[380] | 1 | expdef:
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[401] | 2 | name:Benthic foraminifera reproduction
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[380] | 3 | info:~
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| 4 | Genes and parameter values which control reproduction are stored in user1 and user2 fields.
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| 5 |
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| 6 | user1:
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[402] | 7 | genes which are not encoded in Ff genotype:
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[380] | 8 | Vamin - Minimum stored energy necessary for reproduction
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| 9 | amin - minimal age for reproduction
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| 10 |
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| 11 | user2:
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| 12 | Physiological parameters of foraminifera:
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| 13 | Va - amount of the stored energy
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| 14 | gen - generation: 0 haploid, 1 diploid
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| 15 | ~
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| 16 | code:~
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| 17 |
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[401] | 18 | /*
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| 19 | changes 2015-06-24:
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| 20 | - xxx.get(...) changed to xxx[...]
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| 21 | - xxx.set(...,...) changed to xxx[...]=...
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| 22 | - function placeRandomlyNotColliding(cr) explicitly called when adding a new creature, and removed collision checking from onCreaturesBorn() which is also called when "growing" (since "growing" is implemented as creating a new creature in place of the old one, so onCreaturesBorn() is also called)
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| 23 | - use creature's center (not the bbox corner) when growing
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| 24 | - added "S" receptor to visualize the difference between diplo and haplo generations
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| 25 | - signal.value is a MechPart (a reference) so it does not have to be updated after changing the object location
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| 26 | */
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| 27 |
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[402] | 28 | /* TODO fix
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| 29 | [ERROR] Population.kill: Invalid index 35 (allowed range is 0..34)
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| 30 | [ERROR] Population.kill: ... called from reproduce_haploid() <forams_repro.inc:54>
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| 31 | [ERROR] Population.kill: ... called from onStep() <forams_repro.inc:228>
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| 32 | */
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| 33 |
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[380] | 34 | global foodenergywaiting;
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| 35 | global reprocounter;
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| 36 |
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[401] | 37 | @include "forams_repro.inc"
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| 38 |
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[380] | 39 | // -------------------------------- experiment begin --------------------------------
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| 40 |
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| 41 | function onExpDefLoad()
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| 42 | {
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[401] | 43 |
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[380] | 44 | // define genotype and creature groups
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| 45 | GenePools.clear();
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| 46 | Populations.clear();
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| 47 | GenePools[0].name = "Unused";
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| 48 |
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[401] | 49 | SignalView.mode = 1;
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| 50 |
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[380] | 51 | var pop = Populations[0];
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| 52 | pop.name = "Creatures";
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| 53 | pop.en_assim = 0;
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[404] | 54 | pop.nnsim = 0;
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[380] | 55 | pop.enableperf = 1;
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| 56 | pop.death = 1;
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| 57 | pop.energy = 1;
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| 58 | pop.selfmask = 0x10001;
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[401] | 59 | pop.othermask = 0x20001;
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| 60 | //pop.selfmask = 0x20002; pop.othermask = 0x10002;
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[380] | 61 | pop.perfperiod = 25;
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| 62 |
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| 63 | pop = Populations.addGroup("Food");
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| 64 | pop.nnsim = 0;
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| 65 | pop.enableperf = 0;
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| 66 | pop.death = 1;
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| 67 | pop.energy = 1;
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| 68 | pop.selfmask = 0x20002;
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[401] | 69 | pop.othermask = 0x10000;
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[380] | 70 |
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[404] | 71 | //radius of the chamber
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[405] | 72 | ExpParams.rads = [1.2, 0.6];
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| 73 | //inital genotypes
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| 74 | ExpParams.genh = "//0\np:sh=1,sx=" + ExpParams.rads[0] + ",sy=" + ExpParams.rads[0] + ",sz=" + ExpParams.rads[0] + ", rz=3.14159265358979";
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[404] | 75 | ExpParams.gend = "//0\np:sh=1,sx=" + ExpParams.rads[1] + ",sy=" + ExpParams.rads[1] + ",sz=" + ExpParams.rads[1] + ", rz=3.14159265358979";
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[405] | 76 | ExpParams.gend += "\nn:p=0,d=\"S\"";
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[380] | 77 | ExpParams.e_meta = 0.1;
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[401] | 78 | ExpParams.feedrate = 0.5;
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[380] | 79 | ExpParams.feede0 = 100;
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| 80 | ExpParams.feedtrans = 3;
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| 81 | ExpParams.creath = -0.99; //just above the bottom
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[401] | 82 | ExpParams.foodgen = "//0\np:sh=2,sx=0.1,sy=0.1,sz=0.1\nn:d=T,p=0";
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[380] | 83 | ExpParams.autorestart = 0;
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| 84 | ExpParams.psize = 10;
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[401] | 85 | ExpParams.logging = 0;
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| 86 |
