[380] | 1 | expdef:
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[406] | 2 | name:Reproduction of benthic foraminifera
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[380] | 3 | info:~
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[434] | 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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[476] | 8 | Genes and parameter values which control reproduction are stored in data->genes and data->lifeparams fields.
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[380] | 9 |
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[476] | 10 | genes:
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[402] | 11 | genes which are not encoded in Ff genotype:
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[422] | 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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[380] | 14 |
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[476] | 15 | lifeparams:
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[380] | 16 | Physiological parameters of foraminifera:
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[422] | 17 | max_energy_level - maximum energy level reached so far
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[380] | 18 | gen - generation: 0 haploid, 1 diploid
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[432] | 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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[422] | 21 | reproduce - 0/1 foram isn't/is ready for reproduction
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[380] | 22 | ~
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| 23 | code:~
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| 24 |
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[401] | 25 |
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[421] | 26 | global nutrientenergywaiting;
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[380] | 27 | global reprocounter;
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[422] | 28 | global colors;
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| 29 | global chambers;
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| 30 | global o;
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| 31 | global max_chamber_energ;
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[430] | 32 | global dir_change;
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[474] | 33 | global movePerStep;
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[380] | 34 |
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[406] | 35 | @include "foraminifera.inc"
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[401] | 36 |
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[380] | 37 | // -------------------------------- experiment begin --------------------------------
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| 38 |
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| 39 | function onExpDefLoad()
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| 40 | {
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| 41 | // define genotype and creature groups
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| 42 | GenePools.clear();
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| 43 | Populations.clear();
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| 44 | GenePools[0].name = "Unused";
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| 45 |
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| 46 | var pop = Populations[0];
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[421] | 47 | pop.name = "Forams";
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[380] | 48 | pop.en_assim = 0;
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[404] | 49 | pop.nnsim = 0;
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[380] | 50 | pop.enableperf = 1;
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| 51 | pop.death = 1;
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| 52 | pop.energy = 1;
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| 53 | pop.selfmask = 0x10001;
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[401] | 54 | pop.othermask = 0x20001;
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| 55 | //pop.selfmask = 0x20002; pop.othermask = 0x10002;
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[422] | 56 | pop.perfperiod = 25;
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[380] | 57 |
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[421] | 58 | pop = Populations.addGroup("Nutrients");
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[380] | 59 | pop.nnsim = 0;
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| 60 | pop.enableperf = 0;
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| 61 | pop.death = 1;
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| 62 | pop.energy = 1;
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| 63 | pop.selfmask = 0x20002;
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[401] | 64 | pop.othermask = 0x10000;
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[422] | 65 | //pop.othermask = 0x10002;
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[380] | 66 |
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[444] | 67 | pop = Populations.addGroup("ReticulopodiaNutrients");
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[430] | 68 | pop.nnsim = 0;
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| 69 | pop.enableperf = 0;
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| 70 | pop.death = 0;
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| 71 | pop.energy = 0;
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| 72 | pop.selfmask = 0x20002;
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| 73 | pop.othermask = 0x10000;
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[444] | 74 |
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[422] | 75 | //world
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| 76 | SignalView.mode = 1;
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[430] | 77 | World.wrldwat = 200;
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[447] | 78 | World.wrldsiz = micronsToFrams(40000);
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[422] | 79 | World.wrldbnd = 1;
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| 80 | ExpParams.stress = 1;
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[421] | 81 | ExpParams.creath = -0.99; //just above the bottom
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[380] | 82 | ExpParams.autorestart = 0;
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[422] | 83 |
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[474] | 84 | //time
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| 85 | ExpParams.secPerStep = 60;
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[475] | 86 | ExpParams.foramSpeedMmPerMin = 0.05;
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[474] | 87 | movePerStep = getMovePerStep();
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| 88 |
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[444] | 89 | //ExpParams.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
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| 90 |
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[411] | 91 | //ExpParams.logging = 1; //uncomment to enable logging simulation parameters to log files
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[401] | 92 |
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[422] | 93 | //reproduction
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[430] | 94 | ExpParams.foramPop = 10;
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[474] | 95 | ExpParams.crossprob = 0;
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| 96 | ExpParams.mutationprob = 0;
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[422] | 97 | ExpParams.repro_time = 20;
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| 98 | reprocounter = 0;
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[380] | 99 |
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[422] | 100 | //morphology
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[474] | 101 | dir_change = 30000;
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[475] | 102 | ExpParams.zone1_range = micronsToFrams(1000);
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| 103 | ExpParams.zone2_range = micronsToFrams(3000);
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[422] | 104 | init_chambers();
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[447] | 105 | ExpParams.chamber_proculus_haplo = micronsToFrams(50);
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[422] | 106 | ExpParams.chamber_difference_haplo = 0.0;
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[447] | 107 | ExpParams.chamber_proculus_diplo = micronsToFrams(20);
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[422] | 108 | ExpParams.chamber_difference_diplo = 0.2;
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| 109 | max_chamber_energ = [Vector.new(), Vector.new()];
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| 110 | for (var j = 0; j < 2; j++)
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| 111 | {
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| 112 | for (var i = 0; i < chambers[0].size; i++)
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| 113 | {
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[475] | 114 | max_chamber_energ[j].add(((energyFromVolume(getProperty(j, "chamber_proculus")) + energyFromVolume(getProperty(j, "chamber_proculus") + (i) * getProperty(j, "chamber_difference")))*(i+1))/2);
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[422] | 115 | }
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| 116 | }
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| 117 |
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| 118 | //energetics
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[430] | 119 | ExpParams.min_repro_energ_haplo = 4;
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| 120 | ExpParams.min_repro_energ_diplo = 6;
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| 121 |
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[474] | 122 | ExpParams.e_meta = 0.00005;
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| 123 | ExpParams.energy_hib = 0.000025;
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| 124 | ExpParams.energy_move = 0.00005;
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[430] | 125 |
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| 126 | ExpParams.energies0_haplo = max_chamber_energ[0][0] - 0.001*max_chamber_energ[0][0];
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| 127 | ExpParams.energies0_diplo = max_chamber_energ[1][0] - 0.001*max_chamber_energ[1][0];
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[474] | 128 | ExpParams.feedtrans = 0.125;
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[430] | 129 | ExpParams.e_repro_cost_haplo = 0.7;
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[422] | 130 | ExpParams.e_repro_cost_diplo = 0.3;
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| 131 |
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| 132 | //nutrients
