source: experiments/frams/foraminifera/data/scripts/foraminifera.expdef @ 432

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 is/isn't 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;
global dir_change;

@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;

        //ExpParams.showRet = 1; //uncomment to show reticulopodia

        pop = Populations.addGroup("Reticulopodia");
        pop.nnsim = 0;
        pop.enableperf = 0;
        pop.death = 0;
        pop.energy = 0;
        pop.selfmask = 0x20002;
        pop.othermask = 0x10000;
        
        //world
        SignalView.mode = 1;
        World.wrldwat = 200;
        World.wrldsiz = scale(40000);
        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 = 10;        
        ExpParams.crossprob = 0.4;
        ExpParams.mutationprob = 0.2;
        ExpParams.repro_time = 20;
        reprocounter = 0;

        //morphology
        dir_change = 500;
        ExpParams.zone1_range = scale(5000);
        ExpParams.zone2_range = scale(8000);
        init_chambers();
        ExpParams.chamber_proculus_haplo = scale(50);
        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);
                }                                  
        }

        //energetics
        ExpParams.min_repro_energ_haplo = 4;
        ExpParams.min_repro_energ_diplo = 6;

        ExpParams.e_meta = 0.0002; 
        ExpParams.energy_hib = 0.0001;
        ExpParams.energy_move = 0.00025;

        ExpParams.energies0_haplo = max_chamber_energ[0][0] - 0.001*max_chamber_energ[0][0];
        ExpParams.energies0_diplo = max_chamber_energ[1][0] - 0.001*max_chamber_energ[1][0];
        ExpParams.feedtrans = 0.5;
        ExpParams.e_repro_cost_haplo = 0.7; 
        ExpParams.e_repro_cost_diplo = 0.3;

        //nutrients
        ExpParams.nutrientsize = scale(10);
        ExpParams.energy_nut = 100 * Math.pow(ExpParams.nutrientsize, 3);
        ExpParams.nutrientPop = 1;
        ExpParams.feedrate = 0.1;
        nutrientenergywaiting = ExpParams.energy_nut;
        ExpState.totaltestedcr = 0;
        ExpState.nutrient = "";

        ExpParams.iter = 0;
}

@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();
        Populations[2].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 setForamMeta(cr, gen)
{
        cr.idleen = ExpParams.e_meta * max_chamber_energ[gen][Math.min(lastChamberNum(cr), max_chamber_energ[gen].size-1)];
}

function lastChamberNum(cr)
{
        return cr.numparts-1;
}

function onForamsBorn(cr)
{
        setForamMeta(cr, 1);
        if (ExpParams.showRet == 1)
        {
                var ret = Populations[2].add("//0\np:sh=3,sx=0.01,sy="+ExpParams.zone1_range+",sz="+ExpParams.zone1_range+",ry=1.57");
                cr.user3 = ret;
        }
}

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+1);
        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);
        setForamMeta(cr2, cr2.user2["gen"]);

        if (ExpParams.showRet == 1)
        {
                Populations[2].delete(cr.user3);
        }
        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;
                var eating = 0;

                for (i = 0; i < n.size; i++)
                {
                        mp = n[i].value.getMechPart(0);
                        distvec.set(mp.pos);
                        distvec.sub(p.pos);
                        dist = distvec.length;
                        if (dist < ExpParams.zone1_range)
                        {
                                if (n[i].value != null)
                                {
                                        energyTransfer(cr, n[i].value);
                                        eating = 1;
                                }
                        }
                        else if (eating == 0 && cr.user2["hibernated"] == 0 && dist < mindist)
                        {
                                mindist = dist;
                                mindistvec = distvec.clone();
                        }
                }

                if (!eating && cr.user2["hibernated"] == 0)
                {
                        mindistvec.normalize();
                        mindistvec.scale(-0.08);
                        cr.localDrive = mindistvec;
                        moveEnergyDec(cr);
                }

                return 1;
        }
        
        else
                return 0;
}

function moveEnergyDec(cr)
{
        if (cr.user2["hibernated"] == 0)
        {
                cr.energy_m += ExpParams.energy_move * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)];
        }
}

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

        //adjustment in z axis
        cr.moveAbs(cr.pos_x, cr.pos_y, 0);

        //are there any nutrients in zone 1 or 2?
        {
                var moved = stepToNearest(ExpParams.zone2_range); //TODO weighted sum of distance and energy
                if (moved==1)
                { 
                        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)
        {
                reverseHib(cr);
                cr.localDrive = XYZ.new(0,0,0);
        }
        //random move
        else if (cr.lifespan%dir_change == 0)
        {
                var dir = (Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), 0);  
                dir.normalize();
                dir.scale(-0.08);
                cr.localDrive = dir;
                moveEnergyDec(cr);
        }
}

function energyTransfer(cr1, cr2)
{
        cr1.localDrive = XYZ.new(0,0,0);
        var e = cr2.getPart(0).ing * ExpParams.feedtrans; //TODO efficiency dependent on age
        e = Math.min(cr2.energy, e) + 0.0000001;
        //Simulator.print("transferring "+e+" to "+cr1.name+" from "+cr2.name+" ("+cr2.energy+")");
        cr2.energy_m = cr2.energy_m + e;
        cr1.energy_p = cr1.energy_p + e;
        if (cr1.user2["hibernated"] == 1)
        {
                reverseHib(cr1);
        }
}

function reverseHib(cr)
{
        if (cr.user2["hibernated"] == 1)
        {
                setForamMeta(cr, cr.user2["gen"]); //unhibernate
        } 
        else
        {
                cr.idleen = ExpParams.energy_hib * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)]; //hibernate
        }
        cr.user2["hibernated"] = 1 - cr.user2["hibernated"];
}

function onForamsStep(cr)
{
        cr.getMechPart(0).orient.set(o);
        if (ExpParams.showRet == 1)
                cr.user3.moveAbs(cr.center_x-ExpParams.zone1_range, cr.center_y-ExpParams.zone1_range, cr.center_z-ExpParams.zone1_range-getProperty(cr.user2["gen"], "chamber_proculus"));

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

        foramMove(cr);

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

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

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

function onForamsDied(cr)
{
        if (ExpParams.showRet == 1)
        {
                Populations[2].delete(cr.user3);
        }
        //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+25)+",sy="+nutrientsize+",sz="+nutrientsize+",ry=1.5,vr=0.0,1.0,0.0"; 
}

function onNutrientsStep(cr)
{
        cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, -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;

        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()
{

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

        //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();
                }
        }
        if (ExpParams.stopping == 1)
        {
                if (Simulator.stepNumber == 150000)
                        Simulator.stop();
        }
}

function createStatistics()
{       
        var number = [[0, 0],[0,0]]; // [species][gen]
        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"];
                var species = cr.user2["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 = [number[1][0], number[1][1], number[0][0], number[0][1], Populations[1].size];
        var log_energies = [e_inc[1][0], e_inc[1][1], e_inc[0][0], e_inc[0][1], e_nut];

        log(log_numbers, "forams_log.txt");
        log(log_energies,  "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();
}

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

@include "standard_events.inc"

~

prop:
id:showRet
name:Show reticulopodia
type:d 0 1 0
group:Foraminifera

prop:
id:iter
name:Iteration number
type:d

prop:
id:stopping
name:Stop after the given number of simulation steps
type:d 0 1 0

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:Nutrient energy
type:f 0 1000
group:Energy

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

prop:
id:nutrientsize
name:Nutrient size
type:f 0.1 0.9 0.1
group:Energy

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

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:Nutrient 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