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| 87 | //number of offspring
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| 88 | ExpParams.ofnumh = 40;
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| 89 | ExpParams.ofnumd = 25;
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| 90 | //minial volume for reproduction
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| 91 | ExpParams.v_min_d = 300;
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| 92 | ExpParams.v_min_h = 300;
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| 93 | //minimal age for reproduction
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| 94 | ExpParams.age_min_d = 100;
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| 95 | ExpParams.age_min_h = 100;
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| 96 | //crossover probability
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| 97 | ExpParams.crossprob = 0.4;
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| 98 | //mutation probability
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| 99 | ExpParams.mutationprob = 0.2;
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[380] | 100 | ExpParams.repro_time = 200;
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| 101 | ExpParams.repro_thr = 1;
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| 102 |
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[401] | 103 | //grwoth speed in time steps
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| 104 | ExpParams.growth_step = 50;
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| 105 |
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[380] | 106 | ExpState.totaltestedcr = 0;
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| 107 | ExpState.food = "";
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| 108 | foodenergywaiting = ExpParams.feede0;
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| 109 | reprocounter = 0;
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| 110 |
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[401] | 111 | ExpParams.wsize = 50;
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[380] | 112 | World.wrldwat = 50;
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| 113 | World.wrldsiz = ExpParams.wsize;
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| 114 | World.wrldbnd = 1;
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| 115 | }
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| 116 |
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| 117 | @include "standard_placement.inc"
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| 118 |
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| 119 | function onExpInit()
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| 120 | {
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| 121 | Populations[0].clear();
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| 122 | Populations[1].clear();
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| 123 |
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| 124 | for (var i = 0; i < ExpParams.psize; i++)
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| 125 | {
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| 126 | var cr = Populations[0].add(ExpParams.genh);
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| 127 | cr.name = "Initial creature" + i;
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| 128 | placeCreatureRandomly(cr, 0, 0);
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| 129 | cr.energ0 = ExpParams.v_min_h - ExpParams.repro_thr;
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| 130 | cr.energy = cr.energ0;
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[404] | 131 | cr.user1 = {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h};
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| 132 | cr.user2 = {"Va" : ExpParams.v_min_h - ExpParams.repro_thr, "gen" : 0, "growth_step" : ExpParams.growth_step, "rsize" : ExpParams.rads[0], "vinit" : ExpParams.v_min_h - ExpParams.repro_thr};
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[380] | 133 | }
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| 134 | ExpState.totaltestedcr = 0;
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| 135 | foodenergywaiting = ExpParams.feede0;
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| 136 | }
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| 137 |
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| 138 | function onExpLoad()
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| 139 | {
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| 140 | for (var pop in Populations)
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| 141 | pop.clear();
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| 142 |
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| 143 | Loader.addClass(sim_params.*);
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| 144 | Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
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| 145 | Loader.run();
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| 146 |
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| 147 | Simulator.print("Loaded " + Populations[0].size + " creatures and " + Populations[1].size + " food objects");
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| 148 | }
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| 149 |
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| 150 | function onExpLoad_Unknown()
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| 151 | {
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| 152 | if (Loader.objectName == "org") // saved by the old expdef
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| 153 | {
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| 154 | var g = Genotype.newFromString("");
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| 155 | Loader.currentObject = g;
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| 156 | Interface.makeFrom(g).setAllDefault();
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| 157 | Loader.loadObject();
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| 158 | var cr = Populations[0].add(g);
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| 159 | if (cr != null)
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| 160 | {
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[401] | 161 | //cr.rotate(0,0,Math.rnd01*Math.twopi);
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[380] | 162 | if ((typeof(g.user1) == "Vector") && (g.user1.size >= 3))
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[401] | 163 | {
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| 164 | // [x,y,energy]
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[380] | 165 | cr.move(g.user1[0] - cr.center_x, g.user1[1] - cr.center_y, 0);
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| 166 | cr.energy = g.user1[2];
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| 167 | }
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| 168 | else
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| 169 | {
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[401] | 170 | cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
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[380] | 171 | }
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| 172 | }
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| 173 | }
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| 174 | else if (Loader.objectName == "Creature")
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| 175 | {
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| 176 | Loader.currentObject = CreatureSnapshot.new();
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| 177 | Loader.loadObject();
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| 178 | Populations[0].add(Loader.currentObject);
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| 179 | }
