function create_genotype(proculus_size, number_of_chambers, rgbstring, lastchambergrowth) //lastchambergrowth is 0..1 { const shift = 0.7; const angle_delta = 0.8; const angle_delta_delta = -0.01; const growing = 1.07; //7% growth var str = "//0s\nm:Vstyle=foram\n"; var size = proculus_size; for(var i = 0; i < number_of_chambers; i++) { var effectivesize = size; //'effectivesize' is introduced only to consider the last chamber if (i == number_of_chambers - 1) //last chamber { effectivesize *= lastchambergrowth; size = size * (1.35 - 0.35 * lastchambergrowth); //last iteration: 'size' is only used for shifting (dx). The last chamber emerges at the surface of the previous one if (lastchambergrowth < 1) rgbstring = "0.9,0.9,0.9,i=\"growing=%g\"" % lastchambergrowth; //when the last chamber is growing, make it bright gray and add extra information in its "i" field } str += "p:sh=1,sx=%g,sy=%g,sz=%g,rz=3.14159265358979,vr=%s\n" % effectivesize % effectivesize % effectivesize % rgbstring; if (i > 0) str += "j:%d,%d,sh=1,dx=%g,rz=%g\n" % (i - 1) % i % (size * shift) % (angle_delta + i * angle_delta_delta); size *= growing; } return str; } function setGenotype(mode) { if (mode->opt == "growth") { mode->cr.data->genes = mode->parent_genes; mode->cr.data->lifeparams = mode->parent_lifeparams; } else if (mode->opt == "birth") { foram_uid += 1; var new_id = "c" + string(foram_uid); mode->cr.data->genes = String.deserialize(String.serialize(mode->genes)); mode->cr.data->lifeparams = {"max_energy_level" : mode->energy0, "gen" : mode->gen, "hibernated" : 0, "species" : mode->species, "reproduce" : 0, "dir" : randomDir(), "dir_counter" : Math.random(int(secToSimSteps(ExpProperties.dir_change_sec))), "chamber_growth" : -1, "division_time" : -1, "uid" : new_id}; var oper = "cloning"; var inherit = [1.0]; if (mode->parentsuids.size > 1) { oper = "cross-over"; inherit = [0.5, 0.5]; } var dict = {"Time": Simulator.stepNumber, "FromIDs": mode->parentsuids, "ID": new_id, "Inherited": inherit, "Operation": oper, "Kind" : mode->gen}; Simulator.print("[OFFSPRING] " + String.serialize(dict)); } } function getEnergy0(radius) { return energyFromVolume(micronsToFrams(radius), 1); } function gametsDivision(parent_energy, energy0) { var number = 1; var result = parent_energy; while ((result - ExpProperties.divisionCost) >= energy0) { result = (result - ExpProperties.divisionCost) / 2; number *= 2; } //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number); return {"energy" : result, "number" : number}; } function reproduce_haploid(parent, parent2, clone) { var number, energy0, new_genes, gen; if (clone == 1) { var offspring = gametsDivision(parent.energy, getEnergy0(getGene(parent, "energies0", 0)[0])); energy0 = offspring->energy; number = offspring->number; new_genes = parent.data->genes; parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function gen = parent.data->lifeparams->gen; } else { var offspring1 = gametsDivision(parent.energy, getEnergy0(getGene(parent, "energies0", 0)[1])); var offspring2 = gametsDivision(parent2.energy, getEnergy0(getGene(parent2, "energies0", 0)[1])); energy0 = (offspring1->energy + offspring2->energy); number = ExpProperties.gametSuccessRate * (offspring1->number + offspring2->number) / 2; new_genes = [parent.data->genes, parent2.data->genes]; gen = 1 - parent.data->lifeparams->gen; if (ExpProperties.logging == 1) { log(createLogVector(parent, parent.energy), ExpProperties.logPref + "repro_energies_log.txt"); log(createLogVector(parent2, parent2.energy), ExpProperties.logPref + "repro_energies_log.txt"); log(createLogVector(parent, number), ExpProperties.logPref + "repro_num_log.txt"); log(createLogVector(parent, parent.lifespan), ExpProperties.logPref + "lifespan_log.txt"); log(createLogVector(parent2, parent2.lifespan), ExpProperties.logPref + "lifespan_log.txt"); } } //Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0); for (var j = 0; j < number; j++) { createOffspring(create_genotype(ExpProperties.chamber_proculus_diplo, 1, colors[1], 