1 | expdef:
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2 | name:Reproduction of benthic foraminifera
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3 | info:~
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4 | Basic information about this simulation:
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5 | www.framsticks.com/foraminifera
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6 |
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7 | Technical information:
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8 | Genes and parameter values which control reproduction are stored in data->genes and data->lifeparams fields.
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9 |
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10 | genes:
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11 | genes which are not encoded in Ff genotype:
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12 | min_repro_energy - Minimum energy necessary for reproduction
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13 | hibernation - Defines foram behavior in the case of no nutrients
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14 |
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15 | lifeparams:
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16 | Physiological parameters of foraminifera:
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17 | max_energy_level - maximum energy level reached so far
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18 | gen - generation: 0 haploid, 1 diploid
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19 | species - species: 0 not hibernating 1 hibernating
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20 | hibernated - 0/1 foram is/isn't hibernated
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21 | reproduce - 0/1 foram isn't/is ready for reproduction
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22 | ~
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23 | code:~
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24 |
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25 | global chambers;
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26 | global colors;
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27 | global dir_change;
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28 | global max_chamber_volume;
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29 | global movePerStep;
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30 | global nutrientenergywaiting;
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31 | global o;
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32 | global reprocounter;
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33 | global changePeriod;
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34 | global phase;
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35 |
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36 | @include "foraminifera.inc"
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37 |
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38 | // -------------------------------- experiment begin --------------------------------
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39 |
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40 | function onExpDefLoad()
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41 | {
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42 | // define genotype and creature groups
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43 | GenePools.clear();
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44 | Populations.clear();
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45 | GenePools[0].name = "Unused";
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46 |
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47 | var pop = Populations[0];
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48 | pop.name = "Forams";
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49 | pop.en_assim = 0;
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50 | pop.nnsim = 0;
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51 | pop.enableperf = 1;
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52 | pop.death = 1;
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53 | pop.energy = 1;
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54 | pop.selfmask = 0x10001;
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55 | pop.othermask = 0x20001;
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56 | //pop.selfmask = 0x20002; pop.othermask = 0x10002;
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57 | pop.perfperiod = 25;
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58 |
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59 | pop = Populations.addGroup("Nutrients");
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60 | pop.nnsim = 0;
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61 | pop.enableperf = 0;
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62 | pop.death = 1;
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63 | pop.energy = 1;
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64 | pop.selfmask = 0x20002;
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65 | pop.othermask = 0x10000;
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66 | //pop.othermask = 0x10002;
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67 |
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68 | pop = Populations.addGroup("ReticulopodiaNutrients");
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69 | pop.nnsim = 0;
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70 | pop.enableperf = 0;
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71 | pop.death = 0;
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72 | pop.energy = 0;
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73 | pop.selfmask = 0x20002;
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74 | pop.othermask = 0x10000;
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75 |
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76 | //world
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77 | SignalView.mode = 1;
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78 | World.wrldwat = 200;
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79 | World.wrldsiz = micronsToFrams(40000);
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80 | World.wrldbnd = 1;
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81 | ExpProperties.stress = 1;
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82 | ExpProperties.creath = -0.99; //just above the bottom
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83 | ExpProperties.autorestart = 0;
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84 |
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85 | //time
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86 | ExpProperties.secPerStep = 480;
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87 | ExpProperties.foramSpeedMmPerMin = 0.05;
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88 | movePerStep = getMovePerStep();
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89 |
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90 | //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
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91 |
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92 | //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files
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93 |
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94 | //reproduction
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95 | ExpProperties.foramPop = 20;
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96 | ExpProperties.crossprob = 0;
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97 | ExpProperties.mutationprob = 0;
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98 | ExpProperties.repro_time = 720;
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99 | ExpProperties.gametoPeriod = 43200;
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100 | ExpProperties.divisionCost = 15.6;
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101 | reprocounter = 0;
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102 |
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103 | init_chambers();
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104 |
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105 | //morphology
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106 | dir_change = 30000;
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107 | ExpProperties.zone1_range = micronsToFrams(1000);
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108 | ExpProperties.zone2_range = micronsToFrams(3000);
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109 | ExpProperties.chamber_growth_time = 720;
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110 | ExpProperties.chamberCostPerSec = 0.000001;
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111 | ExpProperties.chamber_proculus_haplo = micronsToFrams(50);
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112 | ExpProperties.chamber_difference_haplo = 0.0;
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113 | ExpProperties.chamber_proculus_diplo = micronsToFrams(20);
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114 | ExpProperties.chamber_difference_diplo = micronsToFrams(8);
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115 |
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116 | max_chamber_volume = [Vector.new(), Vector.new()];
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117 | for (var j = 0; j < 2; j++)
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118 | {
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119 | for (var i = 0; i < chambers[0].size; i++)
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120 | {
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121 | max_chamber_volume[j].add(((volumeInMicrons(getProperty(j, "chamber_proculus")) + volumeInMicrons(getProperty(j, "chamber_proculus") + (i) * getProperty(j, "chamber_difference")))*(i+1))/2);
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122 | }
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123 | }
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124 |
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125 | //energetics
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126 | ExpProperties.min_repro_energ_haplo = 4;
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127 | ExpProperties.min_repro_energ_diplo = 6;
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128 |
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129 | ExpProperties.e_meta = 0.0000005;
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130 | ExpProperties.energy_hib = 0.0000001;
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131 | ExpProperties.energy_move = 0.0000005;
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132 |
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133 | ExpProperties.energies0_haplo = energyFromVolume(micronsToFrams(20),1);
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134 | ExpProperties.energies0_diplo = energyFromVolume(micronsToFrams(1.25),1);
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135 | ExpProperties.feedtrans = 0.001;
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136 | ExpProperties.e_repro_cost_haplo = 0.3;
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137 | ExpProperties.e_repro_cost_diplo = 0.2;
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138 |
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139 | ExpProperties.e_death_level_haplo = 0.5;
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140 | ExpProperties.e_death_level_diplo = 0.5;
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141 |
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142 | //nutrients
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143 | changePeriod = 0;
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144 | phase = "high";
