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 colors;
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26 | global retColors;
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27 | global curColor;
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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 reprocounter;
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32 | global changePeriod;
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33 | global phase;
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34 | global nutrientSqrCm;
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35 | global species_genes;
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36 | global max_chambers_def;
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37 | global foram_uid; //introduced because each replacement of a creature (while growing) would generate a new Creature.uid
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38 | global chamber_vis_denominator;
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39 | global curRadius;
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40 |
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41 | @include "foraminifera.inc"
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42 |
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43 | // -------------------------------- experiment begin --------------------------------
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44 |
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45 | function onExpDefLoad()
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46 | {
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47 | // define genotype and creature groups
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48 | GenePools.clear();
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49 | Populations.clear();
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50 | GenePools[0].name = "Unused";
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51 |
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52 | var pop = Populations[0];
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53 | pop.name = "Forams";
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54 | pop.en_assim = 0;
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55 | pop.nnsim = 0;
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56 | pop.enableperf = 1;
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57 | pop.death = 1;
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58 | pop.energy = 1;
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59 | pop.selfmask = 0;
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60 | pop.othermask = 0;
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61 | //pop.selfmask = 0x20002; pop.othermask = 0x10002;
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62 | pop.perfperiod = 25;
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63 | pop.bodysim = 0;
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64 |
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65 | pop = Populations.addGroup("Nutrients");
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66 | pop.nnsim = 0;
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67 | pop.enableperf = 0;
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68 | pop.death = 1;
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69 | pop.energy = 1;
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70 | pop.selfmask = 0;
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71 | pop.othermask = 0;
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72 | //pop.othermask = 0x10002;
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73 | pop.bodysim = 0;
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74 |
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75 | pop = Populations.addGroup("ReticulopodiaNutrients");
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76 | pop.nnsim = 0;
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77 | pop.enableperf = 0;
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78 | pop.death = 0;
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79 | pop.energy = 0;
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80 | pop.selfmask = 0;
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81 | pop.othermask = 0;
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82 | pop.bodysim = 0;
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83 |
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84 | //world
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85 | SignalView.mode = 1;
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86 | World.wrldwat = 200;
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87 | World.wrldsiz = micronsToFrams(100000);
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88 | World.wrldbnd = 1;
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89 |
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90 | movePerStep = getMovePerStep();
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91 |
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92 | //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
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93 |
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94 | //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files
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95 | ExpProperties.logPref = "";
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96 |
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97 | species_genes = [];
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98 |
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99 | //morphology
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100 | ExpProperties.zone1_range = micronsToFrams(1000);
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101 | ExpProperties.zone2_range = micronsToFrams(3000);
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102 | ExpProperties.chamber_proculus_haplo = micronsToFrams(20);
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103 | ExpProperties.chamber_proculus_diplo = micronsToFrams(10);
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104 | colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
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105 | retColors = ["1.0,1.0,1.0", "1.0,1.0,0.0"];
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106 | curColor = retColors[0];
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107 | curRadius = ExpProperties.zone1_range;
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108 |
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109 | //nutrients
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110 | ExpProperties.nutrientradius = micronsToFrams(10);
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111 | ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
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112 | nutrientSqrCm = 10;
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113 | ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
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114 |
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115 | ExpState.totaltestedcr = 0;
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116 | ExpState.nutrient = "";
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117 |
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118 | max_chambers_def = 35;
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119 | chamber_vis_denominator = 6;
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120 | //addSpecies({"min_repro_energies" : [4,6]});
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121 | //addSpecies({"min_repro_energies" : [4,8]});
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122 |
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123 | //Simulator.print(create_genotype(0.2, 30, "1.0,1.0,0.0", 0.6)); //sample call
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124 | //Simulator.print(create_genotype(0.1, 40, "1.0,0.5,0.0", 0.1)); //sample call
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125 | }
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126 |
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127 | @include "standard_placement.inc"
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128 |
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129 | function onExpInit()
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130 | {
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131 | foram_uid = 0;
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132 |
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133 | Populations[0].clear();
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134 | Populations[1].clear();
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135 | Populations[2].clear(); //reticulopodia and nutrients
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136 |
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137 | if (ExpProperties.max_chamber_num_haplo == max_chambers_def && ExpProperties.max_chamber_num_diplo == max_chambers_def)
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138 | {
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139 | max_chamber_volume = [[30403.5869594578,52812.2546633948,79578.5148482541,113588.815134453,154620.677376218,205094.322220826,262572.712174265,326078.453295303,402342.518962956,498133.985678766,615066.864740109,759500.497626816,937064.025544282,1155915.25563075,1429139.14079748,1762487.92940157,2176286.62046069,2685795.63187845,3316190.12127043,4096436.04462706,5051343.25226193,6231980.1061213,7687880.79524734,9485307.02904958,11716968.9852569,14459866.4934433,17836388.9853663,22004935.7247348,27138607.2546045,33482425.1582986,41336775.1280297,50997910.7842793,62888631.7871037,77563060.9243464,95659468.591964]
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140 | , [3430.07716920763,6159.93090353532,9322.94192815286,13462.9896597283,18399.8550832969,24558.9218126892,31468.8148639192,39189.4977865513,48404.4292075836,60185.8639086061,74490.6048472854,92117.8178412275,113852.779747083,140714.366929552,174450.937643841,215250.242147183,266323.295274072,328858.042352538,406552.379957238,503526.321155323,621060.781025019,767240.824049468,947210.683224091,1169506.19906112,1447211.61255879,1787155.29073739,2205627.64766244,2723413.2837305,3360233.53738709,4147771.02835393,5126445.06973928,6328060.3331703,7805693.278958,9631924.72156452,11884287.1596814]];
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141 | }
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142 |
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143 | else
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144 | {
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145 | max_chamber_volume = [Vector.new(), Vector.new()];
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146 | var density = 100;
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147 | for (var ploid = 0; ploid < 2; ploid++)
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148 | {
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149 | var rad = getPloidRadius(ploid);
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150 | for (var cham_num = 0; cham_num < getProperty(ploid,"max_chamber_num"); cham_num++)
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151 | {
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152 | max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num+1, density));
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153 | }
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154 | }
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155 | }
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156 |
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157 | if (species_genes.size == 0)
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158 | {
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159 | addSpecies({}); //default
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160 | }
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161 |
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162 | for (var spec = 0; spec < species_genes.size; spec++)
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163 | {
