1 | expdef:
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2 | name:Benthic foraminifera reproduction
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3 | info:~
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4 | Genes and parameter values which control reproduction are stored in user1 and user2 fields.
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5 |
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6 | user1:
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7 | genes which are not encoded in ff genotype:
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8 | Vamin - Minimum stored energy necessary for reproduction
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9 | amin - minimal age for reproduction
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10 |
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11 | user2:
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12 | Physiological parameters of foraminifera:
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13 | Va - amount of the stored energy
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14 | gen - generation: 0 haploid, 1 diploid
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15 | ~
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16 | code:~
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17 |
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18 | /*
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19 | changes 2015-06-24:
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20 | - xxx.get(...) changed to xxx[...]
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21 | - xxx.set(...,...) changed to xxx[...]=...
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22 | - function placeRandomlyNotColliding(cr) explicitly called when adding a new creature, and removed collision checking from onCreaturesBorn() which is also called when "growing" (since "growing" is implemented as creating a new creature in place of the old one, so onCreaturesBorn() is also called)
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23 | - use creature's center (not the bbox corner) when growing
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24 | - added "S" receptor to visualize the difference between diplo and haplo generations
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25 | - signal.value is a MechPart (a reference) so it does not have to be updated after changing the object location
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26 | */
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27 |
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28 | global foodenergywaiting;
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29 | global reprocounter;
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30 | global delta_change;
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31 |
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32 | @include "forams_repro.inc"
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33 |
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34 | // -------------------------------- experiment begin --------------------------------
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35 |
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36 | function onExpDefLoad()
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37 | {
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38 |
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39 | // define genotype and creature groups
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40 | GenePools.clear();
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41 | Populations.clear();
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42 | GenePools[0].name = "Unused";
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43 |
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44 | SignalView.mode = 1;
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45 |
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46 | var pop = Populations[0];
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47 | pop.name = "Creatures";
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48 | pop.en_assim = 0;
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49 | pop.nnsim = 1;
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50 | pop.enableperf = 1;
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51 | pop.death = 1;
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52 | pop.energy = 1;
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53 | pop.selfmask = 0x10001;
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54 | pop.othermask = 0x20001;
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55 | //pop.selfmask = 0x20002; pop.othermask = 0x10002;
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56 | pop.perfperiod = 25;
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57 |
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58 | pop = Populations.addGroup("Food");
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59 | pop.nnsim = 0;
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60 | pop.enableperf = 0;
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61 | pop.death = 1;
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62 | pop.energy = 1;
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63 | pop.selfmask = 0x20002;
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64 | pop.othermask = 0x10000;
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65 |
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66 |
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67 | var size_h = ExpParams.haplo_rad * ExpParams.delta_rate + ExpParams.haplo_rad;
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68 | var size_d = ExpParams.diplo_rad * ExpParams.delta_rate + ExpParams.diplo_rad;
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69 | ExpParams.gend = "//0\np:sh=1,sx=" + ExpParams.diplo_rad + ",sy=" + ExpParams.diplo_rad + ",sz=" + ExpParams.diplo_rad + ", rz=3.14159265358979";
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70 | ExpParams.genh = "//0\np:sh=1,sx=" + size_h + ",sy=" + size_h + ",sz=" + size_h + ", rz=3.14159265358979";
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71 | ExpParams.e_meta = 0.1;
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72 | ExpParams.feedrate = 0.5;
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73 | ExpParams.feede0 = 100;
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74 | ExpParams.feedtrans = 3;
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75 | ExpParams.creath = -0.99; //just above the bottom
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76 | ExpParams.foodgen = "//0\np:sh=2,sx=0.1,sy=0.1,sz=0.1\nn:d=T,p=0";
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77 | ExpParams.autorestart = 0;
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78 | ExpParams.psize = 10;
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79 | ExpParams.logging = 0;
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80 |
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81 | //number of offspring
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82 | ExpParams.ofnumh = 40;
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83 | ExpParams.ofnumd = 25;
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84 | //minial volume for reproduction
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85 | ExpParams.v_min_d = 300;
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86 | ExpParams.v_min_h = 300;
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87 | //radius of the chamber
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88 | ExpParams.haplo_rad = 1.2;
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89 | ExpParams.diplo_rad = 0.6;
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90 | //minimal age for reproduction
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91 | ExpParams.age_min_d = 100;
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92 | ExpParams.age_min_h = 100;
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93 | //crossover probability
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94 | ExpParams.crossprob = 0.4;
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95 | //mutation probability
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96 | ExpParams.mutationprob = 0.2;