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145 | ExpProperties.foodperiod = 21600;
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146 | ExpProperties.foodPeriodChange = 0;
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147 | ExpProperties.nutrientradius = micronsToFrams(10);
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148 | ExpProperties.energy_nut = energyFromVolume(ExpProperties.nutrientradius,1);
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149 | ExpProperties.feedrate = 1;
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150 | ExpProperties.ingestion = 0.25;
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151 | nutrientenergywaiting = 0;
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152 | ExpState.totaltestedcr = 0;
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153 | ExpState.nutrient = "";
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154 | }
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155 |
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156 | @include "standard_placement.inc"
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157 |
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158 | function volumeInMicrons(radiusInFrams)
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159 | {
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160 | return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
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161 | }
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162 |
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163 | function energyFromVolume(base, isRadiusInFrams)
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164 | {
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165 | if (isRadiusInFrams == 1) //radius in frams
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166 | {
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167 | return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
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168 | }
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169 | else //volume in microns
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170 | {
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171 | return ExpProperties.picoCarbonPerMikro * base;
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172 | }
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173 | }
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174 |
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175 | function getMovePerStep()
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176 | {
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177 | return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
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178 | }
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179 |
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180 | function micronsToFrams(micrometers)
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181 | {
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182 | return micrometers*0.025;
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183 | }
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184 |
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185 | function framsToMicrons(framsworldunits)
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186 | {
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187 | return framsworldunits/0.025;
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188 | }
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189 |
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190 | function getProperty(gen, prop_id)
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191 | {
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192 | var ploid = "haplo";
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193 | if (gen == 1) ploid = "diplo";
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194 | return ExpProperties.[prop_id + "_" + ploid];
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195 | }
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196 |
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197 | function addForam(species, iter, chambernum, ploid)
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198 | {
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199 | var geno = createForamGenotype(ploid, species, chambernum);
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200 | var cr = Populations[0].add(geno);
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201 | cr.name = "Initial creature" + species + "_" + iter;
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202 | placeCreatureRandomly(cr, 0, 0);
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203 | cr.energy0 = energyFromVolume(max_chamber_volume[ploid][chambernum],0);
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204 | cr.energy = cr.energy0;
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205 | setGenotype({"opt" : 0, "cr" : cr, "species" : species});
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206 | if (ploid == 1)
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207 | {
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208 | cr.data->lifeparams->gen = 1;
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209 | cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
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210 | }
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211 | }
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212 |
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213 | function addInitialForam(species, iter)
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214 | {
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215 | var ploid = 0;
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216 | if (Math.rnd01 > 0.5)
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217 | {
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218 | ploid = 1;
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219 | }
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220 | //add new foram with random energy bewtween starting energy and reproduction treshold
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221 | addForam(species, iter, Math.rndUni(0,getProperty(ploid, "min_repro_energ")),ploid);
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222 | }
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223 |
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224 | function onExpInit()
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225 | {
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226 | Populations[0].clear();
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227 | Populations[1].clear();
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228 | Populations[2].clear(); //reticulopodia and nutrients
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229 |
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230 | for (var i = 0; i < ExpProperties.foramPop; i++)
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231 | {
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232 | addInitialForam(0, i);
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233 | //addInitialForam(1, i);
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234 | }
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235 | o = Populations[0][0].getMechPart(0).orient.clone();
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236 | ExpState.totaltestedcr = 0;
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237 | nutrientenergywaiting = ExpProperties.energy_nut;
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238 | }
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239 |
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240 | function onExpLoad()
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241 | {
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242 | for (var pop in Populations)
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243 | pop.clear();
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244 |
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245 | Loader.addClass(sim_params.*);
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246 | Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
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247 | Loader.run();
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248 |
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249 | Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
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250 | }
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251 |
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252 | function onExpLoad_Unknown()
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253 | {
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254 | if (Loader.objectName == "org") // saved by the old expdef
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255 | {
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256 | var g = Genotype.newFromString("");
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257 | Loader.currentObject = g;
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258 | Interface.makeFrom(g).setAllDefault();
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259 | Loader.loadObject();
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260 | var cr = Populations[0].add(g);
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261 | if (cr != null)
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262 | {
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263 | //cr.rotate(0,0,Math.rnd01*Math.twopi);
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264 | if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
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265 | {
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266 | // [x,y,energy]
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267 | cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
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268 | cr.energy = g.data->genes[2];
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269 | }
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270 | else
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271 | {
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272 | cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
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273 | }
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274 | }
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275 | }
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276 | else if (Loader.objectName == "Creature")
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277 | {
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278 | Loader.currentObject = CreatureSnapshot.new();
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279 | Loader.loadObject();
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280 | Populations[0].add(Loader.currentObject);
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281 | }
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282 | }
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283 |
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284 | function onExpSave()
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285 | {
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286 | File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
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287 |
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288 | var tmpvec = [], i;
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289 |
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290 | for(var cr in Populations[1])
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291 | tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
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292 |
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293 | ExpState.nutrient = tmpvec;
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294 | File.writeObject(sim_params.*);