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164 | for (var i = 0; i < ExpProperties.foramPop; i++)
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165 | {
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166 | addInitialForam(spec, i);
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167 | }
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168 | }
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169 | ExpState.totaltestedcr = 0;
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170 |
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171 | reprocounter = 0;
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172 | nutrientenergywaiting = 0;
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173 | changePeriod = 0;
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174 | phase = "low";
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175 | }
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176 |
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177 | function onExpLoad()
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178 | {
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179 | for (var pop in Populations)
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180 | pop.clear();
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181 |
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182 | Loader.addClass(sim_params.*);
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183 | Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
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184 | Loader.run();
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185 |
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186 | Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
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187 | }
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188 |
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189 | function onExpLoad_Unknown()
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190 | {
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191 | if (Loader.objectName == "org") // saved by the old expdef
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192 | {
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193 | var g = Genotype.newFromString("");
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194 | Loader.currentObject = g;
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195 | Interface.makeFrom(g).setAllDefault();
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196 | Loader.loadObject();
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197 | var cr = Populations[0].add(g);
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198 | if (cr != null)
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199 | {
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200 | //cr.rotate(0,0,Math.rnd01*Math.twopi);
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201 | if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
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202 | {
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203 | // [x,y,energy]
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204 | cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
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205 | cr.energy = g.data->genes[2];
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206 | }
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207 | else
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208 | {
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209 | cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
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210 | }
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211 | }
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212 | }
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213 | else if (Loader.objectName == "Creature")
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214 | {
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215 | Loader.currentObject = CreatureSnapshot.new();
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216 | Loader.loadObject();
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217 | Populations[0].add(Loader.currentObject);
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218 | }
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219 | }
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220 |
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221 | function onExpSave()
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222 | {
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223 | File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
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224 |
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225 | var tmpvec = [], i;
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226 |
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227 | for(var cr in Populations[1])
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228 | tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
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229 |
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230 | ExpState.nutrient = tmpvec;
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231 | File.writeObject(sim_params.*);
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232 | ExpState.nutrient = null; //vectors are only created for saving and then discarded
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233 |
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234 | for (var cr in Populations[0])
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235 | File.writeObject(cr);
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236 | }
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237 |
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238 | // -------------------------------- experiment end --------------------------------
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239 |
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240 | function volumeFromGeno(morphotype, rad, chamber_num, density)
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241 | {
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242 | var geno = create_genotype(rad, chamber_num, colors[morphotype], 1);
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243 | var m=Model.newFromString(geno);
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244 | var mg=ModelGeometry.forModel(m);
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245 | mg.geom_density=density;
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246 | var volumeInFrams = mg.volume();
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247 |
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248 | return volumeInFrams/Math.pow(ExpProperties.scalingFactor,3);
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249 | }
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250 |
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251 | function secToSimSteps(value_in_sec){
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252 | return value_in_sec/ExpProperties.secPerStep;
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253 | }
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254 |
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255 | function volumeInMicrons(radiusInFrams)
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256 | {
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257 | return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
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258 | }
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259 |
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260 | function energyFromVolume(base, isRadiusInFrams)
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261 | {
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262 | if (isRadiusInFrams == 1) //radius in frams
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263 | {
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264 | return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
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265 | }
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266 | else //volume in microns
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267 | {
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268 | return ExpProperties.picoCarbonPerMikro * base;
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269 | }
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270 | }
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271 |
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272 | function getMovePerStep()
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273 | {
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274 | return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
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275 | }
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276 |
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277 | function micronsToFrams(micrometers)
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278 | {
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279 | return micrometers*ExpProperties.scalingFactor;
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280 | }
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281 |
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282 | function framsToMicrons(framsworldunits)
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283 | {
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284 | return framsworldunits/ExpProperties.scalingFactor;
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285 | }
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286 |
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287 | function getProperty(gen, prop_id)
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288 | {
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289 | var ploid = "haplo";
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290 | if (gen == 1) ploid = "diplo";
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291 | return ExpProperties.[prop_id + "_" + ploid];
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292 | }
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293 |
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294 | function getGene(cr, gen_id, gen_set)
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295 | {
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296 | if (cr.data->lifeparams->gen == 0)
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297 | return cr.data->genes[gen_id];
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298 | else
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299 | return cr.data->genes[gen_set][gen_id];
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300 | }
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301 |
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302 | function getPloidRadius(ploid)
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303 | {
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304 | var radius = ExpProperties.chamber_proculus_haplo;
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305 | if (ploid == 1)
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306 | {
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307 | radius = ExpProperties.chamber_proculus_diplo;
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308 | }
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309 | return radius;
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310 | }
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311 |
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312 | function chamberNumFromEnergy(energy, ploid)
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313 | {
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314 | var chamber_num = max_chamber_volume[ploid].size;
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315 | for (var i = 0; i < chamber_num; i++)
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316 | {
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317 | if (energy < energyFromVolume(max_chamber_volume[ploid][i],0))