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97 | ExpParams.repro_time = 200;
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98 | ExpParams.repro_thr = 1;
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99 |
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100 | //size change rate
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101 | ExpParams.delta_rate = 0.1;
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102 | //grwoth speed in time steps
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103 | ExpParams.growth_step = 50;
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104 |
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105 | ExpState.totaltestedcr = 0;
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106 | ExpState.food = "";
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107 | foodenergywaiting = ExpParams.feede0;
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108 | reprocounter = 0;
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109 |
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110 | ExpParams.wsize = 50;
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111 | World.wrldwat = 50;
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112 | World.wrldsiz = ExpParams.wsize;
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113 | World.wrldbnd = 1;
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114 |
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115 | delta_change = 0.5;
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116 | }
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117 |
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118 | @include "standard_placement.inc"
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119 |
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120 | function onExpInit()
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121 | {
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122 | Populations[0].clear();
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123 | Populations[1].clear();
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124 |
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125 | for (var i = 0; i < ExpParams.psize; i++)
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126 | {
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127 | var cr = Populations[0].add(ExpParams.genh);
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128 | cr.name = "Initial creature" + i;
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129 | placeCreatureRandomly(cr, 0, 0);
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130 | cr.energ0 = ExpParams.v_min_h - ExpParams.repro_thr;
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131 | cr.energy = cr.energ0;
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132 | cr.user1 = {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h, "delta_h" : ExpParams.haplo_rad * ExpParams.delta_rate, "delta_d" : ExpParams.diplo_rad * ExpParams.delta_rate};
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133 | cr.user2 = {"Va" : ExpParams.v_min_h - ExpParams.repro_thr, "gen" : 0, "growth_step" : ExpParams.growth_step, "rsize" : ExpParams.haplo_rad, "vinit" : ExpParams.v_min_h - ExpParams.repro_thr};
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134 | }
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135 | ExpState.totaltestedcr = 0;
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136 | foodenergywaiting = ExpParams.feede0;
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137 | }
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138 |
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139 | function onExpLoad()
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140 | {
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141 | for (var pop in Populations)
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142 | pop.clear();
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143 |
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144 | Loader.addClass(sim_params.*);
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145 | Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
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146 | Loader.run();
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147 |
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148 | Simulator.print("Loaded " + Populations[0].size + " creatures and " + Populations[1].size + " food objects");
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149 | }
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150 |
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151 | function onExpLoad_Unknown()
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152 | {
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153 | if (Loader.objectName == "org") // saved by the old expdef
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154 | {
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155 | var g = Genotype.newFromString("");
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156 | Loader.currentObject = g;
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157 | Interface.makeFrom(g).setAllDefault();
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158 | Loader.loadObject();
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159 | var cr = Populations[0].add(g);
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160 | if (cr != null)
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161 | {
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162 | //cr.rotate(0,0,Math.rnd01*Math.twopi);
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163 | if ((typeof(g.user1) == "Vector") && (g.user1.size >= 3))
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164 | {
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165 | // [x,y,energy]
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166 | cr.move(g.user1[0] - cr.center_x, g.user1[1] - cr.center_y, 0);
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167 | cr.energy = g.user1[2];
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168 | }
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169 | else
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170 | {
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171 | cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
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172 | }
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173 | }
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174 | }
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175 | else if (Loader.objectName == "Creature")
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176 | {
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177 | Loader.currentObject = CreatureSnapshot.new();
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178 | Loader.loadObject();
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179 | Populations[0].add(Loader.currentObject);
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180 | }
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181 | }
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182 |
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183 | function onExpSave()
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184 | {
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185 | File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
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186 |
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187 | var tmpvec = [], i;
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188 |
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189 | for(var cr in Populations[1])
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190 | tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
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191 |
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192 | ExpState.food = tmpvec;
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193 | File.writeObject(sim_params.*);
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194 | ExpState.food = null; //vectors are only created for saving and then discarded
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195 |
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196 | for (var cr in Populations[0])
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197 | File.writeObject(cr);