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| 180 | }
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| 181 |
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| 182 | function onExpSave()
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| 183 | {
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| 184 | File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
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| 185 |
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[401] | 186 | var tmpvec = [], i;
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[380] | 187 |
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[401] | 188 | for(var cr in Populations[1])
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[380] | 189 | tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
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| 190 |
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| 191 | ExpState.food = tmpvec;
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| 192 | File.writeObject(sim_params.*);
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| 193 | ExpState.food = null; //vectors are only created for saving and then discarded
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| 194 |
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| 195 | for (var cr in Populations[0])
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| 196 | File.writeObject(cr);
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| 197 | }
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| 198 |
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| 199 | // -------------------------------- experiment end --------------------------------
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| 200 |
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| 201 | // -------------------------------- creature begin --------------------------------
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| 202 |
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| 203 | function onCreaturesBorn(cr)
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| 204 | {
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| 205 | cr.idleen = ExpParams.e_meta;
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| 206 | }
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| 207 |
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[401] | 208 | function placeRandomlyNotColliding(cr)
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| 209 | {
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| 210 | var retry = 100; //try 100 times
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| 211 | while (retry--)
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| 212 | {
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| 213 | placeCreatureRandomly(cr, 0, 0);
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| 214 | if (!cr.boundingBoxCollisions(0))
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| 215 | return cr;
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| 216 | }
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| 217 |
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| 218 | Populations[0].delete(cr);
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| 219 | }
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| 220 |
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[380] | 221 | function readyToRepro(cr)
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| 222 | {
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| 223 | cr.signals.add("repro");
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[401] | 224 | cr.signals[0].power = 1;
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[380] | 225 | }
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| 226 |
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| 227 | function onCreaturesStep(cr)
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| 228 | {
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[405] | 229 | //TODO moving inside sediment?
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| 230 | cr.moveAbs(cr.pos_x, cr.pos_y, 0); //adjustment in z axis
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[380] | 231 | var p = cr.getMechPart(0);
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| 232 | var n = cr.signals.receiveSet("food", ExpParams.food_range);
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| 233 |
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[401] | 234 | //if signals are received find the source of the nearest
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[380] | 235 | if (n.size > 0)
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| 236 | {
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[401] | 237 |
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[380] | 238 | var i;
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| 239 | var mp;
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| 240 | var distvec = XYZ.new(0, 0, 0);
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| 241 | var dist;
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| 242 | var mindist = 100000000000;
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| 243 | var mindistvec = null;
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| 244 |
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[401] | 245 | for (i = 0; i < n.size; i++)
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[380] | 246 | {
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[401] | 247 | mp = n[i].value;
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| 248 | distvec.set(mp.pos);
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| 249 | distvec.sub(p.pos);
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| 250 | dist = distvec.length;
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| 251 | if (dist < mindist)
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[380] | 252 | {
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[401] | 253 | mindist = dist;
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| 254 | mindistvec = distvec.clone();
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[380] | 255 | }
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| 256 | }
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| 257 |
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| 258 | mindistvec.normalize();
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[401] | 259 | mindistvec.scale(-0.08);
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[380] | 260 | cr.localDrive = mindistvec;
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| 261 | }
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[401] | 262 |
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[380] | 263 | else
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| 264 | {
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[401] | 265 | cr.localDrive = (0.1 * Math.rnd01, 0.1 * Math.rnd01, 0);
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[380] | 266 | }
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| 267 |
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[401] | 268 | //energy costs depend on size
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| 269 | if (cr.energy > 100)
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| 270 | {
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[405] | 271 | //TODO energy costs dependent on size
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[401] | 272 | // cr.energy_m = cr.user2["Va"]/cr.user2["vinit"];
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| 273 | }
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[380] | 274 |
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[401] | 275 | if (cr.lifespan >= ExpParams.max_age)
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[380] | 276 | {
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[404] | 277 | //TODO what is max age value? should there be one?