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318 | {
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319 | chamber_num = i+1;
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320 | break;
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321 | }
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322 | }
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323 |
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324 | return chamber_num;
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325 | }
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326 |
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327 | function addForam(species, iter, start_energy, ploid)
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328 | {
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329 | var chambernum = chamberNumFromEnergy(start_energy, ploid);
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330 | var radius = getPloidRadius(ploid);
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331 | var geno = create_genotype(radius, chambernum, colors[ploid], 1);
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332 | curColor = retColors[ploid];
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333 | var cr = Populations[0].add(geno);
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334 | cr.name = "Initial creature" + species + "_" + iter;
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335 | placeCreatureRandomly(cr, 0, 0);
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336 | cr.energy = start_energy;
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337 | setGenotype({"opt" : "birth", "cr" : cr, "gen" : ploid, "species" : species, "energy0" : cr.energy, "genes" : species_genes[species], "parentsuids" : ["c0"]});
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338 | if (ploid == 1)
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339 | {
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340 | cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
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341 | }
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342 | moveReticulopodia(cr);
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343 | }
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344 |
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345 | function addInitialForam(species, iter)
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346 | {
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347 | var ploid = 0;
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348 | if (Math.rnd01 > 0.5)
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349 | {
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350 | ploid = 1;
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351 | }
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352 | //add new foram with random energy bewtween starting energy and reproduction threshold
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353 | var repro_thr = species_genes[species]->min_repro_energies[ploid];
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354 | var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid),1),repro_thr-0.25*repro_thr);
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355 | addForam(species, iter, start_energy,ploid);
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356 | }
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357 |
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358 | //new species can be added as a dictionary with parameter values that are different than default values
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359 | function addSpecies(new_genes)
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360 | {
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361 | species_genes.add({"min_repro_energies" : [ExpProperties.min_repro_energ_haplo,ExpProperties.min_repro_energ_diplo], "energies0" : [ExpProperties.energies0_haplo, ExpProperties.energies0_diplo], "hibernation" : 0, "morphotype" : 0});
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362 | for (var i = 0; i < new_genes.size; i++)
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363 | {
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364 | var key = new_genes.getKey(i);
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365 | species_genes[species_genes.size-1][key] = new_genes[key];
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366 | }
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367 | }
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368 |
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369 | // -------------------------------- foram begin -----------------------------------
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370 |
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371 | function setForamMeta(cr)
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372 | {
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373 | //percent of current energy
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374 | cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
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375 | }
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376 |
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377 | function lastChamberNum(cr)
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378 | {
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379 | return cr.numparts;
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380 | }
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381 |
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382 | function getZoneRange(cr, zone_num)
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383 | {
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384 | return ExpProperties.["zone"+zone_num+"_range"];
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385 | }
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386 |
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387 | function addReticulopodia(cr, radius)
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388 | {
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389 | if (reticulopodiaExists(cr))
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390 | {
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391 | Populations[2].delete(cr.data->reticulopodiacreature);
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392 | }
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393 | var ret = Populations[2].add("//0\nm:Vstyle=reticulopodia\np:sh=1,sx=0.001,sy=0.001,sz=0.001\np:sh=3,sx=0.01,sy="+radius+",sz="+radius+",ry=1.57079633,vr="+curColor+"\nj:0, 1, sh=1");
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394 | cr.data->reticulopodiacreature = ret;
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395 | ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
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396 | ret.moveAbs(cr.center_x-radius, cr.center_y-radius, cr.center_z-radius);
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397 | }
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398 |
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399 | function onForamsBorn(cr)
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400 | {
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401 | setForamMeta(cr);
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402 | if (ExpProperties.visualize == 1)
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403 | {
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404 | addReticulopodia(cr, curRadius);
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405 | }
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406 | moveReticulopodia(cr);
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407 | }
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408 |
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409 | function placeRandomlyNotColliding(cr)
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410 | {
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411 | var retry = 100; //try 100 times
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412 | while (retry--)
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413 | {
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414 | placeCreatureRandomly(cr, 0, 0);
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415 | if (!cr.boundingBoxCollisions(0))
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416 | return cr;
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417 | }
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418 |
|
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419 | Populations[0].delete(cr);
|
---|
420 | }
|
---|
421 |
|
---|
422 | function reticulopodiaExists(cr)
|
---|
423 | {
|
---|
424 | var has_ret = 0;
|
---|
425 |
|
---|
426 | if (cr.data->reticulopodiacreature != null)
|
---|
427 | {
|
---|
428 | if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
|
---|
429 | {
|
---|
430 | has_ret = 1;
|
---|
431 | }
|
---|
432 | }
|
---|
433 |
|
---|
434 | return has_ret;
|
---|
435 | }
|
---|
436 |
|
---|
437 | function visualization(cr)
|
---|
438 | {
|
---|
439 | return reticulopodiaExists(cr);
|
---|
440 | }
|
---|
441 |
|
---|
442 | function foramGrow(cr, chamber_num, lastchambergrowth)
|
---|
443 | {
|
---|
444 | if ((chamber_num+1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
|
---|
445 | {
|
---|
446 | curColor = retColors[cr.data->lifeparams->gen];
|
---|
447 | var ploid = cr.data->lifeparams->gen;
|
---|
448 | var geno = create_genotype(getPloidRadius(ploid), chamber_num+1, colors[ploid], lastchambergrowth);
|
---|
449 | var cr2 = Populations[0].add(geno);
|
---|
450 |
|
---|
451 | cr2.energy0 = cr.energy;
|
---|
452 | cr2.energy = cr2.energy0;
|
---|
453 |
|
---|
454 | setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
|
---|
455 | cr2.moveAbs(cr.pos_x, cr.pos_y,cr.pos_z);
|
---|
456 | setForamMeta(cr2);
|
---|
457 |
|
---|
458 | if (reticulopodiaExists(cr))
|
---|
459 | {
|
---|
460 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
461 | }
|
---|
462 | Populations[0].delete(cr);
|
---|
463 | return cr2;
|
---|
464 | }
|
---|
465 | return cr;
|
---|
466 | }
|
---|
467 |
|
---|
468 | function stepToNearest(cr)
|
---|
469 | {
|
---|
470 | var p = cr.getMechPart(0);
|
---|
471 | var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
|
---|
472 |
|
---|
473 | //if signals are received find the source of the nearest
|
---|
474 | if (n.size > 0)
|
---|
475 | {
|
---|
476 | var i;
|
---|
477 | var mp;
|
---|
478 | var distvec = XYZ.new(0, 0, 0);
|
---|
479 | var dist;
|
---|
480 | var mindist = 100000000000.0;
|
---|
481 | var mindistvec = null;
|
---|
482 | var eating = 0;
|
---|
483 |
|
---|
484 | for (i = 0; i < n.size; i++)
|
---|
485 | {
|
---|
486 | mp = n[i].value.getMechPart(0);
|
---|
487 | distvec.set(mp.pos);
|
---|
488 | distvec.sub(p.pos);
|
---|
489 | dist = distvec.length;
|
---|
490 | if (dist < getZoneRange(cr,1))
|
---|
491 | {
|
---|
492 | if (n[i].value != null)
|
---|
493 | {
|
---|
494 | energyTransfer(cr, n[i].value);
|
---|
495 | eating = 1;
|
---|
496 | }
|
---|
497 | }
|
---|
498 | else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
|
---|
499 | {
|
---|
500 | mindist = dist;
|
---|
501 | mindistvec = distvec.clone();
|
---|
502 | }
|
---|
503 | }
|
---|
504 |
|
---|
505 | if (!eating && cr.data->lifeparams->hibernated == 0)
|
---|
506 | {
|
---|
507 | mindistvec.normalize();
|
---|
508 | mindistvec.scale(-1*movePerStep);
|
---|
509 | cr.localDrive = mindistvec;
|
---|
510 | moveEnergyDec(cr);
|
---|
511 | }
|
---|
512 |
|
---|
513 | return 1;
|
---|
514 | }
|
---|
515 |
|
---|
516 | else
|
---|
517 | {
|
---|
518 | return 0;
|
---|
519 | }
|
---|
520 | }
|
---|
521 |
|
---|
522 | function moveEnergyDec(cr)
|
---|
523 | {
|
---|
524 | if (cr.data->lifeparams->hibernated == 0)
|
---|
525 | {
|
---|
526 | //percent of maximal energy
|
---|
527 | cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
|
---|
528 | }
|
---|
529 | }
|
---|
530 |
|
---|
531 | function fence(pos, zone)
|
---|
532 | {
|
---|
533 | return Math.min(Math.max(0,pos),World.wrldsiz);
|
---|
534 | }
|
---|
535 |
|
---|
536 | function foramMove(cr)
|
---|
537 | {
|
---|
538 | //TODO moving inside sediment?