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295 | ExpState.nutrient = null; //vectors are only created for saving and then discarded
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296 |
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297 | for (var cr in Populations[0])
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298 | File.writeObject(cr);
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299 | }
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300 |
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301 | // -------------------------------- experiment end --------------------------------
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302 |
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303 | // -------------------------------- foram begin -----------------------------------
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304 |
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305 | function setForamMeta(cr)
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306 | {
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307 | //percent of current energy
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308 | cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
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309 | }
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310 |
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311 | function lastChamberNum(cr)
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312 | {
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313 | return cr.numparts-1;
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314 | }
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315 |
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316 | function getZoneRange(cr, zone_num)
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317 | {
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318 | return ExpProperties.["zone"+zone_num+"_range"];
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319 | }
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320 |
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321 | function onForamsBorn(cr)
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322 | {
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323 | setForamMeta(cr);
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324 | if (ExpProperties.visualize == 1)
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325 | {
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326 | var ret = Populations[2].add("//0\np:sh=3,sx=0.01,sy="+getZoneRange(cr,1)+",sz="+getZoneRange(cr,1)+",ry=1.57,vr=1.0,1.0,1.0");
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327 | cr.data->reticulopodiacreature = ret;
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328 | }
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329 | }
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330 |
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331 | function placeRandomlyNotColliding(cr)
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332 | {
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333 | var retry = 100; //try 100 times
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334 | while (retry--)
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335 | {
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336 | placeCreatureRandomly(cr, 0, 0);
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337 | if (!cr.boundingBoxCollisions(0))
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338 | return cr;
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339 | }
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340 |
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341 | Populations[0].delete(cr);
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342 | }
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343 |
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344 | function visualization(cr)
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345 | {
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346 | var has_ret = 0;
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347 |
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348 | if (cr.data->reticulopodiacreature != null)
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349 | {
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350 | if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
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351 | {
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352 | has_ret = 1;
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353 | }
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354 | }
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355 |
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356 | return has_ret;
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357 | }
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358 |
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359 | function foramGrow(cr, chamber_num)
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360 | {
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361 | if ((chamber_num+1) < chambers[cr.data->lifeparams->species].size)
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362 | {
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363 | var geno = createForamGenotype(cr.data->lifeparams->gen, cr.data->lifeparams->species, chamber_num+1);
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364 | var cr2 = Populations[0].add(geno);
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365 |
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366 | cr2.energy0 = cr.energy;
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367 | cr2.energy = cr2.energy0;
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368 |
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369 | setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : 2});
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370 | cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
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371 | setForamMeta(cr2);
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372 |
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373 | if (visualization(cr))
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374 | {
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375 | Populations[2].delete(cr.data->reticulopodiacreature);
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376 | }
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377 | Populations[0].delete(cr);
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378 | }
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379 | }
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380 |
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381 | function stepToNearest(cr)
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382 | {
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383 | var p = cr.getMechPart(0);
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384 | var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
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385 |
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386 | //if signals are received find the source of the nearest
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387 | if (n.size > 0)
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388 | {
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389 | var i;
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390 | var mp;
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391 | var distvec = XYZ.new(0, 0, 0);
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392 | var dist;
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393 | var mindist = 100000000000.0;
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394 | var mindistvec = null;
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395 | var eating = 0;
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396 |
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397 | for (i = 0; i < n.size; i++)
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398 | {
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399 | mp = n[i].value.getMechPart(0);
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400 | distvec.set(mp.pos);
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401 | distvec.sub(p.pos);
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402 | dist = distvec.length;
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403 | if (dist < getZoneRange(cr,1))
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404 | {
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405 | if (n[i].value != null)
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406 | {
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407 | energyTransfer(cr, n[i].value);
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408 | eating = 1;
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409 | }
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410 | }
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411 | else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
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412 | {
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413 | mindist = dist;
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414 | mindistvec = distvec.clone();
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415 | }
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416 | }
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417 |
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418 | if (!eating && cr.data->lifeparams->hibernated == 0)
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419 | {
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420 | mindistvec.normalize();
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421 | mindistvec.scale(-1*movePerStep);
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422 | cr.localDrive = mindistvec;
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423 | moveEnergyDec(cr);
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424 | }
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425 |
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426 | return 1;
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427 | }
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428 |
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429 | else
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430 | {
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431 | return 0;
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432 | }
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433 | }
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434 |
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435 | function moveEnergyDec(cr)
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436 | {
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437 | if (cr.data->lifeparams->hibernated == 0)
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438 | {
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439 | //percent of maximal energy
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440 | cr.energy_m += (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
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441 | }
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442 | }
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443 |
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444 | function foramMove(cr)
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445 | {
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446 | //TODO moving inside sediment?
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447 |
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448 | //adjustment in z axis
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449 | cr.moveAbs(cr.pos_x, cr.pos_y, 0);
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450 |
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451 | //are there any nutrients in zone 1 or 2?
