source: experiments/frams/foraminifera/data/scripts/foraminifera.expdef @ 1100

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.initial_nn_active = 0;
        pop.initial_perf_measuring = 1;
        pop.death = 1;
        pop.energy = 1;
        pop.selfmask = 0;
        pop.othermask = 0;
        //pop.selfmask = 0x20002; pop.othermask = 0x10002;
        pop.perfperiod = 25;
        pop.initial_physics_active = 0;

        pop = Populations.addGroup("Nutrients");
        pop.initial_nn_active = 0;
        pop.initial_perf_measuring = 0;
        pop.death = 1;
        pop.energy = 1;
        pop.selfmask = 0;
        pop.othermask = 0;
        //pop.othermask = 0x10002;
        pop.initial_physics_active = 0;

        pop = Populations.addGroup("ReticulopodiaNutrients");
        pop.initial_nn_active = 0;
        pop.initial_perf_measuring = 0;
        pop.death = 0;
        pop.energy = 0;
        pop.selfmask = 0;
        pop.othermask = 0;
        pop.initial_physics_active = 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("//0s\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.hasKey("reticulopodiacreature"))
        {
                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 "//0s\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("//0s\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: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

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

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

property:
id:print_evol_progress
name:Print evolution progress
help:Print messages on evolution progress
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