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[401] | 278 | Populations[0].kill(cr);
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[405] | 279 | return;
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[401] | 280 | }
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| 281 |
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| 282 | //foram growth
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[404] | 283 | if (cr.lifespan == cr.user2["growth_step"])
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[401] | 284 | {
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[405] | 285 | //TODO how size is related to the energy?
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| 286 | cr.user2["rsize"] = ExpParams.rads[cr.user2["gen"]] * Math.min(Math.max(float(cr.user2["Va"] / cr.user2["vinit"]) * 0.5, 1.0), 2.5);
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[404] | 287 | var geno = "//0\np:sh=1,sx=" + cr.user2["rsize"] + ",sy=" + cr.user2["rsize"] + ",sz=" + cr.user2["rsize"] + ", rz=3.14159265358979";
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| 288 | if (cr.user2["gen"] == 1)
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[380] | 289 | {
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[404] | 290 | geno += "\nn:p=0,d=\"S\""; //TODO why initial genotypes are not used as defined in ExpParams?
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[401] | 291 | //TODO maybe it would be nice if they rotated so the "S" would show where they are going (direction/intention)
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| 292 | }
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[405] | 293 | var cr2 = Populations[0].add(geno);
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[404] | 294 | cr2.energy = cr.energy;
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| 295 | setGenotype(cr2, cr.user1, cr.user2);
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[401] | 296 | cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
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| 297 |
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| 298 | Populations[0].delete(cr);
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[380] | 299 | }
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[401] | 300 | else
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[380] | 301 | {
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[401] | 302 | var properSize = 0;
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| 303 |
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| 304 | if (cr.user2["gen"] == 0)
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| 305 | {
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| 306 | properSize = cr.user2["Va"] >= cr.user1["vamin"];
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| 307 | }
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| 308 | else
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| 309 | {
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| 310 | properSize = cr.user2["Va"] >= cr.user1[0]["vamin"];
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| 311 | }
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| 312 |
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| 313 | //if creature has proper age and cytoplasm amount
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| 314 | if ( properSize )
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| 315 | {
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| 316 | //reproduce with probability repro_prob
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| 317 | if (Math.rnd01 <= ExpParams.repro_prob)
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| 318 | {
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| 319 | readyToRepro(cr);
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| 320 | }
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| 321 | }
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| 322 | if ( properSize && (cr.signals.receive("repro") > 0))
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| 323 | {
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| 324 | readyToRepro(cr);
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| 325 | }
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[380] | 326 | }
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| 327 | }
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| 328 |
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| 329 | function onCreaturesDied(cr)
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| 330 | {
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| 331 | //fossilization
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| 332 | var geno = GenePools[0].add(cr.genotype);
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| 333 | geno.user1 = cr.user1;
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| 334 | geno.user2 = cr.user2;
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| 335 | Simulator.print("\"" + cr.name + "\" died...");
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| 336 | ExpState.totaltestedcr++;
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| 337 | }
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| 338 |
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[404] | 339 | function setGenotype(cr, new_user1, new_user2)
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| 340 | {
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| 341 | cr.user2 = {"Va" : new_user2["Va"], "gen" : new_user2["gen"], "growth_step" : new_user2["growth_step"], "rsize" : new_user2["rsize"], "vinit": new_user2["vinit"]};
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| 342 | if (cr.user2["gen"] == 0)
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| 343 | {
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| 344 | cr.user1 = {"vamin" : new_user1["vamin"], "amin": new_user1["amin"] };
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| 345 | }
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| 346 | else if (cr.user2["gen"] == 1)
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| 347 | {
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| 348 | cr.user1 = [ {"vamin" : new_user1[0]["vamin"], "amin": new_user1[0]["amin"] }, {"vamin" : new_user1[1]["vamin"], "amin": new_user1[1]["amin"] }];
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[405] | 349 | }
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[404] | 350 |
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| 351 | }
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| 352 |
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[380] | 353 | // -------------------------------- creature end --------------------------------
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| 354 |
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| 355 | // -------------------------------- food begin --------------------------------
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| 356 |
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| 357 | function onFoodStep(cr)
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| 358 | {
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| 359 | cr.moveAbs(cr.pos_x % ExpParams.wsize, cr.pos_y % ExpParams.wsize, 0.5);
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| 360 | }
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| 361 |
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| 362 | function addfood()
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| 363 | {
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| 364 | var cr = Populations[1].add(ExpParams.foodgen);
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| 365 |
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| 366 | cr.name = "Food";
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| 367 | cr.idleen = 0;
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| 368 | cr.energ0 = ExpParams.feede0;
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| 369 | cr.energy = cr.energ0;
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| 370 | cr.signals.add("food");
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| 371 |
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[401] | 372 | cr.signals[0].value = cr.getMechPart(0);
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[380] | 373 |
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[404] | 374 | placeRandomlyNotColliding(cr);
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[380] | 375 | }