|
---|
539 |
|
---|
540 | //adjustment in z axis
|
---|
541 | var change_direction = 0;
|
---|
542 | var new_x = fence(cr.pos_x, getZoneRange(cr, 1));
|
---|
543 | var new_y = fence(cr.pos_y,getZoneRange(cr, 1));
|
---|
544 |
|
---|
545 | if ((new_x != cr.pos_x) || (new_y != cr.pos_y) || (cr.data->lifeparams->dir_counter >= int(secToSimSteps(ExpProperties.dir_change_sec))))
|
---|
546 | {
|
---|
547 | change_direction = 1;
|
---|
548 | }
|
---|
549 |
|
---|
550 | cr.moveAbs(new_x, new_y, 0);
|
---|
551 |
|
---|
552 | //are there any nutrients in zone 1 or 2?
|
---|
553 | {
|
---|
554 | var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
|
---|
555 | if (moved==1)
|
---|
556 | {
|
---|
557 | moveReticulopodia(cr);
|
---|
558 | return;
|
---|
559 | }
|
---|
560 | }
|
---|
561 |
|
---|
562 | //no nutrients in zone 2
|
---|
563 | if (getGene(cr, "hibernation",0) == 1)
|
---|
564 | {
|
---|
565 | reverseHib(cr);
|
---|
566 | cr.localDrive = XYZ.new(0,0,0);
|
---|
567 | }
|
---|
568 | //random move
|
---|
569 | else if (change_direction == 1)
|
---|
570 | {
|
---|
571 | cr.data->lifeparams->dir = randomDir();
|
---|
572 | cr.data->lifeparams->dir_counter = 0;
|
---|
573 | cr.localDrive = cr.data->lifeparams->dir;
|
---|
574 | moveEnergyDec(cr);
|
---|
575 | }
|
---|
576 | else
|
---|
577 | {
|
---|
578 | cr.localDrive = cr.data->lifeparams->dir;
|
---|
579 | }
|
---|
580 | moveReticulopodia(cr);
|
---|
581 | }
|
---|
582 |
|
---|
583 | function moveReticulopodia(cr)
|
---|
584 | {
|
---|
585 | if (visualization(cr))
|
---|
586 | {
|
---|
587 | cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
|
---|
588 | cr.data->reticulopodiacreature.localDrive = cr.localDrive;
|
---|
589 | }
|
---|
590 | }
|
---|
591 |
|
---|
592 | function randomDir()
|
---|
593 | {
|
---|
594 | var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0);
|
---|
595 | dir.normalize();
|
---|
596 | dir.scale(-1*movePerStep);
|
---|
597 | return dir;
|
---|
598 | }
|
---|
599 |
|
---|
600 | function energyTransfer(cr1, cr2)
|
---|
601 | {
|
---|
602 | cr1.localDrive = XYZ.new(0,0,0);
|
---|
603 | var e = ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
|
---|
604 | //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
|
---|
605 | var transferred = cr2.transferEnergyTo(cr1, e);
|
---|
606 | cr1.energy -= transferred*(1-ExpProperties.ingestion);
|
---|
607 | if (cr1.data->lifeparams->hibernated == 1)
|
---|
608 | {
|
---|
609 | reverseHib(cr1);
|
---|
610 | }
|
---|
611 | }
|
---|
612 |
|
---|
613 | function reverseHib(cr)
|
---|
614 | {
|
---|
615 | if (cr.data->lifeparams->hibernated == 1)
|
---|
616 | {
|
---|
617 | setForamMeta(cr); //unhibernate
|
---|
618 | }
|
---|
619 | else
|
---|
620 | {
|
---|
621 | cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
|
---|
622 | }
|
---|
623 | cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
|
---|
624 | }
|
---|
625 |
|
---|
626 | function onForamsStep(cr)
|
---|
627 | {
|
---|
628 | //checking for gametogenesis process
|
---|
629 | if (cr.data->lifeparams->division_time > 0)
|
---|
630 | {
|
---|
631 | cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
|
---|
632 | }
|
---|
633 | //checking for end of gametogenesis
|
---|
634 | else if (cr.data->lifeparams->division_time == 0)
|
---|
635 | {
|
---|
636 | //waiting for gamets fusion
|
---|
637 | }
|
---|
638 | //checking for chamber growth process
|
---|
639 | else if (cr.data->lifeparams->chamber_growth > 0)
|
---|
640 | {
|
---|
641 | var chamber_time = Math.max(cr.data->lifeparams->chamber_growth-1,0);
|
---|
642 | cr.data->lifeparams->chamber_growth = chamber_time;
|
---|
643 | cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
|
---|
644 |
|
---|
645 | if (visualization(cr))
|
---|
646 | {
|
---|
647 | var total_time = secToSimSteps(ExpProperties.chamberGrowthSec);
|
---|
648 | var ret_unit = total_time/chamber_vis_denominator;
|
---|
649 | var chamber_unit = total_time-ret_unit;
|
---|
650 |
|
---|
651 | if (chamber_time < ret_unit || chamber_time >= chamber_unit)
|
---|
652 | {
|
---|
653 | var new_rad = Math.min(Math.max((chamber_time%ret_unit)/ret_unit*getZoneRange(cr,1),0.01),getZoneRange(cr,1));
|
---|
654 |
|
---|
655 | if(chamber_time < ret_unit)
|
---|
656 | new_rad = getZoneRange(cr,1)-new_rad;
|
---|
657 |
|
---|
658 | addReticulopodia(cr,new_rad);
|
---|
659 | }
|
---|
660 | else
|
---|
661 | {
|
---|
662 | var new_rad = 1 - Math.min(Math.max((chamber_time-ret_unit)/chamber_unit,0.01),1);
|
---|
663 | curRadius = cr.data->reticulopodiacreature.getPart(1).sy;
|
---|
664 |
|
---|
665 | if (chamber_time == ret_unit){
|
---|
666 | new_rad == 1;
|
---|
667 | }
|
---|
668 |
|
---|
669 | var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen)-1, new_rad);
|
---|