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[447] | 133 | ExpParams.nutrientsize = micronsToFrams(10);
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[475] | 134 | ExpParams.energy_nut = 100 * energyFromVolume(ExpParams.nutrientsize);
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[430] | 135 | ExpParams.nutrientPop = 1;
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[474] | 136 | ExpParams.feedrate = 100;
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| 137 | nutrientenergywaiting = 0;
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[380] | 138 | ExpState.totaltestedcr = 0;
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[421] | 139 | ExpState.nutrient = "";
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[380] | 140 | }
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| 141 |
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| 142 | @include "standard_placement.inc"
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| 143 |
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[475] | 144 | function energyFromVolume(radius)
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| 145 | {
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| 146 | return 4.0/3.0*Math.pi*Math.pow(radius,3);
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| 147 | }
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| 148 |
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[474] | 149 | function getMovePerStep()
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| 150 | {
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| 151 | return micronsToFrams((ExpParams.foramSpeedMmPerMin/60)*1000)*ExpParams.secPerStep;
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| 152 | }
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| 153 |
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[447] | 154 | function micronsToFrams(micrometers)
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[422] | 155 | {
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[445] | 156 | return micrometers*0.025;
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[422] | 157 | }
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| 158 |
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[447] | 159 | function framsToMicrons(framsworldunits)
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[445] | 160 | {
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| 161 | return framsworldunits/0.025;
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| 162 | }
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| 163 |
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[422] | 164 | function getProperty(gen, prop_id)
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| 165 | {
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| 166 | var ploid = "haplo";
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| 167 | if (gen == 1) ploid = "diplo";
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| 168 | return ExpParams.[prop_id + "_" + ploid];
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| 169 | }
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| 170 |
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| 171 | function addInitialForam(species, i)
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| 172 | {
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| 173 | var geno = createForamGenotype(0, species, 0);
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| 174 | var cr = Populations[0].add(geno);
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| 175 | cr.name = "Initial creature" + species + "_" + i;
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| 176 | placeCreatureRandomly(cr, 0, 0);
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| 177 | cr.energy0 = getProperty(0, "energies0");
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| 178 | cr.energy = cr.energy0;
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| 179 | setGenotype({"opt" : 0, "cr" : cr, "species" : species});
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| 180 | }
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| 181 |
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[380] | 182 | function onExpInit()
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| 183 | {
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| 184 | Populations[0].clear();
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| 185 | Populations[1].clear();
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[444] | 186 | Populations[2].clear(); //reticulopodia and nutrients
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[380] | 187 |
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[422] | 188 | for (var i = 0; i < ExpParams.foramPop; i++)
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[380] | 189 | {
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[422] | 190 | addInitialForam(0, i);
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| 191 | addInitialForam(1, i);
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[380] | 192 | }
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[422] | 193 | o = Populations[0][0].getMechPart(0).orient.clone();
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[380] | 194 | ExpState.totaltestedcr = 0;
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[422] | 195 | nutrientenergywaiting = ExpParams.energy_nut;
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[380] | 196 | }
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| 197 |
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| 198 | function onExpLoad()
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| 199 | {
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| 200 | for (var pop in Populations)
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| 201 | pop.clear();
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| 202 |
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| 203 | Loader.addClass(sim_params.*);
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| 204 | Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
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| 205 | Loader.run();
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| 206 |
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[421] | 207 | Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
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[380] | 208 | }
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| 209 |
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| 210 | function onExpLoad_Unknown()
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| 211 | {
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| 212 | if (Loader.objectName == "org") // saved by the old expdef
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| 213 | {
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| 214 | var g = Genotype.newFromString("");
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| 215 | Loader.currentObject = g;
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| 216 | Interface.makeFrom(g).setAllDefault();
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| 217 | Loader.loadObject();
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| 218 | var cr = Populations[0].add(g);
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| 219 | if (cr != null)
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| 220 | {
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[401] | 221 | //cr.rotate(0,0,Math.rnd01*Math.twopi);
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[476] | 222 | if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
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[401] | 223 | {
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| 224 | // [x,y,energy]
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[476] | 225 | cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
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| 226 | cr.energy = g.data->genes[2];
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[380] | 227 | }
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| 228 | else
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| 229 | {
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[401] | 230 | cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
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[380] | 231 | }
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| 232 | }
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| 233 | }
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| 234 | else if (Loader.objectName == "Creature")
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| 235 | {
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| 236 | Loader.currentObject = CreatureSnapshot.new();
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| 237 | Loader.loadObject();
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| 238 | Populations[0].add(Loader.currentObject);
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| 239 | }
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| 240 | }
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| 241 |
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| 242 | function onExpSave()
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| 243 | {
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| 244 | File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
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| 245 |
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[401] | 246 | var tmpvec = [], i;
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[380] | 247 |
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[401] | 248 | for(var cr in Populations[1])
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[380] | 249 | tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
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| 250 |
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[421] | 251 | ExpState.nutrient = tmpvec;
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[380] | 252 | File.writeObject(sim_params.*);
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[432] | 253 | ExpState.nutrient = null; //vectors are only created for saving and then discarded
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[380] | 254 |
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| 255 | for (var cr in Populations[0])
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| 256 | File.writeObject(cr);
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| 257 | }
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| 258 |
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| 259 | // -------------------------------- experiment end --------------------------------
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| 260 |
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[421] | 261 | // -------------------------------- foram begin -----------------------------------
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[380] | 262 |
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[430] | 263 | function setForamMeta(cr, gen)
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| 264 | {
