperties.foodfluxChange;
				phase = "high";
				changePeriod = 0;
			}
		
			else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
			{
				ExpProperties.foodflux = ExpProperties.foodflux*ExpProperties.foodfluxChange;
				phase = "low";
				changePeriod = 0;
			}
	}

	var nutrientNum = getNumberCounter(nutrient_num_counter, ExpProperties.foodflux*wrldsizSquareMeters*ExpProperties.secPerStep,ExpProperties.energy_nut*0.000000000001); 

	nutrient_num_counter = nutrientNum["counter"];

	for (var i = 0; i < nutrientNum["number"]; i++)
	{    
		addNutrient();
	}

	if (ExpProperties.logging == 1 && nutrientNum["number"] > 0)
	{
		log([nutrientNum["number"]],ExpProperties.logPref+"nutrients_log.txt");
	}

}

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

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

function onStep()
{

	nutrientGrowth();
	if (ExpProperties.logging == 1)
	{
		createStatistics();
	}

	//reproduction --------------------------------------------
	reprocounter += 1;
	if (reprocounter > secToSimSteps(ExpProperties.reproTimeSec))
	{
		reprocounter = 0;
		for (var s = 0; s < species_genes.size; s++)
		{
			reproduce_parents(s);
		}
		
	}

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

function createStatistics()
{	
	var number = [];
	var e_inc = [];
	var e_nut = 0.0;

	for (var s = 0; s < species_genes.size; s++)
	{
		number.add([0,0]);// [haplo][diplo]
		e_inc.add([0,0]);
	}

	for (var i = 0; i < Populations[0].size; i++)
	{
		var cr = Populations[0].get(i);
		var gen = cr.data->lifeparams->gen;
		var species = cr.data->lifeparams->species;

		number[species][gen] = number[species][gen] + 1; 
		e_inc[species][gen] = e_inc[species][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 = [];
	var log_energies = [];

	for (var s = 0; s < species_genes.size; s++)
	{
		for (var p = 0; p < 2; p++)
		{
			log_numbers.add(number[s][p]);
			log_energies.add(e_inc[s][p]);
		}
	}
	
	log_numbers.add(Populations[1].size);
	log_energies.add(e_nut);

	log(log_numbers, ExpProperties.logPref+"forams_log.txt");
    log(log_energies,  ExpProperties.logPref+"energies_log.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();
}

function createLogVector(cr, value)
{
	var vec = Vector.new();
	for (var i = 0; i < species_genes.size; i++)
	{
		for (var j = 0; j < 2; j++)
		{
			vec.add(0);
		}
		if (cr.data->lifeparams->species == i)
		{
			vec[i*2+cr.data->lifeparams->gen] = value;		
		}
	}
	return vec;
}


// -------------------------------- step end --------------------------------
//TODO default params values in frams instead of microns/seconds

@include "standard_events.inc"

~

property:
id:visualize
name:Show reticulopodia and nutrients
type:d 0 1 0
group:

property:
id:maxSteps
name:Maximum number of steps
type:d 0 10000000 0
group:

property:
id:scalingFactor
name:Scaling factor for micrometers
type:f 0 -1 0.01
group:

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

property:
id:logPref
name:Log prefix
type:s

property:
id:secPerStep
name:Seconds per simulation step
help:~
Number of seconds of foraminifera time per simulation step.
Lower values mean smoother animation.~
type:f 1 480 300
flags: 16
group:

property:
id:foramSpeedMmPerMin
name:Speed of foraminfera in mm/min
type:f 0.01 0.1 0.05
flags: 16
group:Foraminifera

property:
id:dir_change_sec
name:Number of seconds before direction change
type:d 300 300000 6000
group:Foraminifera

property:
id:foramPop
name:Initial forams population size
type:d 1 1000 20
group:Foraminifera

property:
id:gametoPeriodSec
name:Time of gametogenesis
type:f 300 300000 21600
group:Reproduction

property:
id:gametSuccessRate
name:Ratio of successful gamets
type:f 0.0001 0.01 0.001
group:Reproduction

property:
id:divisionCost
name:Cost of division in pG
type:f 15 25 20
group:Reproduction

property:
id:min_repro_energ_haplo
name:Min reproduction energy of haploid in pg
type:f 0 -1 350000
group:Energy

property:
id:min_repro_energ_diplo
name:Min reproduction energy of diploid in pg
type:f 0 -1 600000
group:Energy

property:
id:repro_prob
name:Probability of reproduction
type:f 0 1 0.8
group:Reproduction

property:
id:energies0_haplo
name:Energy of offspring from diploid forams
type:f 0 -1 20
group:Energy

property:
id:energies0_diplo
name:Energy of offspring from diploid forams
type:f 0 -1 1.25
group:Energy

property:
id:max_chamber_num_haplo
name:Maximum number of haploid chambers
type:f 1 50 35
group:Energy

property:
id:max_chamber_num_diplo
name:Maximum number of diploid chambers
type:f 1 50 35
group:Energy

property:
id:crossprob
name:Crossover probability
type:f 0 1 0
group:Reproduction

property:
id:mutationprob
name:Mutation probability
type:f 0 1 0
group:Reproduction

property:
id:reproTimeSec
name:Time before reproduction
type:d 0 10000 720
group:Reproduction

property:
id:chamberGrowthSec
name:Time of the chamber growth in seconds
type:f 720 43200 43200
group:Foraminifera

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

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

property:
id:hunted_prob
name:Probability of being hunted
type:f 0 1 0
group:Foraminifera

property:
id:zone1_range
name:Zone 1 range in frams units
type:f 0 200 10
group:Foraminifera

property:
id:zone2_range
name:Zone 2 range in frams units
type:f 0 3000 30
group:Foraminifera

property:
id:chamberCostPerSec
name:Cost of growning chamber per second
type:f 0 1 0.000001
group:Energy

property:
id:e_death_level_haplo
name:Minimal level of energy to sustain life of haploid
type:f 0 1 0.5
group:Energy

property:
id:e_death_level_diplo
name:Minimal level of energy to sustain life of diploid
type:f 0 1 0.5
group:Energy

property:
id:energy_hib
name:Energy used for hibernation during one step
type:f 0 1 0.0000001
group:Energy

property:
id:energy_move
name:Energy used for movement during one step
type:f 0 1 0.0000005
group:Energy

property:
id:e_meta
name:Idle metabolism
type:f 0 1 0.0000005
group:Energy
help:Foraminifera consumes this proportion of its energy in one time step

property:
id:ingestion
name:Ingestion rate
type:f 0 -1 0.25
group:Energy

property:
id:nutrient_pop
name:Nutrient population
type:f 0 1000000
group:Energy
help:How fast energy is created in the world

property:
id:energy_nut
name:Nutrient energy
type:f 0 10000000
group:Energy

property:
id:nutrientradius
name:Nutrient size
type:f 0.001 0.9 0.1
group:Energy

property:
id:picoCarbonPerMikro
name:Picograms of carbon in cubic micrometer
type:f 0 -1 0.13
group:Energy

property:
id:feedtrans
name:Energy transfer per second
type:f 0 1 0.001
group:Energy

property:
id:foodflux
name:POM flux in grams per second per square meter
type:f 0 1 0.0000000075631
group:Energy

property:
id:foodfluxChange
name:Set variable feed rate
type:f 0 -1 0
group:Energy

property:
id:stress
name:Environmental stress
type:d 0 1 1
group:

property:
id:repro_trigger
name:Reproduction trigger
type:d 0 1 1
group:Reproduction

property:
id:creath
name:Creation height
type:f -1 50 -0.99
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~

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

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

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