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198 | }
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199 |
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200 | // -------------------------------- experiment end --------------------------------
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201 |
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202 | // -------------------------------- creature begin --------------------------------
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203 |
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204 | function onCreaturesBorn(cr)
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205 | {
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206 | cr.idleen = ExpParams.e_meta;
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207 | }
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208 |
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209 | function placeRandomlyNotColliding(cr)
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210 | {
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211 | var retry = 100; //try 100 times
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212 | while (retry--)
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213 | {
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214 | placeCreatureRandomly(cr, 0, 0);
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215 | if (!cr.boundingBoxCollisions(0))
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216 | return cr;
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217 | }
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218 |
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219 | Populations[0].delete(cr);
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220 | }
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221 |
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222 | function readyToRepro(cr)
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223 | {
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224 | cr.signals.add("repro");
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225 | cr.signals[0].power = 1;
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226 |
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227 | }
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228 |
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229 | function onCreaturesStep(cr)
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230 | {
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231 | cr.moveAbs(cr.pos_x, cr.pos_y, 0); //adjustment in z axis
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232 | var p = cr.getMechPart(0);
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233 | var n = cr.signals.receiveSet("food", ExpParams.food_range);
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234 |
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235 | //if signals are received find the source of the nearest
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236 | if (n.size > 0)
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237 | {
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238 |
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239 | var i;
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240 | var mp;
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241 | var distvec = XYZ.new(0, 0, 0);
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242 | var dist;
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243 | var mindist = 100000000000;
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244 | var mindistvec = null;
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245 |
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246 | for (i = 0; i < n.size; i++)
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247 | {
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248 | mp = n[i].value;
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249 | distvec.set(mp.pos);
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250 | distvec.sub(p.pos);
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251 | dist = distvec.length;
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252 | if (dist < mindist)
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253 | {
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254 | mindist = dist;
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255 | mindistvec = distvec.clone();
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256 | }
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257 | }
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258 |
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259 | mindistvec.normalize();
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260 | mindistvec.scale(-0.08);
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261 | cr.localDrive = mindistvec;
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262 | }
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263 |
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264 | else
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265 | {
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266 | cr.localDrive = (0.1 * Math.rnd01, 0.1 * Math.rnd01, 0);
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267 | }
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268 |
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269 | //energy costs depend on size
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270 | if (cr.energy > 100)
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271 | {
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272 | // cr.energy_m = cr.user2["Va"]/cr.user2["vinit"];
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273 | }
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274 |
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275 | if (cr.lifespan >= ExpParams.max_age)
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276 | {
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277 | Populations[0].kill(cr);
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278 | }
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279 |
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280 | //foram growth
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281 | else if (cr.lifespan == cr.user2["growth_step"])
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282 | {
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283 | var pos = [cr.center_x, cr.center_y, cr.center_z];
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284 | var energy = cr.energy;
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285 | var cr2 = null;
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286 | if (cr.user2["gen"] == 0)
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287 | {
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288 | var new_r = ExpParams.haplo_rad * Math.min(Math.max(cr.user2["Va"] / cr.user2["vinit"] * 0.5, 1), 2.5);
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289 | cr.user2["rsize"] = new_r;
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290 | cr2 = Populations[0].add("//0\np:sh=1,sx=" + cr.user2["rsize"] + ",sy=" + cr.user2["rsize"] + ",sz=" + cr.user2["rsize"] + ", rz=3.14159265358979");
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291 | cr2.user1 = {"vamin" : cr.user1["vamin"], "amin": cr.user1["amin"], "delta_h" : cr.user1["delta_h"], "delta_d" : cr.user1["delta_d"]};
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292 | }
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293 | else if (cr.user2["gen"] == 1)
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294 | {
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295 | var new_r = ExpParams.diplo_rad * Math.min(Math.max(cr.user2["Va"] / cr.user2["vinit"] * 0.5, 1), 2.5);
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296 | cr.user2["rsize"] = new_r;
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297 |
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298 | var geno = "//0\np:sh=1,sx=" + cr.user2["rsize"] + ",sy=" + cr.user2["rsize"] + ",sz=" + cr.user2["rsize"] + ", rz=3.14159265358979";
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299 | geno += "\nn:p=0,d=\"S\""; //TODO is this the only difference with haploid code? TODO why initial genotypes are not used as defined in ExpParams?