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[475] | 265 | //cr.idleen = (ExpParams.e_meta * max_chamber_energ[gen][Math.min(lastChamberNum(cr), max_chamber_energ[gen].size-1)])*ExpParams.secPerStep;
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| 266 | cr.idleen = (ExpParams.e_meta * cr.energy)*ExpParams.secPerStep;
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[430] | 267 | }
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| 268 |
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| 269 | function lastChamberNum(cr)
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| 270 | {
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| 271 | return cr.numparts-1;
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| 272 | }
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| 273 |
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[421] | 274 | function onForamsBorn(cr)
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| 275 | {
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[430] | 276 | setForamMeta(cr, 1);
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[444] | 277 | if (ExpParams.visualize == 1)
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[430] | 278 | {
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[450] | 279 | var ret = Populations[2].add("//0\np:sh=3,sx=0.01,sy="+ExpParams.zone1_range+",sz="+ExpParams.zone1_range+",ry=1.57,vr=1.0,1.0,1.0");
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[476] | 280 | cr.data->reticulopodiacreature = ret;
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[430] | 281 | }
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[380] | 282 | }
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| 283 |
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[401] | 284 | function placeRandomlyNotColliding(cr)
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| 285 | {
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| 286 | var retry = 100; //try 100 times
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| 287 | while (retry--)
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| 288 | {
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| 289 | placeCreatureRandomly(cr, 0, 0);
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| 290 | if (!cr.boundingBoxCollisions(0))
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| 291 | return cr;
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| 292 | }
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| 293 |
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| 294 | Populations[0].delete(cr);
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| 295 | }
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| 296 |
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[444] | 297 | function visualization(cr)
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| 298 | {
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| 299 | var has_ret = 0;
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| 300 |
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[476] | 301 | if (cr.data->reticulopodiacreature != null)
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[444] | 302 | {
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[476] | 303 | if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
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[444] | 304 | {
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| 305 | has_ret = 1;
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| 306 | }
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| 307 | }
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| 308 |
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| 309 | return has_ret;
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| 310 | }
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| 311 |
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[422] | 312 | function foramGrow(cr, chamber_num)
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[380] | 313 | {
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[476] | 314 | if ((chamber_num+1) < chambers[cr.data->lifeparams->species].size)
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[474] | 315 | {
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[476] | 316 | var geno = createForamGenotype(cr.data->lifeparams->gen, cr.data->lifeparams->species, chamber_num+1);
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[474] | 317 | var cr2 = Populations[0].add(geno);
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[422] | 318 |
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[474] | 319 | cr2.energy0 = cr.energy;
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| 320 | cr2.energy = cr2.energy0;
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[422] | 321 |
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[476] | 322 | setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : 2});
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[474] | 323 | cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
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[476] | 324 | setForamMeta(cr2, cr2.data->lifeparams->gen);
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[422] | 325 |
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[474] | 326 | if (visualization(cr))
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| 327 | {
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[476] | 328 | Populations[2].delete(cr.data->reticulopodiacreature);
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[474] | 329 | }
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| 330 | Populations[0].delete(cr);
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[430] | 331 | }
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[380] | 332 | }
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| 333 |
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[435] | 334 | function stepToNearest(cr)
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[380] | 335 | {
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| 336 | var p = cr.getMechPart(0);
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[422] | 337 | var n = cr.signals.receiveSet("nutrient", ExpParams.zone2_range);
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[380] | 338 |
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[401] | 339 | //if signals are received find the source of the nearest
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[380] | 340 | if (n.size > 0)
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| 341 | {
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| 342 | var i;
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| 343 | var mp;
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| 344 | var distvec = XYZ.new(0, 0, 0);
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| 345 | var dist;
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[470] | 346 | var mindist = 100000000000.0;
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[380] | 347 | var mindistvec = null;
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[430] | 348 | var eating = 0;
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[380] | 349 |
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[401] | 350 | for (i = 0; i < n.size; i++)
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[380] | 351 | {
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[430] | 352 | mp = n[i].value.getMechPart(0);
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[401] | 353 | distvec.set(mp.pos);
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| 354 | distvec.sub(p.pos);
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| 355 | dist = distvec.length;
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[430] | 356 | if (dist < ExpParams.zone1_range)
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[380] | 357 | {
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[430] | 358 | if (n[i].value != null)
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| 359 | {
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| 360 | energyTransfer(cr, n[i].value);
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| 361 | eating = 1;
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| 362 | }
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| 363 | }
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[476] | 364 | else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
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[430] | 365 | {
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[401] | 366 | mindist = dist;
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| 367 | mindistvec = distvec.clone();
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[380] | 368 | }
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| 369 | }
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| 370 |
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[476] | 371 | if (!eating && cr.data->lifeparams->hibernated == 0)
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[430] | 372 | {
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| 373 | mindistvec.normalize();
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[474] | 374 | mindistvec.scale(-1*movePerStep);
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[430] | 375 | cr.localDrive = mindistvec;
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| 376 | moveEnergyDec(cr);
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| 377 | }
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| 378 |
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[422] | 379 | return 1;
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[380] | 380 | }
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[422] | 381 |
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| 382 | else
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[474] | 383 | {
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[422] | 384 | return 0;
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[474] | 385 | }
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[422] | 386 | }
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[401] | 387 |
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[422] | 388 | function moveEnergyDec(cr)
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| 389 | {
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[476] | 390 | if (cr.data->lifeparams->hibernated == 0)
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[422] | 391 | {
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[476] | 392 | //cr.energy_m += (ExpParams.energy_move * max_chamber_energ[cr.data->lifeparams->gen][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.data->lifeparams->gen].size)-1)])*ExpParams.secPerStep;
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[475] | 393 | cr.energy_m += (ExpParams.energy_move * cr.energy)*ExpParams.secPerStep;
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[422] | 394 | }
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[421] | 395 | }
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[380] | 396 |
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[422] | 397 | function foramMove(cr)
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[421] | 398 | {
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[422] | 399 | //TODO moving inside sediment?
