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2 | function create_genotype(proculus_size, number_of_chambers, rgbstring, lastchambergrowth) //lastchambergrowth is 0..1
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3 | {
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4 | const shift=0.7;
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5 | const angle_delta=0.8;
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6 | const angle_delta_delta=-0.01;
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7 | const growing=1.07; //7% growth
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8 |
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9 | var str="//0\n";
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10 | var size=proculus_size;
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11 | for(var i=0;i<number_of_chambers;i++)
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12 | {
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13 | var effectivesize=size; //'effectivesize' is introduced only to consider the last chamber
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14 | if (i==number_of_chambers-1) //last chamber
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15 | {
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16 | effectivesize*=lastchambergrowth;
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17 | 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
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18 | if (lastchambergrowth<1)
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19 | rgbstring="0.8,0.8,0.8,i=\"growing=%g\"" % lastchambergrowth; //when the last chamber is growing, make it gray and add extra information in its "i" field
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20 | }
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21 | str += "p:sh=1,sx=%g,sy=%g,sz=%g,rz=3.14159265358979,vr=%s\n" % effectivesize % effectivesize % effectivesize % rgbstring;
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22 | if (i>0)
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23 | str+="j:%d,%d,sh=1,dx=%g,rz=%g\n" % (i-1) % i % (size*shift) % (angle_delta+i*angle_delta_delta);
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24 | size*=growing;
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25 | }
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26 | return str;
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27 | }
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28 |
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29 | function setGenotype(mode)
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30 | {
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31 | if (mode->opt == "growth")
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32 | {
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33 | mode->cr.data->genes = mode->parent_genes;
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34 | mode->cr.data->lifeparams = mode->parent_lifeparams;
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35 | }
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36 |
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37 | else if (mode->opt == "birth")
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38 | {
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39 | foram_uid += 1;
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40 | var new_id = "c"+string(foram_uid);
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41 | mode->cr.data->genes = String.deserialize(String.serialize(mode->genes));
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42 | 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};
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43 |
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44 | var oper = "cloning";
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45 | var inherit = [1.0];
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46 | if (mode->parentsuids.size > 1)
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47 | {
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48 | oper = "cross-over";
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49 | inherit = [0.5, 0.5];
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50 | }
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51 |
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52 | var dict={"Time":Simulator.stepNumber,"FromIDs":mode->parentsuids,"ID":new_id, "Inherited":inherit, "Operation": oper, "Kind" : mode->gen};
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53 | Simulator.print("[OFFSPRING] " + String.serialize(dict));
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54 | }
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55 | }
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56 |
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57 | function getEnergy0(radius)
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58 | {
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59 | return energyFromVolume(micronsToFrams(radius),1);
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60 | }
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61 |
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62 | function gametsDivision(parent_energy, energy0)
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63 | {
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64 | var number = 1;
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65 | var result = parent_energy;
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66 | while ((result-ExpProperties.divisionCost) >= energy0)
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67 | {
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68 | result = (result-ExpProperties.divisionCost)/2;
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69 | number *= 2;
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70 | }
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71 | //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
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72 | return {"energy" : result, "number" : number};
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73 | }
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74 |
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75 | function reproduce_haploid(parent, parent2, clone)
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76 | {
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77 | var number, energy0, new_genes, gen;
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78 | if (clone == 1)
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79 | {
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80 | var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0",0)[0]));
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81 | energy0 = offspring->energy;
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82 | number = offspring->number;
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83 | new_genes = parent.data->genes;
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84 | parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function
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85 | gen = parent.data->lifeparams->gen;
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86 | }
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87 | else
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88 | {
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89 | var offspring1 = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[1]));
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90 | var offspring2 = gametsDivision(parent2.energy,getEnergy0(getGene(parent2,"energies0", 0)[1]));
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91 | energy0 = (offspring1->energy+offspring2->energy);
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92 | number = ExpProperties.gametSuccessRate*(offspring1->number+offspring2->number)/2;
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93 | new_genes = [parent.data->genes, parent2.data->genes];
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94 | gen = 1 - parent.data->lifeparams->gen;
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95 |
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96 | if (ExpProperties.logging == 1)
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97 | {
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98 | log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
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99 | log(createLogVector(parent2, parent2.energy),ExpProperties.logPref+"repro_energies_log.txt");
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100 | log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
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101 | log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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102 | log(createLogVector(parent2, parent2.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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103 | }
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104 | }
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105 |
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106 | //Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);
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107 |
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108 | for (var j = 0; j < number; j++)
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109 | {
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110 | 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]);
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111 | }
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112 | }
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113 |
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114 | function reproduce_diploid(parent)
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115 | {
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116 | var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[0]));
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117 | var energy0 = offspring->energy;
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118 | var number = offspring->number;
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119 |
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120 | if (ExpProperties.logging == 1)
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121 | {
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122 | log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
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123 | log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
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124 | log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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125 | }
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126 |
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127 | //Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
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128 |
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129 | for (var j = 0; j < number / 2; j++)
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130 | {
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131 | var crossed = 0;
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132 | //crossover
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133 | if (Math.rnd01 < ExpProperties.crossprob)
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134 | {
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135 | crossover(parent, "min_repro_energies");
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136 | crossed = 1;
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137 | }
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138 |