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452 | {
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453 | var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
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454 | if (moved==1)
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455 | {
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456 | return;
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457 | }
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458 | }
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459 |
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460 | //no nutrients in zone 2
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461 | var hibernation = 0;
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462 | if (cr.data->lifeparams->gen == 0) hibernation = cr.data->genes->hibernation;
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463 | else hibernation = cr.data->genes[0]->hibernation;
|
---|
464 | //hibernation
|
---|
465 | if (hibernation == 1)
|
---|
466 | {
|
---|
467 | reverseHib(cr);
|
---|
468 | cr.localDrive = XYZ.new(0,0,0);
|
---|
469 | }
|
---|
470 | //random move
|
---|
471 | else if (cr.lifespan%int(dir_change/ExpProperties.secPerStep) == 0)
|
---|
472 | {
|
---|
473 | cr.data->lifeparams->dir = randomDir();
|
---|
474 | cr.localDrive = cr.data->lifeparams->dir;
|
---|
475 | moveEnergyDec(cr);
|
---|
476 | }
|
---|
477 | else
|
---|
478 | {
|
---|
479 | cr.localDrive = cr.data->lifeparams->dir;
|
---|
480 | }
|
---|
481 | }
|
---|
482 |
|
---|
483 | function randomDir()
|
---|
484 | {
|
---|
485 | var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0);
|
---|
486 | dir.normalize();
|
---|
487 | dir.scale(-1*movePerStep);
|
---|
488 | return dir;
|
---|
489 | }
|
---|
490 |
|
---|
491 | function energyTransfer(cr1, cr2)
|
---|
492 | {
|
---|
493 | cr1.localDrive = XYZ.new(0,0,0);
|
---|
494 | var e = ExpProperties.feedtrans*cr1.energy;//ExpProperties.feedtrans*cr1.energy*ExpProperties.ingestion*ExpProperties.secPerStep; //TODO efficiency dependent on age
|
---|
495 | e = Math.min(cr2.energy, e);
|
---|
496 | e *= ExpProperties.secPerStep;
|
---|
497 | //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.name+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
|
---|
498 | cr2.energy_m = cr2.energy_m + e + 0.0000001;
|
---|
499 | cr1.energy_p = cr1.energy_p + e*ExpProperties.ingestion;
|
---|
500 | if (cr1.data->lifeparams->hibernated == 1)
|
---|
501 | {
|
---|
502 | reverseHib(cr1);
|
---|
503 | }
|
---|
504 | }
|
---|
505 |
|
---|
506 | function reverseHib(cr)
|
---|
507 | {
|
---|
508 | if (cr.data->lifeparams->hibernated == 1)
|
---|
509 | {
|
---|
510 | setForamMeta(cr); //unhibernate
|
---|
511 | }
|
---|
512 | else
|
---|
513 | {
|
---|
514 | cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
|
---|
515 | }
|
---|
516 | cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
|
---|
517 | }
|
---|
518 |
|
---|
519 |
|
---|
520 | function onForamsStep(cr)
|
---|
521 | {
|
---|
522 | //checking for gametogenesis process
|
---|
523 | if (cr.data->lifeparams->division_time > 0)
|
---|
524 | {
|
---|
525 | cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
|
---|
526 | }
|
---|
527 | //checking for end of gametogenesis
|
---|
528 | else if (cr.data->lifeparams->division_time == 0)
|
---|
529 | {
|
---|
530 | //waiting for gamets fusion
|
---|
531 | }
|
---|
532 | //checking for chamber growth process
|
---|
533 | else if (cr.data->lifeparams->chamber_growth > 0)
|
---|
534 | {
|
---|
535 | cr.data->lifeparams->chamber_growth = Math.max(cr.data->lifeparams->chamber_growth-1,0);
|
---|
536 | //Simulator.print("chamber growing, time left = " + cr.data->lifeparams->chamber_growth*ExpProperties.secPerStep);
|
---|
537 | cr.energy_m += ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
|
---|
538 |
|
---|
539 | //Simulator.print("energy " + cr2.energy + " subtracting " + growth_cost);
|
---|
540 | }
|
---|
541 | //checking for end of chamber growth process
|
---|
542 | else if (cr.data->lifeparams->chamber_growth == 0)
|
---|
543 | {
|
---|
544 | foramGrow(cr, lastChamberNum(cr));
|
---|
545 | cr.data->lifeparams->chamber_growth = -1;
|
---|
546 | //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
|
---|
547 | }