|
---|
[421] | 400 |
|
---|
[422] | 401 | //adjustment in z axis
|
---|
[430] | 402 | cr.moveAbs(cr.pos_x, cr.pos_y, 0);
|
---|
[421] | 403 |
|
---|
[430] | 404 | //are there any nutrients in zone 1 or 2?
|
---|
[401] | 405 | {
|
---|
[435] | 406 | var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
|
---|
[422] | 407 | if (moved==1)
|
---|
[430] | 408 | {
|
---|
[422] | 409 | return;
|
---|
| 410 | }
|
---|
[401] | 411 | }
|
---|
| 412 |
|
---|
[422] | 413 | //no nutrients in zone 2
|
---|
| 414 | var hibernation = 0;
|
---|
[476] | 415 | if (cr.data->lifeparams->gen == 0) hibernation = cr.data->genes->hibernation;
|
---|
| 416 | else hibernation = cr.data->genes[0]->hibernation;
|
---|
[422] | 417 | //hibernation
|
---|
| 418 | if (hibernation == 1)
|
---|
[401] | 419 | {
|
---|
[430] | 420 | reverseHib(cr);
|
---|
[422] | 421 | cr.localDrive = XYZ.new(0,0,0);
|
---|
[380] | 422 | }
|
---|
[422] | 423 | //random move
|
---|
[474] | 424 | else if (cr.lifespan%(dir_change/ExpParams.secPerStep) == 0)
|
---|
[380] | 425 | {
|
---|
[476] | 426 | cr.data->lifeparams->dir = randomDir();
|
---|
| 427 | cr.localDrive = cr.data->lifeparams->dir;
|
---|
[422] | 428 | moveEnergyDec(cr);
|
---|
| 429 | }
|
---|
[474] | 430 | else
|
---|
| 431 | {
|
---|
[476] | 432 | cr.localDrive = cr.data->lifeparams->dir;
|
---|
[474] | 433 | }
|
---|
[422] | 434 | }
|
---|
[401] | 435 |
|
---|
[474] | 436 | function randomDir()
|
---|
| 437 | {
|
---|
| 438 | var dir = (Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), 0);
|
---|
| 439 | dir.normalize();
|
---|
| 440 | dir.scale(-1*movePerStep);
|
---|
| 441 | return dir;
|
---|
| 442 | }
|
---|
| 443 |
|
---|
[430] | 444 | function energyTransfer(cr1, cr2)
|
---|
[422] | 445 | {
|
---|
[430] | 446 | cr1.localDrive = XYZ.new(0,0,0);
|
---|
[474] | 447 | var e = ExpParams.feedtrans*ExpParams.secPerStep; //TODO efficiency dependent on age
|
---|
[430] | 448 | e = Math.min(cr2.energy, e) + 0.0000001;
|
---|
| 449 | //Simulator.print("transferring "+e+" to "+cr1.name+" from "+cr2.name+" ("+cr2.energy+")");
|
---|
| 450 | cr2.energy_m = cr2.energy_m + e;
|
---|
| 451 | cr1.energy_p = cr1.energy_p + e;
|
---|
[476] | 452 | if (cr1.data->lifeparams->hibernated == 1)
|
---|
[422] | 453 | {
|
---|
[430] | 454 | reverseHib(cr1);
|
---|
[422] | 455 | }
|
---|
| 456 | }
|
---|
[401] | 457 |
|
---|
[430] | 458 | function reverseHib(cr)
|
---|
| 459 | {
|
---|
[476] | 460 | if (cr.data->lifeparams->hibernated == 1)
|
---|
[430] | 461 | {
|
---|
[476] | 462 | setForamMeta(cr, cr.data->lifeparams->gen); //unhibernate
|
---|
[430] | 463 | }
|
---|
| 464 | else
|
---|
| 465 | {
|
---|
[476] | 466 | //cr.idleen = (ExpParams.energy_hib * max_chamber_energ[cr.data->lifeparams->gen][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.data->lifeparams->gen].size)-1)])*ExpParams.secPerStep; //hibernate
|
---|
[475] | 467 | cr.idleen = (ExpParams.energy_hib * cr.energy)*ExpParams.secPerStep; //hibernate
|
---|
[430] | 468 | }
|
---|
[476] | 469 | cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
|
---|
[430] | 470 | }
|
---|
| 471 |
|
---|
[422] | 472 | function onForamsStep(cr)
|
---|
| 473 | {
|
---|
| 474 | cr.getMechPart(0).orient.set(o);
|
---|
[444] | 475 | if (visualization(cr))
|
---|
| 476 | {
|
---|
[476] | 477 | cr.data->reticulopodiacreature.moveAbs(cr.center_x-ExpParams.zone1_range, cr.center_y-ExpParams.zone1_range, cr.center_z-ExpParams.zone1_range-getProperty(cr.data->lifeparams->gen, "chamber_proculus"));
|
---|
[444] | 478 | }
|
---|
[422] | 479 |
|
---|
| 480 | if (deathConditions(cr) == 1)
|
---|
| 481 | {
|
---|
| 482 | Populations[0].kill(cr);
|
---|
| 483 | return;
|
---|
| 484 | }
|
---|
| 485 |
|
---|
| 486 | foramMove(cr);
|
---|
| 487 |
|
---|
[430] | 488 | var repro = foramReproduce(cr);
|
---|
| 489 | if (repro == 1)
|
---|
| 490 | {
|
---|
| 491 | return;
|
---|
| 492 | }
|
---|
| 493 |
|
---|
[476] | 494 | cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