670 | curRadius = getZoneRange(new_cr,1);
|
---|
671 |
|
---|
672 | if (chamber_time == 0)//checking for end of chamber growth process
|
---|
673 | {
|
---|
674 | new_cr.data->lifeparams->chamber_growth = -1;
|
---|
675 | }
|
---|
676 | }
|
---|
677 | }
|
---|
678 | }
|
---|
679 | //checking for end of chamber growth process
|
---|
680 | else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr)==0)
|
---|
681 | {
|
---|
682 | foramGrow(cr, lastChamberNum(cr), 1);
|
---|
683 | cr.data->lifeparams->chamber_growth = -1;
|
---|
684 | //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
|
---|
685 | }
|
---|
686 | else
|
---|
687 | {
|
---|
688 | //update of metabolism rate
|
---|
689 | if (cr.data->lifeparams->hibernated == 0)
|
---|
690 | {
|
---|
691 | setForamMeta(cr);
|
---|
692 | }
|
---|
693 |
|
---|
694 | if (deathConditions(cr) == 1)
|
---|
695 | {
|
---|
696 | if (ExpProperties.logging == 1)
|
---|
697 | {
|
---|
698 | log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
|
---|
699 | log(createLogVector(cr, cr.lifespan),ExpProperties.logPref+"lifespan_log.txt");
|
---|
700 | }
|
---|
701 | Populations[0].kill(cr);
|
---|
702 | return;
|
---|
703 | }
|
---|
704 |
|
---|
705 | //update direction change counter
|
---|
706 | cr.data->lifeparams->dir_counter += 1;
|
---|
707 |
|
---|
708 | foramMove(cr);
|
---|
709 |
|
---|
710 | var repro = foramReproduce(cr);
|
---|
711 | if (repro == 1)
|
---|
712 | {
|
---|
713 | return;
|
---|
714 | }
|
---|
715 |
|
---|
716 | cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
|
---|
717 |
|
---|
718 | //cheking conditions of chamber growth process start
|
---|
719 | if (lastChamberNum(cr) < max_chamber_volume[cr.data->lifeparams->gen].size)
|
---|
720 | {
|
---|
721 | if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)-1],0)))
|
---|
722 | {
|
---|
723 | cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
|
---|
724 | }
|
---|
725 | }
|
---|
726 | }
|
---|
727 | }
|
---|
728 |
|
---|
729 | function deathConditions(cr)
|
---|
730 | {
|
---|
731 | if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
|
---|
732 | {
|
---|
733 | return 1;
|
---|
734 | }
|
---|
735 | else
|
---|
736 | return 0;
|
---|
737 | }
|
---|
738 |
|
---|
739 | function onForamsDied(cr)
|
---|
740 | {
|
---|
741 | if (visualization(cr))
|
---|
742 | {
|
---|
743 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
744 | }
|
---|
745 | //fossilization
|
---|
746 | var geno = GenePools[0].add(cr.genotype);
|
---|
747 | geno.data->genes = cr.data->genes;
|
---|
748 | geno.data->lifeparams = cr.data->lifeparams;
|
---|
749 | if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
|
---|
750 | ExpState.totaltestedcr++;
|
---|
751 | }
|
---|
752 |
|
---|
753 | // --------------------------------foram end -------------------------------------
|
---|
754 |
|
---|
755 | // -------------------------------- nutrient begin --------------------------------
|
---|
756 |
|
---|
757 | function createNutrientGenotype(nutrientradius)
|
---|
758 | {
|
---|
759 | return "//0\nm:Vstyle=nutrient\np:sh=3,sx="+nutrientradius+",sy="+nutrientradius+",sz="+nutrientradius+",ry=1.57,vr=0.0,1.0,0.0";
|
---|
760 | }
|
---|
761 |
|
---|
762 | function onNutrientsStep(cr)
|
---|
763 | {
|
---|
764 | cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
|
---|
765 | }
|
---|
766 |
|
---|
767 | function addNutrient()
|
---|
768 | {
|
---|
769 | var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
|
---|
770 |
|
---|
771 | cr.name = "Nutrients";
|
---|
772 | cr.idleen = 0;
|
---|
773 | cr.energy0 = ExpProperties.energy_nut;
|
---|
774 | cr.energy = cr.energy0;
|
---|
775 | cr.signals.add("nutrient");
|
---|
776 |
|
---|
777 | cr.signals[0].value = cr;
|
---|
778 |
|
---|
779 | placeCreatureRandomly(cr, 0, 0);
|
---|
780 | if (ExpProperties.visualize == 1)
|
---|
781 | {
|
---|
782 | var nutsize = ExpProperties.nutrientradius*10;
|
---|
783 | var nut = Populations[2].add("//0\nm:Vstyle=nutrient_visual\np:sh=2,sx="+nutsize+",sy="+nutsize+",sz="+nutsize+",ry=1.5,vr=0.0,1.0,0.0");
|
---|
784 | cr.data->reticulopodiacreature = nut;
|
---|
785 | nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
|
---|
786 | }
|
---|
787 | }
|
---|
788 |
|
---|
789 | function onNutrientsDied(cr)
|
---|
790 | {
|
---|
791 | if (visualization(cr))
|
---|
792 | {
|
---|
793 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
794 | }
|
---|
795 | }
|
---|
796 |
|
---|
797 | function nutrientGrowth()
|
---|
798 | {
|
---|
799 | if (ExpProperties.foodPeriodChange > 0)
|
---|
800 | {
|
---|
801 | changePeriod += 1;
|
---|
802 | if (phase=="low" && changePeriod >= secToSimSteps(23328000)) //9 months
|
---|
803 | {
|
---|
804 | ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
|
---|
805 | phase = "high";
|
---|