|
---|
548 | else
|
---|
549 | {
|
---|
550 | //update of metabolism rate
|
---|
551 | if (cr.data->lifeparams->hibernated == 0)
|
---|
552 | {
|
---|
553 | setForamMeta(cr);
|
---|
554 | }
|
---|
555 |
|
---|
556 | cr.getMechPart(0).orient.set(o);
|
---|
557 | if (visualization(cr))
|
---|
558 | {
|
---|
559 | cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1)-getProperty(cr.data->lifeparams->gen, "chamber_proculus"));
|
---|
560 | }
|
---|
561 |
|
---|
562 | if (deathConditions(cr) == 1)
|
---|
563 | {
|
---|
564 | Populations[0].kill(cr);
|
---|
565 | return;
|
---|
566 | }
|
---|
567 |
|
---|
568 | foramMove(cr);
|
---|
569 |
|
---|
570 | var repro = foramReproduce(cr);
|
---|
571 | if (repro == 1)
|
---|
572 | {
|
---|
573 | return;
|
---|
574 | }
|
---|
575 |
|
---|
576 | cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
|
---|
577 |
|
---|
578 | //cheking conditions of chamber growth process start
|
---|
579 | if (lastChamberNum(cr) != chambers[0].size-1)
|
---|
580 | {
|
---|
581 | if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)],0)))
|
---|
582 | {
|
---|
583 | cr.data->lifeparams->chamber_growth = int(ExpProperties.chamber_growth_time/ExpProperties.secPerStep);
|
---|
584 | }
|
---|
585 | }
|
---|
586 | }
|
---|
587 | }
|
---|
588 |
|
---|
589 | function deathConditions(cr)
|
---|
590 | {
|
---|
591 | if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
|
---|
592 | {
|
---|
593 | return 1;
|
---|
594 | }
|
---|
595 | else
|
---|
596 | return 0;
|
---|
597 | }
|
---|
598 |
|
---|
599 | function onForamsDied(cr)
|
---|
600 | {
|
---|
601 | if (visualization(cr))
|
---|
602 | {
|
---|
603 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
604 | }
|
---|
605 | //fossilization
|
---|
606 | var geno = GenePools[0].add(cr.genotype);
|
---|
607 | geno.data->genes = cr.data->genes;
|
---|
608 | geno.data->lifeparams = cr.data->lifeparams;
|
---|
609 | if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
|
---|
610 | ExpState.totaltestedcr++;
|
---|
611 | }
|
---|
612 |
|
---|
613 | // --------------------------------foram end -------------------------------------
|
---|
614 |
|
---|
615 | // -------------------------------- nutrient begin --------------------------------
|
---|
616 |
|
---|
617 | function createNutrientGenotype(nutrientradius)
|
---|
618 | {
|
---|
619 | return "//0\np:sh=3,sx="+nutrientradius+",sy="+nutrientradius+",sz="+nutrientradius+",ry=1.5,vr=0.0,1.0,0.0";
|
---|
620 | }
|
---|
621 |
|
---|
622 | function onNutrientsStep(cr)
|
---|
623 | {
|
---|
624 | cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
|
---|
625 | }
|
---|
626 |
|
---|
627 | function addNutrient()
|
---|
628 | {
|
---|
629 | var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
|
---|
630 |
|
---|
631 | cr.name = "Nutrients";
|
---|
632 | cr.idleen = 0;
|
---|
633 | cr.energy0 = ExpProperties.energy_nut;
|
---|
634 | cr.energy = cr.energy0;
|
---|
635 | cr.signals.add("nutrient");
|
---|
636 |
|
---|
637 | cr.signals[0].value = cr;
|
---|
638 |
|
---|
639 | placeCreatureRandomly(cr, 0, 0);
|
---|
640 | if (ExpProperties.visualize == 1)
|
---|
641 | {
|
---|
642 | var nutsize = ExpProperties.nutrientradius*10;
|
---|
643 | var nut = Populations[2].add("//0\np:sh=2,sx="+nutsize+",sy="+nutsize+",sz="+nutsize+",ry=1.5,vr=0.0,1.0,0.0");
|
---|
644 | cr.data->reticulopodiacreature = nut;
|
---|
645 | nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
|
---|
646 | }
|
---|
647 | }
|
---|
648 |
|
---|
649 | function onNutrientsDied(cr)
|
---|
650 | {
|
---|
651 | if (visualization(cr))
|
---|
652 | {
|
---|
653 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
654 | }
|
---|
655 | }
|
---|
656 |
|
---|
657 | function nutrientGrowth()
|
---|
658 | {
|
---|
659 | if (ExpProperties.foodPeriodChange > 0)
|
---|
660 | {
|
---|
661 | changePeriod += 1;
|
---|
662 | if (phase=="low" && (changePeriod*ExpProperties.secPerStep) >= 23328000) //9 months
|
---|
663 | {
|
---|
664 | ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
|
---|
665 | phase = "high";
|
---|
666 | changePeriod = 0;
|
---|
667 | }
|
---|
668 |
|
---|
669 | else if (phase == "high" && (changePeriod*ExpProperties.secPerStep) >= 7776000) //3 months
|
---|
670 | {
|
---|
671 | ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