|
---|
[430] | 495 | if (lastChamberNum(cr) <= chambers[0].size-1)
|
---|
[422] | 496 | {
|
---|
[476] | 497 | if ((cr.data->lifeparams->max_energy_level >= max_chamber_energ[cr.data->lifeparams->gen][lastChamberNum(cr)]))
|
---|
[401] | 498 | {
|
---|
[430] | 499 | foramGrow(cr, lastChamberNum(cr));
|
---|
[422] | 500 | }
|
---|
[430] | 501 | }
|
---|
[380] | 502 | }
|
---|
| 503 |
|
---|
[422] | 504 | function deathConditions(cr)
|
---|
| 505 | {
|
---|
[476] | 506 | if ((cr.energy <= getProperty(cr.data->lifeparams->species,"e_death_level")) || (Math.rnd01 < ExpParams.hunted_prob))
|
---|
[422] | 507 | return 1;
|
---|
| 508 | else
|
---|
| 509 | return 0;
|
---|
| 510 | }
|
---|
| 511 |
|
---|
[421] | 512 | function onForamsDied(cr)
|
---|
[380] | 513 | {
|
---|
[444] | 514 | if (visualization(cr))
|
---|
[430] | 515 | {
|
---|
[476] | 516 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[430] | 517 | }
|
---|
[380] | 518 | //fossilization
|
---|
| 519 | var geno = GenePools[0].add(cr.genotype);
|
---|
[476] | 520 | geno.data->genes = cr.data->genes;
|
---|
| 521 | geno.data->lifeparams = cr.data->lifeparams;
|
---|
[418] | 522 | if (ExpParams.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
|
---|
[380] | 523 | ExpState.totaltestedcr++;
|
---|
| 524 | }
|
---|
| 525 |
|
---|
[421] | 526 | // --------------------------------foram end -------------------------------------
|
---|
[380] | 527 |
|
---|
[421] | 528 | // -------------------------------- nutrient begin --------------------------------
|
---|
[380] | 529 |
|
---|
[422] | 530 | function createNutrientGenotype(nutrientsize, zone1_range)
|
---|
| 531 | {
|
---|
[444] | 532 | return "//0\np:sh=3,sx="+nutrientsize+",sy="+nutrientsize+",sz="+nutrientsize+",ry=1.5,vr=0.0,1.0,0.0";
|
---|
[422] | 533 | }
|
---|
| 534 |
|
---|
[421] | 535 | function onNutrientsStep(cr)
|
---|
[380] | 536 | {
|
---|
[444] | 537 | cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
|
---|
[380] | 538 | }
|
---|
| 539 |
|
---|
[421] | 540 | function addNutrient()
|
---|
[380] | 541 | {
|
---|
[422] | 542 | var cr = Populations[1].add(createNutrientGenotype(ExpParams.nutrientsize, ExpParams.zone1_range));
|
---|
[380] | 543 |
|
---|
[421] | 544 | cr.name = "Nutrients";
|
---|
[380] | 545 | cr.idleen = 0;
|
---|
[422] | 546 | cr.energy0 = ExpParams.energy_nut;
|
---|
[416] | 547 | cr.energy = cr.energy0;
|
---|
[421] | 548 | cr.signals.add("nutrient");
|
---|
[380] | 549 |
|
---|
[430] | 550 | cr.signals[0].value = cr;
|
---|
[380] | 551 |
|
---|
[422] | 552 | placeCreatureRandomly(cr, 0, 0);
|
---|
[444] | 553 | if (ExpParams.visualize == 1)
|
---|
| 554 | {
|
---|
| 555 | var nutsize = ExpParams.nutrientsize*10;
|
---|
| 556 | 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");
|
---|
[476] | 557 | cr.data->reticulopodiacreature = nut;
|
---|
[444] | 558 | nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
|
---|
| 559 | }
|
---|
[380] | 560 | }
|
---|
| 561 |
|
---|
[444] | 562 | function onNutrientsDied(cr)
|
---|
| 563 | {
|
---|
| 564 | if (visualization(cr))
|
---|
| 565 | {
|
---|
[476] | 566 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[444] | 567 | }
|
---|
| 568 | }
|
---|
| 569 |
|
---|
[422] | 570 | function nutrientGrowth()
|
---|
[380] | 571 | {
|
---|
[474] | 572 | nutrientenergywaiting = nutrientenergywaiting + 1;
|
---|
| 573 | if (nutrientenergywaiting > ExpParams.feedrate/ExpParams.secPerStep)
|
---|
[380] | 574 | {
|
---|
[422] | 575 | for (var i = 0; i < ExpParams.nutrientPop; i++)
|
---|
[432] | 576 | {
|
---|
[422] | 577 | addNutrient();
|
---|
| 578 | }
|
---|
| 579 |
|
---|
| 580 | nutrientenergywaiting = 0.0;
|
---|
| 581 | Simulator.checkpoint();
|
---|
[380] | 582 | }
|
---|
| 583 | }
|
---|
| 584 |
|
---|
[421] | 585 | // -------------------------------- nutrient end --------------------------------
|
---|
[380] | 586 |
|
---|
[422] | 587 | // -------------------------------- step begin --------------------------------