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| 376 |
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| 377 | function onFoodCollision()
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| 378 | {
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| 379 | if (Collision.Creature2.user2 != null)
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| 380 | {
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| 381 | var e = Collision.Part2.ing * ExpParams.feedtrans;
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| 382 | //Simulator.print("transferring "+e+" from "+Collision.Creature1.name+" to "+Collision.Creature2.name+" ("+Collision.Creature2.energy+")");
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| 383 | Collision.Creature1.energy_m = Collision.Creature1.energy_m + e;
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| 384 | Collision.Creature2.energy_p = Collision.Creature2.energy_p + e;
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[404] | 385 | Collision.Creature2.user2["Va"] = float(Collision.Creature2.user2["Va"]) + float(e);
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[380] | 386 | }
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| 387 | }
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| 388 |
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| 389 | // -------------------------------- food end --------------------------------
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| 390 |
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| 391 |
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| 392 | function log(tolog, fname)
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| 393 | {
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[401] | 394 | var f = File.appendDirect(fname, "forams data");
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[380] | 395 | f.writeString("" + Simulator.stepNumber);
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[401] | 396 | for (var i = 0; i < tolog.size; i++)
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[380] | 397 | {
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| 398 | f.writeString(";" + tolog[i]);
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| 399 | }
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| 400 | f.writeString("\n");
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| 401 | f.close();
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| 402 | }
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| 403 |
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| 404 |
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| 405 |
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| 406 |
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[401] | 407 | @include "standard_events.inc"
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[380] | 408 |
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[401] | 409 | ~
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[380] | 410 |
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[401] | 411 | prop:
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| 412 | id:max_age
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| 413 | name:Maximal age
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| 414 | type:d 100 1000 500
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[380] | 415 |
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[401] | 416 | prop:
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| 417 | id:wsize
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| 418 | name:World size
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| 419 | type:d 10 1000 20
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[380] | 420 |
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[401] | 421 | prop:
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| 422 | id:growth_step
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| 423 | name:Growth step
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[404] | 424 | type:d 10 10000 1000
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[380] | 425 |
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[401] | 426 | prop:
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[404] | 427 | id:rads
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[405] | 428 | name:Haploid and diploid radius
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[404] | 429 | type:x
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[380] | 430 |
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| 431 | prop:
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| 432 | id:age_min_h
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| 433 | name:Min reproduction age of haploid forams
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| 434 | type:d 100 10000 300
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| 435 | group:Foraminifera
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| 436 |
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| 437 | prop:
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| 438 | id:age_min_d
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| 439 | name:Min reproduction age of diploid forams
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| 440 | type:d 100 10000 200
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| 441 | group:Foraminifera
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| 442 |
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| 443 | prop:
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| 444 | id:v_min_h
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| 445 | name:Min reproduction energy of haploid forams
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[401] | 446 | type:f 10 10000 300
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[380] | 447 | group:Foraminifera
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| 448 |
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| 449 | prop:
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| 450 | id:v_min_d
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| 451 | name:Min reproduction energy of diploid forams
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[401] | 452 | type:f 10 10000 150
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[380] | 453 | group:Foraminifera
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| 454 |
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| 455 | prop:
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| 456 | id:repro_thr
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[405] | 457 | name:Energy creatures need to gather to reproduce
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[380] | 458 | type:d 1 1000 1
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| 459 |
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| 460 | prop:
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| 461 | id:food_range
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[401] | 462 | name:Range of food smell
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[380] | 463 | type:d 0 10000 10000
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| 464 |
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| 465 | prop:
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| 466 | id:repro_time
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[401] | 467 | name:Time before reproduction
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[380] | 468 | type:d 0 1000
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| 469 |
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| 470 | prop:
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| 471 | id:psize
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[401] | 472 | name:Initial population size
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[380] | 473 | type:d 1 1000 100
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| 474 |
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| 475 | prop:
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[401] | 476 | id:logging
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| 477 | name:Log statistics to file
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| 478 | type:d 0 1 0
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| 479 |
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| 480 | prop:
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[380] | 481 | id:ofnumh
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| 482 | name:Number of offspring from haploid forams