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300 | //TODO maybe it would be nice if they rotated so the "S" would show where they are going (direction/intention)
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301 | cr2 = Populations[0].add(geno);
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302 |
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303 |
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304 | cr2.user1 = [ {"vamin" : cr.user1[0]["vamin"], "amin": cr.user1[0]["amin"], "delta_h" : cr.user1[0].get("delta_h"), "delta_d" : cr.user1[0]["delta_d"] }, {"vamin" : cr.user1[1]["vamin"], "amin": cr.user1[1]["amin"], "delta_h" : cr.user1[1]["delta_h"], "delta_d" : cr.user1[1]["delta_d"] }];
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305 | }
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306 | cr2.energy = energy;
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307 | cr2.user2 = {"Va" : cr.user2["Va"], "gen" : cr.user2["gen"], "growth_step" : cr.user2["growth_step"], "rsize" : cr.user2["rsize"], "vinit": cr.user2["vinit"]};
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308 | cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
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309 |
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310 | Populations[0].delete(cr);
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311 | }
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312 | else
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313 | {
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314 | var properSize = 0;
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315 |
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316 | if (cr.user2["gen"] == 0)
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317 | {
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318 | properSize = cr.user2["Va"] >= cr.user1["vamin"];
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319 | }
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320 | else
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321 | {
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322 | properSize = cr.user2["Va"] >= cr.user1[0]["vamin"];
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323 | }
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324 |
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325 | //if creature has proper age and cytoplasm amount
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326 | if ( properSize )
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327 | {
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328 | //reproduce with probability repro_prob
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329 | if (Math.rnd01 <= ExpParams.repro_prob)
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330 | {
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331 | readyToRepro(cr);
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332 | }
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333 | }
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334 | if ( properSize && (cr.signals.receive("repro") > 0))
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335 | {
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336 | readyToRepro(cr);
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337 | }
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338 | }
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339 | }
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340 |
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341 | function onCreaturesDied(cr)
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342 | {
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343 | //fossilization
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344 | var geno = GenePools[0].add(cr.genotype);
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345 | geno.user1 = cr.user1;
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346 | geno.user2 = cr.user2;
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347 | Simulator.print("\"" + cr.name + "\" died...");
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348 | ExpState.totaltestedcr++;
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349 | }
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350 |
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351 | // -------------------------------- creature end --------------------------------
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352 |
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353 | // -------------------------------- food begin --------------------------------
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354 |
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355 | function onFoodStep(cr)
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356 | {
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357 | cr.moveAbs(cr.pos_x % ExpParams.wsize, cr.pos_y % ExpParams.wsize, 0.5);
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358 | }
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359 |
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360 | function addfood()
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361 | {
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362 | var cr = Populations[1].add(ExpParams.foodgen);
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363 |