|
---|
672 | phase = "low";
|
---|
673 | changePeriod = 0;
|
---|
674 | }
|
---|
675 | }
|
---|
676 | nutrientenergywaiting = nutrientenergywaiting + 1;
|
---|
677 | if (nutrientenergywaiting*ExpProperties.secPerStep >= ExpProperties.foodperiod)
|
---|
678 | {
|
---|
679 | for (var i = 0; i < ExpProperties.feedrate; i++)
|
---|
680 | {
|
---|
681 | addNutrient();
|
---|
682 | }
|
---|
683 |
|
---|
684 | nutrientenergywaiting = 0.0;
|
---|
685 | Simulator.checkpoint();
|
---|
686 | }
|
---|
687 | }
|
---|
688 |
|
---|
689 | // -------------------------------- nutrient end --------------------------------
|
---|
690 |
|
---|
691 | // -------------------------------- step begin --------------------------------
|
---|
692 |
|
---|
693 | function onStep()
|
---|
694 | {
|
---|
695 |
|
---|
696 | nutrientGrowth();
|
---|
697 | if (ExpProperties.logging == 1)
|
---|
698 | {
|
---|
699 | createStatistics();
|
---|
700 | }
|
---|
701 |
|
---|
702 | //reproduction --------------------------------------------
|
---|
703 | reprocounter += 1;
|
---|
704 | if (reprocounter*ExpProperties.secPerStep > ExpProperties.repro_time)
|
---|
705 | {
|
---|
706 | reprocounter = 0;
|
---|
707 | reproduce_parents(0);
|
---|
708 | reproduce_parents(1);
|
---|
709 | }
|
---|
710 |
|
---|
711 | //check for extinction -----------------------------------------------
|
---|
712 | if (Populations[0].size == 0)
|
---|
713 | {
|
---|
714 | if (ExpProperties.autorestart)
|
---|
715 | {
|
---|
716 | Simulator.print("no more creatures, restarting...");
|
---|
717 | onExpInit();
|
---|
718 | }
|
---|
719 | else
|
---|
720 | {
|
---|
721 | Simulator.print("no more creatures, stopped.");
|
---|
722 | Simulator.stop();
|
---|
723 | }
|
---|
724 | }
|
---|
725 | if (ExpProperties.maxSteps > 0)
|
---|
726 | {
|
---|
727 | if (Simulator.stepNumber >= ExpProperties.maxSteps)
|
---|
728 | Simulator.stop();
|
---|
729 | }
|
---|
730 | }
|
---|
731 |
|
---|
732 | function createStatistics()
|
---|
733 | {
|
---|
734 | var number = [[0, 0],[0,0]]; // [species][gen]
|
---|
735 | var e_inc = [[0, 0],[0,0]];
|
---|
736 | var e_nut = 0.0;
|
---|
737 |
|
---|
738 | for (var i = 0; i < Populations[0].size; i++)
|
---|
739 | {
|
---|
740 | var cr = Populations[0].get(i);
|
---|
741 | var gen = cr.data->lifeparams->gen;
|
---|
742 | var species = cr.data->lifeparams->species;
|
---|
743 |
|
---|
744 | number[species][gen] = number[species][gen] + 1;
|
---|
745 | e_inc[species][gen] = e_inc[species][gen] + cr.energy;
|
---|
746 | }
|
---|
747 |
|
---|
748 | for (var i = 0; i < Populations[1].size; i++)
|
---|
749 | {
|
---|
750 | var cr = Populations[1].get(i);
|
---|
751 | e_nut += cr.energy;
|
---|
752 | }
|
---|
753 |
|
---|
754 | var log_numbers = [number[1][0], number[1][1], number[0][0], number[0][1], Populations[1].size];
|
---|
755 | var log_energies = [e_inc[1][0], e_inc[1][1], e_inc[0][0], e_inc[0][1], e_nut];
|
---|
756 |
|
---|
757 | log(log_numbers, "forams_log.txt");
|
---|
758 | log(log_energies, "energies_log.txt");
|
---|
759 | }
|
---|
760 |
|
---|
761 | function log(tolog, fname)
|
---|
762 | {
|
---|
763 | var f = File.appendDirect(fname, "forams data");
|
---|
764 | f.writeString("" + Simulator.stepNumber);
|
---|
765 | for (var i = 0; i < tolog.size; i++)
|
---|
766 | {
|
---|
767 | f.writeString(";" + tolog[i]);
|
---|
768 | }
|
---|
769 | f.writeString("\n");
|
---|
770 | f.close();
|
---|
771 | }
|
---|
772 |
|
---|
773 | // -------------------------------- step end --------------------------------
|
---|
774 | //TODO default params values in frams instead of microns/seconds
|
---|
775 |
|
---|
776 | @include "standard_events.inc"
|
---|
777 |
|
---|
778 | ~
|
---|
779 |
|
---|
780 | property:
|
---|
781 | id:visualize
|
---|
782 | name:Show reticulopodia and nutrients
|
---|
783 | type:d 0 1 0
|
---|
784 | group:Foraminifera
|
---|
785 |
|
---|
786 | property:
|
---|
787 | id:maxSteps
|
---|
788 | name:Stop after the given number of simulation steps
|
---|
789 | type:d 0 1000000 0
|
---|
790 |
|
---|
791 | property:
|
---|
792 | id:foramSpeedMmPerMin
|
---|
793 | name:Speed of foraminfera in mm/min
|
---|
794 | type:f 0.1
|
---|
795 | flags: 16
|
---|
796 | group:Foraminifera
|
---|
797 |
|
---|
798 | property:
|
---|
799 | id:gametSuccessRate