|
---|
[380] | 588 |
|
---|
[422] | 589 | function onStep()
|
---|
| 590 | {
|
---|
[432] | 591 |
|
---|
| 592 | nutrientGrowth();
|
---|
[422] | 593 | if (ExpParams.logging == 1)
|
---|
| 594 | {
|
---|
| 595 | createStatistics();
|
---|
| 596 | }
|
---|
| 597 |
|
---|
| 598 | //reproduction --------------------------------------------
|
---|
| 599 | reprocounter += 1;
|
---|
[474] | 600 | if (reprocounter*ExpParams.secPerStep > ExpParams.repro_time)
|
---|
[422] | 601 | {
|
---|
| 602 | reprocounter = 0;
|
---|
| 603 | reproduce_parents(0);
|
---|
| 604 | reproduce_parents(1);
|
---|
| 605 | }
|
---|
| 606 |
|
---|
| 607 | //check for extinction -----------------------------------------------
|
---|
| 608 | if (Populations[0].size == 0)
|
---|
| 609 | {
|
---|
| 610 | if (ExpParams.autorestart)
|
---|
| 611 | {
|
---|
| 612 | Simulator.print("no more creatures, restarting...");
|
---|
| 613 | onExpInit();
|
---|
| 614 | }
|
---|
| 615 | else
|
---|
| 616 | {
|
---|
| 617 | Simulator.print("no more creatures, stopped.");
|
---|
| 618 | Simulator.stop();
|
---|
| 619 | }
|
---|
| 620 | }
|
---|
[434] | 621 | if (ExpParams.maxSteps > 0)
|
---|
[432] | 622 | {
|
---|
[434] | 623 | if (Simulator.stepNumber >= ExpParams.maxSteps)
|
---|
[432] | 624 | Simulator.stop();
|
---|
| 625 | }
|
---|
[422] | 626 | }
|
---|
| 627 |
|
---|
| 628 | function createStatistics()
|
---|
| 629 | {
|
---|
[430] | 630 | var number = [[0, 0],[0,0]]; // [species][gen]
|
---|
| 631 | var e_inc = [[0, 0],[0,0]];
|
---|
[422] | 632 | var e_nut = 0.0;
|
---|
| 633 |
|
---|
| 634 | for (var i = 0; i < Populations[0].size; i++)
|
---|
| 635 | {
|
---|
| 636 | var cr = Populations[0].get(i);
|
---|
[476] | 637 | var gen = cr.data->lifeparams->gen;
|
---|
| 638 | var species = cr.data->lifeparams->species;
|
---|
[430] | 639 |
|
---|
| 640 | number[species][gen] = number[species][gen] + 1;
|
---|
| 641 | e_inc[species][gen] = e_inc[species][gen] + cr.energy;
|
---|
[422] | 642 | }
|
---|
| 643 |
|
---|
| 644 | for (var i = 0; i < Populations[1].size; i++)
|
---|
| 645 | {
|
---|
| 646 | var cr = Populations[1].get(i);
|
---|
| 647 | e_nut += cr.energy;
|
---|
| 648 | }
|
---|
| 649 |
|
---|
[432] | 650 | var log_numbers = [number[1][0], number[1][1], number[0][0], number[0][1], Populations[1].size];
|
---|
| 651 | var log_energies = [e_inc[1][0], e_inc[1][1], e_inc[0][0], e_inc[0][1], e_nut];
|
---|
[422] | 652 |
|
---|
[430] | 653 | log(log_numbers, "forams_log.txt");
|
---|
[474] | 654 | log(log_energies, "energies_log.txt");
|
---|
[422] | 655 | }
|
---|
| 656 |
|
---|
[380] | 657 | function log(tolog, fname)
|
---|
| 658 | {
|
---|
[430] | 659 | var f = File.appendDirect(fname, "forams data");
|
---|
[380] | 660 | f.writeString("" + Simulator.stepNumber);
|
---|
[401] | 661 | for (var i = 0; i < tolog.size; i++)
|
---|
[380] | 662 | {
|
---|
| 663 | f.writeString(";" + tolog[i]);
|
---|
| 664 | }
|
---|
| 665 | f.writeString("\n");
|
---|
| 666 | f.close();
|
---|
| 667 | }
|
---|
| 668 |
|
---|
[422] | 669 | // -------------------------------- step end --------------------------------
|
---|
[380] | 670 |
|
---|
[401] | 671 | @include "standard_events.inc"
|
---|
[380] | 672 |
|
---|
[401] | 673 | ~
|
---|
[380] | 674 |
|
---|
[401] | 675 | prop:
|
---|
[444] | 676 | id:visualize
|
---|
| 677 | name:Show reticulopodia and nutrients
|
---|
[430] | 678 | type:d 0 1 0
|
---|
| 679 | group:Foraminifera
|
---|
| 680 |
|
---|
| 681 | prop:
|
---|
[434] | 682 | id:maxSteps
|
---|
[432] | 683 | name:Stop after the given number of simulation steps
|
---|
[434] | 684 | type:d 0 1000000 0
|
---|
[432] | 685 |
|
---|
| 686 | prop:
|
---|
[474] | 687 | id:foramSpeedMmPerMin
|
---|
| 688 | name:Speed of foraminfera in mm/min
|
---|
| 689 | type:f 0.1
|
---|
| 690 | flags: 16
|
---|
| 691 | group:Foraminifera
|
---|
| 692 |
|
---|
| 693 | prop:
|
---|
| 694 | id:secPerStep
|
---|
| 695 | name:Seconds per simulation step