806 | changePeriod = 0;
|
---|
807 | }
|
---|
808 |
|
---|
809 | else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
|
---|
810 | {
|
---|
811 | ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
|
---|
812 | phase = "low";
|
---|
813 | changePeriod = 0;
|
---|
814 | }
|
---|
815 | }
|
---|
816 | nutrientenergywaiting = nutrientenergywaiting + 1;
|
---|
817 | if (nutrientenergywaiting >= secToSimSteps(ExpProperties.foodperiod))
|
---|
818 | {
|
---|
819 | for (var i = 0; i < ExpProperties.nutrient_pop; i++)
|
---|
820 | {
|
---|
821 | addNutrient();
|
---|
822 | }
|
---|
823 |
|
---|
824 | nutrientenergywaiting = 0.0;
|
---|
825 | Simulator.checkpoint();
|
---|
826 |
|
---|
827 | if (ExpProperties.logging == 1)
|
---|
828 | {
|
---|
829 | log([ExpProperties.nutrient_pop],ExpProperties.logPref+"nutrients_log.txt");
|
---|
830 | }
|
---|
831 | }
|
---|
832 |
|
---|
833 | }
|
---|
834 |
|
---|
835 | // -------------------------------- nutrient end --------------------------------
|
---|
836 |
|
---|
837 | // -------------------------------- step begin --------------------------------
|
---|
838 |
|
---|
839 | function onStep()
|
---|
840 | {
|
---|
841 |
|
---|
842 | nutrientGrowth();
|
---|
843 | if (ExpProperties.logging == 1)
|
---|
844 | {
|
---|
845 | createStatistics();
|
---|
846 | }
|
---|
847 |
|
---|
848 | //reproduction --------------------------------------------
|
---|
849 | reprocounter += 1;
|
---|
850 | if (reprocounter > secToSimSteps(ExpProperties.reproTimeSec))
|
---|
851 | {
|
---|
852 | reprocounter = 0;
|
---|
853 | for (var s = 0; s < species_genes.size; s++)
|
---|
854 | {
|
---|
855 | reproduce_parents(s);
|
---|
856 | }
|
---|
857 |
|
---|
858 | }
|
---|
859 |
|
---|
860 | //check for extinction -----------------------------------------------
|
---|
861 | if (Populations[0].size == 0)
|
---|
862 | {
|
---|
863 | if (ExpProperties.autorestart)
|
---|
864 | {
|
---|
865 | Simulator.print("no more creatures, restarting...");
|
---|
866 | onExpInit();
|
---|
867 | }
|
---|
868 | else
|
---|
869 | {
|
---|
870 | Simulator.print("no more creatures, stopped.");
|
---|
871 | Simulator.stop();
|
---|
872 | }
|
---|
873 | }
|
---|
874 | if (ExpProperties.maxSteps > 0)
|
---|
875 | {
|
---|
876 | if (Simulator.stepNumber >= ExpProperties.maxSteps)
|
---|
877 | Simulator.stop();
|
---|
878 | }
|
---|
879 | }
|
---|
880 |
|
---|
881 | function createStatistics()
|
---|
882 | {
|
---|
883 | var number = [];
|
---|
884 | var e_inc = [];
|
---|
885 | var e_nut = 0.0;
|
---|
886 |
|
---|
887 | for (var s = 0; s < species_genes.size; s++)
|
---|
888 | {
|
---|
889 | number.add([0,0]);// [haplo][diplo]
|
---|
890 | e_inc.add([0,0]);
|
---|
891 | }
|
---|
892 |
|
---|
893 | for (var i = 0; i < Populations[0].size; i++)
|
---|
894 | {
|
---|
895 | var cr = Populations[0].get(i);
|
---|
896 | var gen = cr.data->lifeparams->gen;
|
---|
897 | var species = cr.data->lifeparams->species;
|
---|
898 |
|
---|
899 | number[species][gen] = number[species][gen] + 1;
|
---|
900 | e_inc[species][gen] = e_inc[species][gen] + cr.energy;
|
---|
901 | }
|
---|
902 |
|
---|
903 | for (var i = 0; i < Populations[1].size; i++)
|
---|
904 | {
|
---|
905 | var cr = Populations[1].get(i);
|
---|
906 | e_nut += cr.energy;
|
---|
907 | }
|
---|
908 |
|
---|
909 | var log_numbers = [];
|
---|
910 | var log_energies = [];
|
---|
911 |
|
---|
912 | for (var s = 0; s < species_genes.size; s++)
|
---|
913 | {
|
---|
914 | for (var p = 0; p < 2; p++)
|
---|
915 | {
|
---|
916 | log_numbers.add(number[s][p]);
|
---|
917 | log_energies.add(e_inc[s][p]);
|
---|
918 | }
|
---|
919 | }
|
---|
920 |
|
---|
921 | log_numbers.add(Populations[1].size);
|
---|
922 | log_energies.add(e_nut);
|
---|
923 |
|
---|
924 | log(log_numbers, ExpProperties.logPref+"forams_log.txt");
|
---|
925 | log(log_energies, ExpProperties.logPref+"energies_log.txt");
|
---|
926 | }
|
---|
927 |
|
---|
928 | function log(tolog, fname)
|
---|
929 | {
|
---|
930 | var f = File.appendDirect(fname, "forams data");
|
---|
931 | f.writeString("" + Simulator.stepNumber);
|
---|
932 | for (var i = 0; i < tolog.size; i++)
|
---|
933 | {
|
---|
934 | f.writeString(";" + tolog[i]);
|
---|
935 | }
|
---|
936 | f.writeString("\n");
|
---|
937 | f.close();
|
---|
938 | }
|
---|
939 |
|
---|
940 | function createLogVector(cr, value)
|
---|
941 | {
|
---|
942 | var vec = Vector.new();
|
---|
943 | for (var i = 0; i < species_genes.size; i++)
|
---|
944 | {
|
---|
945 | for (var j = 0; j < 2; j++)
|
---|
946 | {
|
---|
947 | vec.add(0);
|
---|
948 | }
|
---|
949 | if (cr.data->lifeparams->species == i)
|
---|
950 | {
|
---|
951 | vec[i*2+cr.data->lifeparams->gen] = value;
|
---|
952 | }
|
---|
953 | }
|
---|
954 | return vec;
|
---|
955 | }
|
---|
956 |