|
---|
800 | name:Ratio of successful gamets
|
---|
801 | type:f 0.001
|
---|
802 | group:Foraminifera
|
---|
803 |
|
---|
804 | property:
|
---|
805 | id:gametoPeriod
|
---|
806 | name:Time of gametogenesis
|
---|
807 | type:f 720
|
---|
808 | group:Foraminifera
|
---|
809 |
|
---|
810 | property:
|
---|
811 | id:picoCarbonPerMikro
|
---|
812 | name:Picograms of carbon in cubed micrometer
|
---|
813 | type:f 0.13
|
---|
814 | group:Foraminifera
|
---|
815 |
|
---|
816 | property:
|
---|
817 | id:secPerStep
|
---|
818 | name:Seconds per simulation step
|
---|
819 | type:f 60.0
|
---|
820 | flags: 16
|
---|
821 | group:Foraminifera
|
---|
822 |
|
---|
823 | property:
|
---|
824 | id:e_repro_cost_haplo
|
---|
825 | name:Cost of reproduction
|
---|
826 | type:f 0.1 0.9 0.5
|
---|
827 | group:Foraminifera
|
---|
828 |
|
---|
829 | property:
|
---|
830 | id:divisionCost
|
---|
831 | name:Cost of division in pG
|
---|
832 | type:f
|
---|
833 | group:Foraminifera
|
---|
834 |
|
---|
835 | property:
|
---|
836 | id:e_repro_cost_diplo
|
---|
837 | name:Cost of reproduction
|
---|
838 | type:f 0.1 0.9 0.3
|
---|
839 | group:Foraminifera
|
---|
840 |
|
---|
841 | property:
|
---|
842 | id:chamber_growth_time
|
---|
843 | name:Time of the chamber growth in seconds
|
---|
844 | type:f
|
---|
845 | group:Foraminifera
|
---|
846 |
|
---|
847 | property:
|
---|
848 | id:chamberCostPerSec
|
---|
849 | name:Cost of growning chamber per second
|
---|
850 | type:f
|
---|
851 | group:Foraminifera
|
---|
852 |
|
---|
853 | property:
|
---|
854 | id:chamber_proculus_haplo
|
---|
855 | name:Size of proculus
|
---|
856 | type:f
|
---|
857 | group:Foraminifera
|
---|
858 |
|
---|
859 | property:
|
---|
860 | id:chamber_proculus_diplo
|
---|
861 | name:Size of proculus
|
---|
862 | type:f
|
---|
863 | group:Foraminifera
|
---|
864 |
|
---|
865 | property:
|
---|
866 | id:chamber_difference_haplo
|
---|
867 | name:Difference in size between subsequent chambers
|
---|
868 | type:f
|
---|
869 | group:Foraminifera
|
---|
870 |
|
---|
871 | property:
|
---|
872 | id:chamber_difference_diplo
|
---|
873 | name:Difference in size between subsequent chambers
|
---|
874 | type:f
|
---|
875 | group:Foraminifera
|
---|
876 |
|
---|
877 | property:
|
---|
878 | id:hunted_prob
|
---|
879 | name:Probability of being hunted
|
---|
880 | type:f 0 1 0
|
---|
881 | group:Forminifera
|
---|
882 |
|
---|
883 | property:
|
---|
884 | id:zone1_range
|
---|
885 | name:Zone 1 range
|
---|
886 | type:f 0 200
|
---|
887 | group:Foraminifera
|
---|
888 |
|
---|
889 | property:
|
---|
890 | id:zone2_range
|
---|
891 | name:Zone 2 range
|
---|
892 | type:f 0 3000
|
---|
893 | group:Foraminifera
|
---|
894 |
|
---|
895 | property:
|
---|
896 | id:colors
|
---|
897 | name:Haploid and diploid colors
|
---|
898 | type:x
|
---|
899 | group:Foraminifera
|
---|
900 |
|
---|
901 | property:
|
---|
902 | id:min_repro_energ_haplo
|
---|
903 | name:Min reproduction energy of forams
|
---|
904 | type:f
|
---|
905 | group:Foraminifera
|
---|
906 |
|
---|
907 | property:
|
---|
908 | id:min_repro_energ_diplo
|
---|
909 | name:Min reproduction energy of forams
|
---|
910 | type:f
|
---|
911 | group:Foraminifera
|
---|
912 |
|
---|
913 | property:
|
---|
914 | id:repro_prob
|
---|
915 | name:Probability of reproduction
|
---|
916 | type:f 0 1 0.8
|
---|
917 | group:Foraminifera
|
---|
918 |
|
---|
919 | property:
|
---|
920 | id:energies0_haplo
|
---|
921 | name:Energy of offspring from diploid forams
|
---|
922 | type:f
|
---|
923 | group:Foraminifera
|
---|
924 |
|
---|
925 | property:
|
---|
926 | id:energies0_diplo
|
---|
927 | name:Energy of offspring from diploid forams
|
---|
928 | type:f
|
---|
929 | group:Foraminifera
|
---|
930 |
|
---|
931 | property:
|
---|
932 | id:e_death_level_haplo
|
---|
933 | name:Minimal level of energy to sustain life of haploid
|
---|
934 | type:f 0 20 0.2
|
---|
935 | group:Foraminifera
|
---|
936 |
|
---|
937 | property:
|
---|
938 | id:e_death_level_diplo
|
---|
939 | name:Minimal level of energy to sustain life of diploid
|
---|
940 | type:f 0 20 0.2
|
---|
941 | group:Foraminifera
|
---|
942 |
|
---|
943 | property:
|
---|
944 | id:energy_hib
|
---|
945 | name:Energy used for hibernation during one step
|
---|
946 | type:f 0 1 0.001