1), energy0, new_genes, parent.data->lifeparams, [parent.data->lifeparams->uid, parent2.data->lifeparams->uid]); } } function reproduce_diploid(parent) { var offspring = gametsDivision(parent.energy, getEnergy0(getGene(parent, "energies0", 0)[0])); var energy0 = offspring->energy; var number = offspring->number; if (ExpProperties.logging == 1) { log(createLogVector(parent, parent.energy), ExpProperties.logPref + "repro_energies_log.txt"); log(createLogVector(parent, number), ExpProperties.logPref + "repro_num_log.txt"); log(createLogVector(parent, parent.lifespan), ExpProperties.logPref + "lifespan_log.txt"); } //Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0); for (var j = 0; j < number / 2; j++) { var crossed = 0; //crossover if (Math.rnd01 < ExpProperties.crossprob) { crossover(parent, "min_repro_energies"); crossed = 1; } for (var k = 0; k < 2; k++) { createOffspring(create_genotype(ExpProperties.chamber_proculus_haplo, 1, colors[0], 1), energy0, parent.data->genes[0], parent.data->lifeparams, [parent.data->lifeparams->uid]); } //reverse of crossover for fossilization if (crossed == 1) { crossover(parent, "min_repro_energies"); crossed = 0; } } } function reproduce_parents(species) { var parent1 = null; var parent2 = null; var pop = Populations[0]; for (var i = pop.size - 1; i >= 0; i--) { if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species) { if ((pop[i].data->lifeparams->gen == 1) || ((pop[i].data->lifeparams->gen == 0) && ExpProperties.stress == 0)) { continue; } else if (parent1 == null) { parent1 = pop[i]; } else if (parent2 == null) { parent2 = pop[i]; } if (parent1 != null && parent2 != null) { //when parents are ready for reproduction start gametogenesis if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1) { var time = int(secToSimSteps(ExpProperties.gametoPeriodSec)); parent1.data->lifeparams->division_time = time; parent2.data->lifeparams->division_time = time; parent1.idleen = 0; parent2.idleen = 0; //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber); } //when gametogenesis is finished fuse gamets else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0) { reproduce_haploid(parent1, parent2, 0); //print_repro_info(parent1); //print_repro_info(parent2); pop.kill(parent1); pop.kill(parent2); parent1 = null; parent2 = null; } } } } } function readyToRepro(cr) { var reproduced = 1; if (cr.data->lifeparams->gen == 1) { reproduce_diploid(cr); } else if (ExpProperties.stress == 0) { reproduce_haploid(cr, null, 1); } else { if (cr.signals.size == 0) { cr.signals.add("repro" + cr.data->lifeparams->species); cr.signals[0].power = 1; } reproduced = 0; cr.data->lifeparams->reproduce = 1; } if (reproduced == 1) { //print_repro_info(cr); Populations[0].kill(cr); } return reproduced; } function foramReproduce(cr) { var properEnergy = cr.energy >= getGene(cr, "min_repro_energies", 0)[cr.data->lifeparams->gen]; var reproduced = 0; //if creature has proper energy if ( properEnergy ) { //reproduce with probability repro_prob if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger { reproduced = readyToRepro(cr); } else if (cr.signals.receive("repro" + cr.data->lifeparams->species) > 0) { reproduced = readyToRepro(cr); } if (reproduced == 1) return 1; } else if (!properEnergy) { cr.signals.clear(); cr.data->lifeparams->reproduce = 0; } return 0; } function crossover(parent, gene) { var tmp = parent.data->genes[0][gene]; parent.data->genes[0][gene] = parent.data->genes[1][gene]; parent.data->genes[1][gene] = tmp; } function createOffspring(geno, energy, parent_genes, parent_lifeparams, parentsuids) { curColor = colors[1 - parent_lifeparams->gen]; var cr = createAndRotate(geno, 0, 2 * Math.pi, 0); cr.energy0 = energy; cr.energy = cr.energy0; setGenotype({"opt" : "birth", "cr" : cr, "gen" : 1 - parent_lifeparams->gen, "species" : parent_lifeparams->species, "energy0" : cr.energy0, "genes" : parent_genes, "parentsuids" : parentsuids}); placeRandomlyNotColliding(cr); } function print_repro_info(cr) { Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy); }