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| 483 | type:d
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| 484 | group:Foraminifera
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| 485 |
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| 486 | prop:
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| 487 | id:ofnumd
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| 488 | name:Number of offspring from diploid forams
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| 489 | type:d
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| 490 | group:Foraminifera
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| 491 |
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| 492 | prop:
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| 493 | id:repro_prob
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[401] | 494 | name:Probability of reproduction
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[380] | 495 | type:f 0 1 0.9
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| 496 |
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| 497 | prop:
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| 498 | id:crossprob
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[401] | 499 | name:Crossover probability
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| 500 | type:f 0 1 0
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[380] | 501 |
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| 502 | prop:
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[401] | 503 | id:mutationprob
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| 504 | name:Mutation probability
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| 505 | type:f 0 1 0
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| 506 |
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| 507 | prop:
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[380] | 508 | id:genh
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| 509 | name:Initial genotype of haploid forams
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| 510 | type:s 1
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| 511 | group:Foraminifera
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| 512 |
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| 513 | prop:
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| 514 | id:gend
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| 515 | name:Initial genotype of diploid forams
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| 516 | type:s 1
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| 517 | group:Foraminifera
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| 518 |
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| 519 | prop:
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| 520 | id:creath
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| 521 | name:Creation height
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| 522 | type:f -1 50
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| 523 | help:~
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| 524 | Vertical position (above the surface) where new creatures are revived.
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| 525 | Negative values are only used in the water area:
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| 526 | 0 = at the surface
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| 527 | -0.5 = half depth
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| 528 | -1 = just above the bottom~
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| 529 |
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| 530 | prop:
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| 531 | id:e_meta
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| 532 | name:Idle metabolism
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| 533 | type:f 0 1
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| 534 | group:Energy
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| 535 | help:Each stick consumes this amount of energy in one time step
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| 536 |
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| 537 | prop:
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| 538 | id:feedrate
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| 539 | name:Feeding rate
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| 540 | type:f 0 100
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| 541 | group:Energy
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| 542 | help:How fast energy is created in the world
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| 543 |
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| 544 | prop:
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| 545 | id:feede0
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| 546 | name:Food's energy
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| 547 | group:Energy
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| 548 | type:f 0 1000
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| 549 |
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| 550 | prop:
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| 551 | id:feedtrans
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| 552 | name:Ingestion multiplier
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| 553 | group:Energy
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| 554 | type:f 0 100
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| 555 |
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| 556 | prop:
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| 557 | id:foodgen
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| 558 | name:Food's genotype
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| 559 | group:Energy
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| 560 | type:s 1
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| 561 |
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| 562 | prop:
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| 563 | id:autorestart
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| 564 | name:Restart after extinction
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| 565 | help:Restart automatically this experiment after the last creature has died?
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| 566 | type:d 0 1
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| 567 |
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| 568 | state:
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| 569 | id:notes
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| 570 | name:Notes
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| 571 | type:s 1
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| 572 | help:~
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| 573 | You can write anything here
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| 574 | (it will be saved to the experiment file)~
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| 575 |
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| 576 | state:
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| 577 | id:totaltestedcr
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| 578 | name:Evaluated creatures
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| 579 | help:Total number of the creatures evaluated in the experiment
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| 580 | type:d
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| 581 | flags:16
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| 582 |
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[404] | 583 | prop:
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| 584 | id:foodPop
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[405] | 585 | name:Food size
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[404] | 586 | type:d 1 1000 10
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| 587 |
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[380] | 588 | state:
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| 589 | id:food
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| 590 | name:Food locations
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| 591 | help:vector of vectors [x,y,energy]
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| 592 | type:x
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| 593 | flags:32
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