|
---|
947 | group:Foraminifera
|
---|
948 |
|
---|
949 | property:
|
---|
950 | id:energy_move
|
---|
951 | name:Energy used for movement during one step
|
---|
952 | type:f 0 20 0.001
|
---|
953 | group:Foraminifera
|
---|
954 |
|
---|
955 | property:
|
---|
956 | id:min_vol
|
---|
957 | name:Minimal volume for reproduction
|
---|
958 | type:f 100 900 100
|
---|
959 | group:Foraminifera
|
---|
960 |
|
---|
961 | property:
|
---|
962 | id:max_size
|
---|
963 | name:Maximal size
|
---|
964 | type:d 1 10 5
|
---|
965 | group:Foraminifera
|
---|
966 |
|
---|
967 | property:
|
---|
968 | id:foramPop
|
---|
969 | name:Initial forams population size
|
---|
970 | type:d 1 1000 100
|
---|
971 | group:Foraminifera
|
---|
972 |
|
---|
973 | property:
|
---|
974 | id:crossprob
|
---|
975 | name:Crossover probability
|
---|
976 | type:f 0 1 0
|
---|
977 | group:Foraminifera
|
---|
978 |
|
---|
979 | property:
|
---|
980 | id:mutationprob
|
---|
981 | name:Mutation probability
|
---|
982 | type:f 0 1 0
|
---|
983 | group:Foraminifera
|
---|
984 |
|
---|
985 | property:
|
---|
986 | id:e_meta
|
---|
987 | name:Idle metabolism
|
---|
988 | type:f 0 1
|
---|
989 | group:Energy
|
---|
990 | help:Each stick consumes this amount of energy in one time step
|
---|
991 |
|
---|
992 | property:
|
---|
993 | id:feedrate
|
---|
994 | name:Feeding rate
|
---|
995 | type:f 0 1000000
|
---|
996 | group:Energy
|
---|
997 | help:How fast energy is created in the world
|
---|
998 |
|
---|
999 | property:
|
---|
1000 | id:foodPeriodChange
|
---|
1001 | name:Set variable feed rate
|
---|
1002 | type:f 0
|
---|
1003 | group:Energy
|
---|
1004 |
|
---|
1005 | property:
|
---|
1006 | id:ingestion
|
---|
1007 | name:Ingestion rate
|
---|
1008 | type:f
|
---|
1009 | group:Energy
|
---|
1010 |
|
---|
1011 | property:
|
---|
1012 | id:energy_nut
|
---|
1013 | name:Nutrient energy
|
---|
1014 | type:f 0 100000
|
---|
1015 | group:Energy
|
---|
1016 |
|
---|
1017 | property:
|
---|
1018 | id:feedtrans
|
---|
1019 | name:Energy transfer per second
|
---|
1020 | type:f 0 100000
|
---|
1021 | group:Energy
|
---|
1022 |
|
---|
1023 | property:
|
---|
1024 | id:foodperiod
|
---|
1025 | name:Time between food occurrences
|
---|
1026 | type:f 0 1000000
|
---|
1027 | group:Energy
|
---|
1028 |
|
---|
1029 | property:
|
---|
1030 | id:nutrientradius
|
---|
1031 | name:Nutrient size
|
---|
1032 | type:f 0.1 0.9 0.1
|
---|
1033 | group:Energy
|
---|
1034 |
|
---|
1035 | property:
|
---|
1036 | id:stress
|
---|
1037 | name:Environmental stress
|
---|
1038 | type:d 0 1 1
|
---|
1039 | group:World
|
---|
1040 |
|
---|
1041 | property:
|
---|
1042 | id:repro_trigger
|
---|
1043 | name:Reproduction trigger
|
---|
1044 | type:d 0 1 1
|
---|
1045 | group:World
|
---|
1046 |
|
---|
1047 | property:
|
---|
1048 | id:repro_time
|
---|
1049 | name:Time before reproduction
|
---|
1050 | type:d 0 10000
|
---|
1051 |
|
---|
1052 | property:
|
---|
1053 | id:creath
|
---|
1054 | name:Creation height
|
---|
1055 | type:f -1 50
|
---|
1056 | help:~
|
---|
1057 | Vertical position (above the surface) where new Forams are revived.
|
---|
1058 | Negative values are only used in the water area:
|
---|
1059 | 0 = at the surface
|
---|
1060 | -0.5 = half depth
|
---|
1061 | -1 = just above the bottom~
|
---|
1062 |
|
---|
1063 | state:
|
---|
1064 | id:nutrient
|
---|
1065 | name:Nutrient locations
|
---|
1066 | help:vector of vectors [x,y,energy]
|
---|
1067 | type:x
|
---|
1068 | flags:32
|
---|
1069 |
|
---|
1070 | property:
|
---|
1071 | id:autorestart
|
---|
1072 | name:Restart after extinction
|
---|
1073 | help:Restart automatically this experiment after the last creature has died?
|
---|
1074 | type:d 0 1
|
---|
1075 |
|
---|
1076 | state:
|
---|
1077 | id:notes
|
---|
1078 | name:Notes
|
---|
1079 | type:s 1
|
---|
1080 | help:~
|
---|
1081 | You can write anything here
|
---|
1082 | (it will be saved to the experiment file)~
|
---|
1083 |
|
---|
1084 | state:
|
---|
1085 | id:totaltestedcr
|
---|
1086 | name:Evaluated Forams
|
---|
1087 | help:Total number of the Forams evaluated in the experiment
|
---|
1088 | type:d
|
---|
1089 | flags:16
|
---|
1090 |
|
---|
1091 | property:
|
---|
1092 | id:logging
|
---|
1093 | name:Log statistics to file
|
---|
1094 | type:d 0 1 0
|
---|