|
---|
957 |
|
---|
958 | // -------------------------------- step end --------------------------------
|
---|
959 | //TODO default params values in frams instead of microns/seconds
|
---|
960 |
|
---|
961 | @include "standard_events.inc"
|
---|
962 |
|
---|
963 | ~
|
---|
964 |
|
---|
965 | property:
|
---|
966 | id:visualize
|
---|
967 | name:Show reticulopodia and nutrients
|
---|
968 | type:d 0 1 0
|
---|
969 | group:
|
---|
970 |
|
---|
971 | property:
|
---|
972 | id:maxSteps
|
---|
973 | name:Maximum number of steps
|
---|
974 | type:d 0 10000000 0
|
---|
975 | group:
|
---|
976 |
|
---|
977 | property:
|
---|
978 | id:scalingFactor
|
---|
979 | name:Scaling factor for micrometers
|
---|
980 | type:f 0 -1 0.01
|
---|
981 | group:
|
---|
982 |
|
---|
983 | property:
|
---|
984 | id:logging
|
---|
985 | name:Log statistics to file
|
---|
986 | type:d 0 1 0
|
---|
987 | group:
|
---|
988 |
|
---|
989 | property:
|
---|
990 | id:logPref
|
---|
991 | name:Log prefix
|
---|
992 | type:s
|
---|
993 |
|
---|
994 | property:
|
---|
995 | id:secPerStep
|
---|
996 | name:Seconds per simulation step
|
---|
997 | help:Number of seconds of foraminifera time per simulation step
|
---|
998 | type:f 1 480 300
|
---|
999 | flags: 16
|
---|
1000 | group:
|
---|
1001 |
|
---|
1002 | property:
|
---|
1003 | id:foramSpeedMmPerMin
|
---|
1004 | name:Speed of foraminfera in mm/min
|
---|
1005 | type:f 0.01 0.1 0.05
|
---|
1006 | flags: 16
|
---|
1007 | group:Foraminifera
|
---|
1008 |
|
---|
1009 | property:
|
---|
1010 | id:dir_change_sec
|
---|
1011 | name:Number of seconds before direction change
|
---|
1012 | type:d 300 300000 6000
|
---|
1013 | group:Foraminifera
|
---|
1014 |
|
---|
1015 | property:
|
---|
1016 | id:foramPop
|
---|
1017 | name:Initial forams population size
|
---|
1018 | type:d 1 1000 20
|
---|
1019 | group:Foraminifera
|
---|
1020 |
|
---|
1021 | property:
|
---|
1022 | id:gametoPeriodSec
|
---|
1023 | name:Time of gametogenesis
|
---|
1024 | type:f 300 300000 21600
|
---|
1025 | group:Reproduction
|
---|
1026 |
|
---|
1027 | property:
|
---|
1028 | id:gametSuccessRate
|
---|
1029 | name:Ratio of successful gamets
|
---|
1030 | type:f 0.0001 0.01 0.001
|
---|
1031 | group:Reproduction
|
---|
1032 |
|
---|
1033 | property:
|
---|
1034 | id:divisionCost
|
---|
1035 | name:Cost of division in pG
|
---|
1036 | type:f 15 25 20
|
---|
1037 | group:Reproduction
|
---|
1038 |
|
---|
1039 | property:
|
---|
1040 | id:min_repro_energ_haplo
|
---|
1041 | name:Min reproduction energy of haploid in pg
|
---|
1042 | type:f 0 -1 350000
|
---|
1043 | group:Energy
|
---|
1044 |
|
---|
1045 | property:
|
---|
1046 | id:min_repro_energ_diplo
|
---|
1047 | name:Min reproduction energy of diploid in pg
|
---|
1048 | type:f 0 -1 600000
|
---|
1049 | group:Energy
|
---|
1050 |
|
---|
1051 | property:
|
---|
1052 | id:repro_prob
|
---|
1053 | name:Probability of reproduction
|
---|
1054 | type:f 0 1 0.8
|
---|
1055 | group:Reproduction
|
---|
1056 |
|
---|
1057 | property:
|
---|
1058 | id:energies0_haplo
|
---|
1059 | name:Energy of offspring from diploid forams
|
---|
1060 | type:f 0 -1 20
|
---|
1061 | group:Energy
|
---|
1062 |
|
---|
1063 | property:
|
---|
1064 | id:energies0_diplo
|
---|
1065 | name:Energy of offspring from diploid forams
|
---|
1066 | type:f 0 -1 1.25
|
---|
1067 | group:Energy
|
---|
1068 |
|
---|
1069 | property:
|
---|
1070 | id:max_chamber_num_haplo
|
---|
1071 | name:Maximum number of haploid chambers
|
---|
1072 | type:f 1 50 35
|
---|
1073 | group:Energy
|
---|
1074 |
|
---|
1075 | property:
|
---|
1076 | id:max_chamber_num_diplo
|
---|
1077 | name:Maximum number of diploid chambers
|
---|
1078 | type:f 1 50 35
|
---|
1079 | group:Energy
|
---|
1080 |
|
---|
1081 |
|
---|
1082 | property:
|
---|
1083 | id:crossprob
|
---|
1084 | name:Crossover probability
|
---|
1085 | type:f 0 1 0
|
---|
1086 | group:Reproduction
|
---|
1087 |
|
---|
1088 | property:
|
---|
1089 | id:mutationprob
|
---|
1090 | name:Mutation probability
|
---|
1091 | type:f 0 1 0
|
---|
1092 | group:Reproduction
|
---|
1093 |
|
---|
1094 | property:
|
---|
1095 | id:reproTimeSec
|
---|
1096 | name:Time before reproduction
|
---|
1097 | type:d 0 10000 720
|
---|
1098 | group:Reproduction
|
---|
1099 |
|
---|
1100 | property:
|
---|
1101 | id:chamberGrowthSec
|
---|
1102 | name:Time of the chamber growth in seconds
|
---|
1103 | type:f 720 43200 43200
|
---|
1104 | group:Foraminifera
|
---|
1105 |
|
---|
1106 | property:
|
---|
1107 | id:chamber_proculus_haplo
|
---|
1108 | name:Size of proculus
|
---|
1109 | type:f
|
---|
1110 | group:Foraminifera
|
---|
1111 |
|
---|
1112 | property:
|
---|
1113 | id:chamber_proculus_diplo
|
---|
1114 | name:Size of proculus
|
---|
1115 | type:f
|
---|