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364 | cr.name = "Food";
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365 | cr.idleen = 0;
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366 | cr.energ0 = ExpParams.feede0;
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367 | cr.energy = cr.energ0;
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368 | cr.signals.add("food");
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369 |
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370 | cr.signals[0].value = cr.getMechPart(0);
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371 |
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372 | var retry = 100; //try 100 times
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373 | while (retry--)
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374 | {
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375 | placeCreatureRandomly(cr, 0, 0);
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376 | if (!cr.boundingBoxCollisions(0))
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377 | return cr;
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378 | }
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379 |
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380 | return cr;
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381 | }
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382 |
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383 | function onFoodCollision()
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384 | {
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385 | if (Collision.Creature2.user2 != null)
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386 | {
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387 | var e = Collision.Part2.ing * ExpParams.feedtrans;
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388 | //Simulator.print("transferring "+e+" from "+Collision.Creature1.name+" to "+Collision.Creature2.name+" ("+Collision.Creature2.energy+")");
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389 | Collision.Creature1.energy_m = Collision.Creature1.energy_m + e;
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390 | Collision.Creature2.energy_p = Collision.Creature2.energy_p + e;
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391 | var ener = float(Collision.Creature2.user2["Va"]);
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392 | var sum = float(float(ener) + float(e));
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393 | Collision.Creature2.user2["Va"] = float(sum);
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394 | }
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395 | }
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396 |
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397 | // -------------------------------- food end --------------------------------
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398 |
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399 |
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400 | function log(tolog, fname)
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401 | {
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402 | var f = File.appendDirect(fname, "forams data");
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403 | f.writeString("" + Simulator.stepNumber);
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404 | for (var i = 0; i < tolog.size; i++)
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405 | {
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406 | f.writeString(";" + tolog[i]);
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407 | }
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408 | f.writeString("\n");
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409 | f.close();
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410 | }
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411 |
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412 |
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413 |
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414 |
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415 | @include "standard_events.inc"
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416 |
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417 | ~
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418 |
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419 | prop:
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420 | id:max_age
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421 | name:Maximal age
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422 | type:d 100 1000 500
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423 |
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424 | prop:
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425 | id:wsize
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426 | name:World size
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427 | type:d 10 1000 20
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428 |
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429 | prop:
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430 | id:haplo_rad
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431 | name:Haploid radius
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432 | type:f 0.1 3 1.2
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433 |