|
---|
| 696 | type:f 60.0
|
---|
| 697 | flags: 16
|
---|
| 698 | group:Foraminifera
|
---|
| 699 |
|
---|
| 700 | prop:
|
---|
[422] | 701 | id:e_repro_cost_haplo
|
---|
[423] | 702 | name:Cost of reproduction
|
---|
[422] | 703 | type:f 0.1 0.9 0.5
|
---|
[421] | 704 | group:Foraminifera
|
---|
[380] | 705 |
|
---|
[401] | 706 | prop:
|
---|
[422] | 707 | id:e_repro_cost_diplo
|
---|
[423] | 708 | name:Cost of reproduction
|
---|
[422] | 709 | type:f 0.1 0.9 0.3
|
---|
| 710 | group:Foraminifera
|
---|
[380] | 711 |
|
---|
[401] | 712 | prop:
|
---|
[422] | 713 | id:chamber_proculus_haplo
|
---|
[423] | 714 | name:Size of proculus
|
---|
[422] | 715 | type:f
|
---|
[421] | 716 | group:Foraminifera
|
---|
[380] | 717 |
|
---|
[401] | 718 | prop:
|
---|
[422] | 719 | id:chamber_proculus_diplo
|
---|
[423] | 720 | name:Size of proculus
|
---|
[422] | 721 | type:f
|
---|
[380] | 722 | group:Foraminifera
|
---|
| 723 |
|
---|
| 724 | prop:
|
---|
[422] | 725 | id:chamber_difference_haplo
|
---|
[423] | 726 | name:Difference in size between subsequent chambers
|
---|
[422] | 727 | type:f
|
---|
[380] | 728 | group:Foraminifera
|
---|
| 729 |
|
---|
| 730 | prop:
|
---|
[422] | 731 | id:chamber_difference_diplo
|
---|
[423] | 732 | name:Difference in size between subsequent chambers
|
---|
[422] | 733 | type:f
|
---|
[380] | 734 | group:Foraminifera
|
---|
| 735 |
|
---|
| 736 | prop:
|
---|
[422] | 737 | id:hunted_prob
|
---|
| 738 | name:Probability of being hunted
|
---|
| 739 | type:f 0 1 0
|
---|
| 740 | group:Forminifera
|
---|
[380] | 741 |
|
---|
| 742 | prop:
|
---|
[422] | 743 | id:zone1_range
|
---|
| 744 | name:Zone 1 range
|
---|
| 745 | type:f 0 200
|
---|
| 746 | group:Foraminifera
|
---|
[380] | 747 |
|
---|
| 748 | prop:
|
---|
[422] | 749 | id:zone2_range
|
---|
| 750 | name:Zone 2 range
|
---|
| 751 | type:f 0 3000
|
---|
[421] | 752 | group:Foraminifera
|
---|
[380] | 753 |
|
---|
| 754 | prop:
|
---|
[422] | 755 | id:colors
|
---|
| 756 | name:Haploid and diploid colors
|
---|
| 757 | type:x
|
---|
[380] | 758 | group:Foraminifera
|
---|
| 759 |
|
---|
| 760 | prop:
|
---|
[422] | 761 | id:min_repro_energ_haplo
|
---|
| 762 | name:Min reproduction energy of forams
|
---|
| 763 | type:f
|
---|
[380] | 764 | group:Foraminifera
|
---|
| 765 |
|
---|
| 766 | prop:
|
---|
[422] | 767 | id:min_repro_energ_diplo
|
---|
| 768 | name:Min reproduction energy of forams
|
---|
| 769 | type:f
|
---|
| 770 | group:Foraminifera
|
---|
| 771 |
|
---|
| 772 | prop:
|
---|
[380] | 773 | id:repro_prob
|
---|
[401] | 774 | name:Probability of reproduction
|
---|
[422] | 775 | type:f 0 1 0.8
|
---|
[421] | 776 | group:Foraminifera
|
---|
[380] | 777 |
|
---|
| 778 | prop:
|
---|
[422] | 779 | id:energies0_haplo
|
---|
| 780 | name:Energy of offspring from diploid forams
|
---|
| 781 | type:f
|
---|
| 782 | group:Foraminifera
|
---|
| 783 |
|
---|
| 784 | prop:
|
---|
| 785 | id:energies0_diplo
|
---|
| 786 | name:Energy of offspring from diploid forams
|
---|
| 787 | type:f
|
---|
| 788 | group:Foraminifera
|
---|
| 789 |
|
---|
| 790 | prop:
|
---|
[475] | 791 | id:e_death_level_haplo
|
---|
| 792 | name:Minimal level of energy to sustain life of haploid
|
---|
| 793 | type:f 0 20 4
|
---|
| 794 | group:Foraminifera
|
---|
| 795 |
|
---|
| 796 | prop:
|
---|
| 797 | id:e_death_level_diplo
|
---|
| 798 | name:Minimal level of energy to sustain life of diploid
|
---|
| 799 | type:f 0 20 0.25
|
---|
| 800 | group:Foraminifera
|
---|
| 801 |
|
---|
| 802 | prop:
|
---|
[422] | 803 | id:energy_hib
|
---|
| 804 | name:Energy used for hibernation during one step
|
---|
| 805 | type:f 0 1 0.001
|
---|
| 806 | group:Foraminifera
|
---|
| 807 |
|
---|
| 808 | prop:
|
---|
| 809 | id:energy_move
|
---|
| 810 | name:Energy used for movement during one step
|
---|
| 811 | type:f 0 20 0.001
|
---|
| 812 | group:Foraminifera
|
---|
| 813 |
|
---|
| 814 | prop:
|
---|
| 815 | id:min_vol
|
---|