1116 | group:Foraminifera
|
---|
1117 |
|
---|
1118 | property:
|
---|
1119 | id:hunted_prob
|
---|
1120 | name:Probability of being hunted
|
---|
1121 | type:f 0 1 0
|
---|
1122 | group:Foraminifera
|
---|
1123 |
|
---|
1124 | property:
|
---|
1125 | id:zone1_range
|
---|
1126 | name:Zone 1 range in frams units
|
---|
1127 | type:f 0 200 10
|
---|
1128 | group:Foraminifera
|
---|
1129 |
|
---|
1130 | property:
|
---|
1131 | id:zone2_range
|
---|
1132 | name:Zone 2 range in frams units
|
---|
1133 | type:f 0 3000 30
|
---|
1134 | group:Foraminifera
|
---|
1135 |
|
---|
1136 | property:
|
---|
1137 | id:chamberCostPerSec
|
---|
1138 | name:Cost of growning chamber per second
|
---|
1139 | type:f 0 1 0.000001
|
---|
1140 | group:Energy
|
---|
1141 |
|
---|
1142 | property:
|
---|
1143 | id:e_death_level_haplo
|
---|
1144 | name:Minimal level of energy to sustain life of haploid
|
---|
1145 | type:f 0 1 0.5
|
---|
1146 | group:Energy
|
---|
1147 |
|
---|
1148 | property:
|
---|
1149 | id:e_death_level_diplo
|
---|
1150 | name:Minimal level of energy to sustain life of diploid
|
---|
1151 | type:f 0 1 0.5
|
---|
1152 | group:Energy
|
---|
1153 |
|
---|
1154 | property:
|
---|
1155 | id:energy_hib
|
---|
1156 | name:Energy used for hibernation during one step
|
---|
1157 | type:f 0 1 0.0000001
|
---|
1158 | group:Energy
|
---|
1159 |
|
---|
1160 | property:
|
---|
1161 | id:energy_move
|
---|
1162 | name:Energy used for movement during one step
|
---|
1163 | type:f 0 1 0.0000005
|
---|
1164 | group:Energy
|
---|
1165 |
|
---|
1166 | property:
|
---|
1167 | id:e_meta
|
---|
1168 | name:Idle metabolism
|
---|
1169 | type:f 0 1 0.0000005
|
---|
1170 | group:Energy
|
---|
1171 | help:Foraminifera consumes this proportion of its energy in one time step
|
---|
1172 |
|
---|
1173 | property:
|
---|
1174 | id:ingestion
|
---|
1175 | name:Ingestion rate
|
---|
1176 | type:f 0 -1 0.25
|
---|
1177 | group:Energy
|
---|
1178 |
|
---|
1179 | property:
|
---|
1180 | id:nutrient_pop
|
---|
1181 | name:Nutrient population
|
---|
1182 | type:f 0 1000000
|
---|
1183 | group:Energy
|
---|
1184 | help:How fast energy is created in the world
|
---|
1185 |
|
---|
1186 | property:
|
---|
1187 | id:energy_nut
|
---|
1188 | name:Nutrient energy
|
---|
1189 | type:f 0 10000000
|
---|
1190 | group:Energy
|
---|
1191 |
|
---|
1192 | property:
|
---|
1193 | id:nutrientradius
|
---|
1194 | name:Nutrient size
|
---|
1195 | type:f 0.001 0.9 0.1
|
---|
1196 | group:Energy
|
---|
1197 |
|
---|
1198 | property:
|
---|
1199 | id:picoCarbonPerMikro
|
---|
1200 | name:Picograms of carbon in cubic micrometer
|
---|
1201 | type:f 0 -1 0.13
|
---|
1202 | group:Energy
|
---|
1203 |
|
---|
1204 | property:
|
---|
1205 | id:feedtrans
|
---|
1206 | name:Energy transfer per second
|
---|
1207 | type:f 0 1 0.001
|
---|
1208 | group:Energy
|
---|
1209 |
|
---|
1210 | property:
|
---|
1211 | id:foodperiod
|
---|
1212 | name:Time between food occurrences
|
---|
1213 | type:f 0 1000000 14400
|
---|
1214 | group:Energy
|
---|
1215 |
|
---|
1216 | property:
|
---|
1217 | id:foodPeriodChange
|
---|
1218 | name:Set variable feed rate
|
---|
1219 | type:f 0 -1 0
|
---|
1220 | group:Energy
|
---|
1221 |
|
---|
1222 | property:
|
---|
1223 | id:stress
|
---|
1224 | name:Environmental stress
|
---|
1225 | type:d 0 1 1
|
---|
1226 | group:
|
---|
1227 |
|
---|
1228 | property:
|
---|
1229 | id:repro_trigger
|
---|
1230 | name:Reproduction trigger
|
---|
1231 | type:d 0 1 1
|
---|
1232 | group:Reproduction
|
---|
1233 |
|
---|
1234 | property:
|
---|
1235 | id:creath
|
---|
1236 | name:Creation height
|
---|
1237 | type:f -1 50 -0.99
|
---|
1238 | help:~
|
---|
1239 | Vertical position (above the surface) where new Forams are revived.
|
---|
1240 | Negative values are only used in the water area:
|
---|
1241 | 0 = at the surface
|
---|
1242 | -0.5 = half depth
|
---|
1243 | -1 = just above the bottom~
|
---|
1244 |
|
---|
1245 | property:
|
---|
1246 | id:autorestart
|
---|
1247 | name:Restart after extinction
|
---|
1248 | help:Restart automatically this experiment after the last creature has died?
|
---|
1249 | type:d 0 1 0
|
---|
1250 |
|
---|
1251 | state:
|
---|
1252 | id:nutrient
|
---|
1253 | name:Nutrient locations
|
---|
1254 | help:vector of vectors [x,y,energy]
|
---|
1255 | type:x
|
---|
1256 | flags:32
|
---|
1257 |
|
---|
1258 | state:
|
---|
1259 | id:notes
|
---|
1260 | name:Notes
|
---|
1261 | type:s 1
|
---|
1262 | help:~
|
---|
1263 | You can write anything here
|
---|
1264 | (it will be saved to the experiment file)~
|
---|
1265 |
|
---|
1266 | state:
|
---|
1267 | id:totaltestedcr
|
---|
1268 | name:Evaluated Forams
|
---|
1269 | help:Total number of the Forams evaluated in the experiment
|
---|
1270 | type:d
|
---|
1271 | flags:16
|
---|