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434 | prop:
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435 | id:growth_step
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436 | name:Growth step
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437 | type:d 50 10000 1000
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438 |
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439 | prop:
|
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440 | id:delta_rate
|
---|
441 | name:Delta rate
|
---|
442 | type:f 0.0001 0.1 0.001
|
---|
443 |
|
---|
444 | prop:
|
---|
445 | id:diplo_rad
|
---|
446 | name:Diploid radius
|
---|
447 | type:f 0.1 3 0.6
|
---|
448 |
|
---|
449 | prop:
|
---|
450 | id:foodPop
|
---|
451 | name:Food size
|
---|
452 | type:d 1 1000 10
|
---|
453 |
|
---|
454 | prop:
|
---|
455 | id:age_min
|
---|
456 | name:Minimal age for reproduction
|
---|
457 | type:d 100 10000 200
|
---|
458 |
|
---|
459 | prop:
|
---|
460 | id:age_min_h
|
---|
461 | name:Min reproduction age of haploid forams
|
---|
462 | type:d 100 10000 300
|
---|
463 | group:Foraminifera
|
---|
464 |
|
---|
465 | prop:
|
---|
466 | id:age_min_d
|
---|
467 | name:Min reproduction age of diploid forams
|
---|
468 | type:d 100 10000 200
|
---|
469 | group:Foraminifera
|
---|
470 |
|
---|
471 | prop:
|
---|
472 | id:v_min_h
|
---|
473 | name:Min reproduction energy of haploid forams
|
---|
474 | type:f 10 10000 300
|
---|
475 | group:Foraminifera
|
---|
476 |
|
---|
477 | prop:
|
---|
478 | id:v_min_d
|
---|
479 | name:Min reproduction energy of diploid forams
|
---|
480 | type:f 10 10000 150
|
---|
481 | group:Foraminifera
|
---|
482 |
|
---|
483 | prop:
|
---|
484 | id:repro_thr
|
---|
485 | name:Threshold for reproduction
|
---|
486 | type:d 1 1000 1
|
---|
487 |
|
---|
488 | prop:
|
---|
489 | id:food_range
|
---|
490 | name:Range of food smell
|
---|
491 | type:d 0 10000 10000
|
---|
492 |
|
---|
493 | prop:
|
---|
494 | id:repro_time
|
---|
495 | name:Time before reproduction
|
---|
496 | type:d 0 1000
|
---|
497 |
|
---|
498 | prop:
|
---|
499 | id:psize
|
---|
500 | name:Initial population size
|
---|
501 | type:d 1 1000 100
|
---|
502 |
|
---|
503 | prop:
|
---|
504 | id:logging
|
---|
505 | name:Log statistics to file
|
---|
506 | type:d 0 1 0
|
---|
507 |
|
---|
508 | prop:
|
---|
509 | id:ofnumh
|
---|
510 | name:Number of offspring from haploid forams
|
---|
511 | type:d
|
---|
512 | group:Foraminifera
|
---|
513 |
|
---|
514 | prop:
|
---|
515 | id:ofnumd
|
---|
516 | name:Number of offspring from diploid forams
|
---|
517 | type:d
|
---|
518 | group:Foraminifera
|
---|
519 |
|
---|
520 | prop:
|
---|
521 | id:repro_prob
|
---|
522 | name:Probability of reproduction
|
---|
523 | type:f 0 1 0.9
|
---|
524 |
|
---|
525 | prop:
|
---|
526 | id:crossprob
|
---|
527 | name:Crossover probability
|
---|
528 | type:f 0 1 0
|
---|
529 |
|
---|
530 | prop:
|
---|
531 | id:mutationprob
|
---|
532 | name:Mutation probability
|
---|
533 | type:f 0 1 0
|
---|
534 |
|
---|
535 | prop:
|
---|
536 | id:genh
|
---|
537 | name:Initial genotype of haploid forams
|
---|
538 | type:s 1
|
---|
539 | group:Foraminifera
|
---|
540 |
|
---|
541 | prop:
|
---|
542 | id:gend
|
---|
543 | name:Initial genotype of diploid forams
|
---|
544 | type:s 1
|
---|
545 | group:Foraminifera
|
---|
546 |
|
---|
547 | prop:
|
---|
548 | id:creath
|
---|
549 | name:Creation height
|
---|
550 | type:f -1 50
|
---|
551 | help:~
|
---|
552 | Vertical position (above the surface) where new creatures are revived.
|
---|
553 | Negative values are only used in the water area:
|
---|
554 | 0 = at the surface
|
---|
555 | -0.5 = half depth
|
---|
556 | -1 = just above the bottom~
|
---|
557 |
|
---|
558 | prop:
|
---|
559 | id:e_meta
|
---|
560 | name:Idle metabolism
|
---|
561 | type:f 0 1
|
---|
562 | group:Energy
|
---|
563 | help:Each stick consumes this amount of energy in one time step
|
---|
564 |
|
---|
565 | prop:
|
---|
566 | id:feedrate
|
---|
567 | name:Feeding rate
|
---|
568 | type:f 0 100
|
---|
569 | group:Energy
|
---|
570 | help:How fast energy is created in the world
|
---|
571 |
|
---|
572 | prop:
|
---|
573 | id:feede0
|
---|
574 | name:Food's energy
|
---|
575 | group:Energy
|
---|
576 | type:f 0 1000
|
---|
577 |
|
---|
578 | prop:
|
---|
579 | id:feedtrans
|
---|
580 | name:Ingestion multiplier
|
---|
581 | group:Energy
|
---|
582 | type:f 0 100
|
---|
583 |
|
---|
584 | prop:
|
---|
585 | id:foodgen
|
---|
586 | name:Food's genotype
|
---|
587 | group:Energy
|
---|
588 | type:s 1
|
---|
589 |
|
---|
590 | prop:
|
---|
591 | id:autorestart
|
---|
592 | name:Restart after extinction
|
---|
593 | help:Restart automatically this experiment after the last creature has died?
|
---|
594 | type:d 0 1
|
---|
595 |
|
---|
596 | state:
|
---|
597 | id:notes
|
---|
598 | name:Notes
|
---|
599 | type:s 1
|
---|
600 | help:~
|
---|
601 | You can write anything here
|
---|
602 | (it will be saved to the experiment file)~
|
---|
603 |
|
---|
604 | state:
|
---|
605 | id:totaltestedcr
|
---|
606 | name:Evaluated creatures
|
---|
607 | help:Total number of the creatures evaluated in the experiment
|
---|
608 | type:d
|
---|
609 | flags:16
|
---|
610 |
|
---|
611 | state:
|
---|
612 | id:food
|
---|
613 | name:Food locations
|
---|
614 | help:vector of vectors [x,y,energy]
|
---|
615 | type:x
|
---|
616 | flags:32
|
---|
617 |
|
---|