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139 | for (var k = 0; k < 2; k++)
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140 | {
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141 | createOffspring(create_genotype(ExpProperties.chamber_proculus_haplo, 1, colors[0], 1), energy0, parent.data->genes[0], parent.data->lifeparams, [parent.data->lifeparams->uid]);
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142 | }
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143 |
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144 | //reverse of crossover for fossilization
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145 | if (crossed == 1)
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146 | {
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147 | crossover(parent, "min_repro_energies");
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148 | crossed = 0;
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149 | }
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150 |
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151 | }
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152 | }
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153 |
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154 | function reproduce_parents(species)
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155 | {
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156 | var parent1 = null;
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157 | var parent2 = null;
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158 | var pop = Populations[0];
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159 | for (var i = pop.size-1; i >= 0; i--)
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160 | {
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161 | if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species)
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162 | {
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163 | if ((pop[i].data->lifeparams->gen==1) || ((pop[i].data->lifeparams->gen==0) && ExpProperties.stress == 0))
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164 | {
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165 | continue;
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166 | }
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167 | else if (parent1 == null)
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168 | {
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169 | parent1 = pop[i];
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170 | }
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171 | else if (parent2 == null)
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172 | {
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173 | parent2 = pop[i];
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174 | }
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175 | if (parent1 != null && parent2 != null)
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176 | {
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177 | //when parents are ready for reproduction start gametogenesis
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178 | if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
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179 | {
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180 | var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
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181 | parent1.data->lifeparams->division_time = time;
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182 | parent2.data->lifeparams->division_time = time;
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183 | parent1.idleen = 0;
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184 | parent2.idleen = 0;
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185 | //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber);
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186 | }
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187 | //when gametogenesis is finished fuse gamets
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188 | else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
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189 | {
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190 | reproduce_haploid(parent1, parent2, 0);
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191 | //print_repro_info(parent1);
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192 | //print_repro_info(parent2);
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193 | pop.kill(parent1);
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194 | pop.kill(parent2);
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195 | parent1 = null;
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196 | parent2 = null;
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197 | }
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198 | }
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199 | }
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200 | }
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201 | }
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202 |
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203 | function readyToRepro(cr)
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204 | {
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205 | var reproduced = 1;
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206 |
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207 | if (cr.data->lifeparams->gen == 1)
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208 | {
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209 | reproduce_diploid(cr);
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210 | }
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211 |
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212 | else if (ExpProperties.stress == 0)
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213 | {
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214 | reproduce_haploid(cr, null, 1);
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215 | }
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216 |
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217 | else
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218 | {
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219 | if (cr.signals.size == 0)
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220 | {
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221 | cr.signals.add("repro"+cr.data->lifeparams->species);
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222 | cr.signals[0].power = 1;
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223 | }
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224 | reproduced = 0;
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225 | cr.data->lifeparams->reproduce = 1;
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226 | }
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227 |
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228 | if (reproduced == 1)
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229 | {
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230 | //print_repro_info(cr);
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231 | Populations[0].kill(cr);
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232 | }
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233 |
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234 | return reproduced;
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235 | }
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236 |
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237 | function foramReproduce(cr)
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238 | {
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239 | var properEnergy = cr.energy >= getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen];
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240 | var reproduced = 0;
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241 |
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242 | //if creature has proper energy
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243 | if ( properEnergy && cr.signals.size == 0)
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244 | {
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245 | //reproduce with probability repro_prob
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246 | if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger
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247 | {
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248 | reproduced = readyToRepro(cr);
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249 | }
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250 | else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
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251 | {
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252 | reproduced = readyToRepro(cr);
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253 | }
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254 | if (reproduced == 1)
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255 | return 1;
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256 | }
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257 |
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258 | else if (!properEnergy)
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259 | {
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260 | cr.signals.clear();
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261 | cr.data->lifeparams->reproduce = 0;
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262 | }
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263 |
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264 | return 0;
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265 | }
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266 |
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267 | function crossover(parent, gene)
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268 | {
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269 | var tmp = parent.data->genes[0][gene];
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270 | parent.data->genes[0][gene] = parent.data->genes[1][gene];
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271 | parent.data->genes[1][gene] = tmp;
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272 | }
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273 |
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274 | function createOffspring(geno, energy, parent_genes, parent_lifeparams, parentsuids)
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275 | {
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276 | curColor = colors[1-parent_lifeparams->gen];
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277 | var cr = Populations[0].add(geno);
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278 | cr.energy0 = energy;
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279 | cr.energy = cr.energy0;
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280 | setGenotype({"opt" : "birth", "cr" : cr, "gen" : 1 - parent_lifeparams->gen, "species" : parent_lifeparams->species, "energy0" : cr.energy0, "genes" : parent_genes, "parentsuids" : parentsuids});
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281 | placeRandomlyNotColliding(cr);
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282 | }
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283 |
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284 | function print_repro_info(cr)
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285 | {
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286 | Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
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287 | }
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