| 816 | name:Minimal volume for reproduction
|
---|
| 817 | type:f 100 900 100
|
---|
| 818 | group:Foraminifera
|
---|
| 819 |
|
---|
| 820 | prop:
|
---|
| 821 | id:max_size
|
---|
| 822 | name:Maximal size
|
---|
| 823 | type:d 1 10 5
|
---|
| 824 | group:Foraminifera
|
---|
| 825 |
|
---|
| 826 | prop:
|
---|
| 827 | id:foramPop
|
---|
| 828 | name:Initial forams population size
|
---|
| 829 | type:d 1 1000 100
|
---|
| 830 | group:Foraminifera
|
---|
| 831 |
|
---|
| 832 | prop:
|
---|
[380] | 833 | id:crossprob
|
---|
[401] | 834 | name:Crossover probability
|
---|
| 835 | type:f 0 1 0
|
---|
[421] | 836 | group:Foraminifera
|
---|
[380] | 837 |
|
---|
| 838 | prop:
|
---|
[401] | 839 | id:mutationprob
|
---|
| 840 | name:Mutation probability
|
---|
| 841 | type:f 0 1 0
|
---|
[421] | 842 | group:Foraminifera
|
---|
[401] | 843 |
|
---|
| 844 | prop:
|
---|
[380] | 845 | id:e_meta
|
---|
| 846 | name:Idle metabolism
|
---|
| 847 | type:f 0 1
|
---|
| 848 | group:Energy
|
---|
| 849 | help:Each stick consumes this amount of energy in one time step
|
---|
| 850 |
|
---|
| 851 | prop:
|
---|
| 852 | id:feedrate
|
---|
| 853 | name:Feeding rate
|
---|
[474] | 854 | type:f 0 1000000
|
---|
[380] | 855 | group:Energy
|
---|
| 856 | help:How fast energy is created in the world
|
---|
| 857 |
|
---|
| 858 | prop:
|
---|
[422] | 859 | id:energy_nut
|
---|
[428] | 860 | name:Nutrient energy
|
---|
[422] | 861 | type:f 0 1000
|
---|
[380] | 862 | group:Energy
|
---|
| 863 |
|
---|
| 864 | prop:
|
---|
| 865 | id:feedtrans
|
---|
| 866 | name:Ingestion multiplier
|
---|
[422] | 867 | type:f 0 100
|
---|
[380] | 868 | group:Energy
|
---|
[422] | 869 |
|
---|
| 870 | prop:
|
---|
| 871 | id:nutrientsize
|
---|
[428] | 872 | name:Nutrient size
|
---|
[423] | 873 | type:f 0.1 0.9 0.1
|
---|
[422] | 874 | group:Energy
|
---|
| 875 |
|
---|
| 876 | prop:
|
---|
[421] | 877 | id:nutrientPop
|
---|
[428] | 878 | name:Nutrient population size
|
---|
[421] | 879 | group:Energy
|
---|
| 880 | type:d 1 1000 10
|
---|
| 881 |
|
---|
[422] | 882 | prop:
|
---|
| 883 | id:stress
|
---|
| 884 | name:Environmental stress
|
---|
| 885 | type:d 0 1 1
|
---|
| 886 | group:World
|
---|
| 887 |
|
---|
| 888 | prop:
|
---|
| 889 | id:repro_trigger
|
---|
| 890 | name:Reproduction trigger
|
---|
| 891 | type:d 0 1 1
|
---|
| 892 | group:World
|
---|
| 893 |
|
---|
| 894 | prop:
|
---|
| 895 | id:repro_time
|
---|
| 896 | name:Time before reproduction
|
---|
[474] | 897 | type:d 0 10000
|
---|
[422] | 898 |
|
---|
| 899 | prop:
|
---|
| 900 | id:creath
|
---|
| 901 | name:Creation height
|
---|
| 902 | type:f -1 50
|
---|
| 903 | help:~
|
---|
| 904 | Vertical position (above the surface) where new Forams are revived.
|
---|
| 905 | Negative values are only used in the water area:
|
---|
| 906 | 0 = at the surface
|
---|
| 907 | -0.5 = half depth
|
---|
| 908 | -1 = just above the bottom~
|
---|
| 909 |
|
---|
[421] | 910 | state:
|
---|
| 911 | id:nutrient
|
---|
[428] | 912 | name:Nutrient locations
|
---|
[421] | 913 | help:vector of vectors [x,y,energy]
|
---|
| 914 | type:x
|
---|
| 915 | flags:32
|
---|
| 916 |
|
---|
| 917 | prop:
|
---|
[380] | 918 | id:autorestart
|
---|
| 919 | name:Restart after extinction
|
---|
| 920 | help:Restart automatically this experiment after the last creature has died?
|
---|
| 921 | type:d 0 1
|
---|
| 922 |
|
---|
| 923 | state:
|
---|
| 924 | id:notes
|
---|
| 925 | name:Notes
|
---|
| 926 | type:s 1
|
---|
| 927 | help:~
|
---|
| 928 | You can write anything here
|
---|
| 929 | (it will be saved to the experiment file)~
|
---|
| 930 |
|
---|
| 931 | state:
|
---|
| 932 | id:totaltestedcr
|
---|
[421] | 933 | name:Evaluated Forams
|
---|
| 934 | help:Total number of the Forams evaluated in the experiment
|
---|
[380] | 935 | type:d
|
---|
| 936 | flags:16
|
---|
| 937 |
|
---|
[404] | 938 | prop:
|
---|
[421] | 939 | id:logging
|
---|
| 940 | name:Log statistics to file
|
---|
| 941 | type:d 0 1 0
|
---|