[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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[422] | 25 | global colors;
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[493] | 26 | global curColor;
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[479] | 27 | global max_chamber_volume;
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[474] | 28 | global movePerStep;
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[479] | 29 | global reprocounter;
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[481] | 30 | global changePeriod;
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| 31 | global phase;
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[493] | 32 | global nutrientSqrCm;
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[567] | 33 | global species_genes;
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| 34 | global max_chambers_def;
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| 35 | global foram_uid; //introduced because each replacement of a creature (while growing) would generate a new Creature.uid
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| 36 | global chamber_vis_denominator;
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| 37 | global curRadius;
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[590] | 38 | global nutrient_num_counter;
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| 39 | global wrldsizSquareMeters;
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[380] | 40 |
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[406] | 41 | @include "foraminifera.inc"
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[401] | 42 |
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[380] | 43 | // -------------------------------- experiment begin --------------------------------
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| 44 |
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| 45 | function onExpDefLoad()
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| 46 | {
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| 47 | // define genotype and creature groups
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| 48 | GenePools.clear();
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| 49 | Populations.clear();
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| 50 | GenePools[0].name = "Unused";
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| 51 |
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| 52 | var pop = Populations[0];
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[421] | 53 | pop.name = "Forams";
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[380] | 54 | pop.en_assim = 0;
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[404] | 55 | pop.nnsim = 0;
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[380] | 56 | pop.enableperf = 1;
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| 57 | pop.death = 1;
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| 58 | pop.energy = 1;
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[487] | 59 | pop.selfmask = 0;
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| 60 | pop.othermask = 0;
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[401] | 61 | //pop.selfmask = 0x20002; pop.othermask = 0x10002;
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[847] | 62 | pop.perfperiod = 25;
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[487] | 63 | pop.bodysim = 0;
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[380] | 64 |
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[421] | 65 | pop = Populations.addGroup("Nutrients");
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[380] | 66 | pop.nnsim = 0;
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| 67 | pop.enableperf = 0;
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| 68 | pop.death = 1;
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| 69 | pop.energy = 1;
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[487] | 70 | pop.selfmask = 0;
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| 71 | pop.othermask = 0;
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[422] | 72 | //pop.othermask = 0x10002;
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[487] | 73 | pop.bodysim = 0;
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[380] | 74 |
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[444] | 75 | pop = Populations.addGroup("ReticulopodiaNutrients");
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[430] | 76 | pop.nnsim = 0;
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| 77 | pop.enableperf = 0;
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| 78 | pop.death = 0;
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| 79 | pop.energy = 0;
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[487] | 80 | pop.selfmask = 0;
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| 81 | pop.othermask = 0;
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| 82 | pop.bodysim = 0;
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[444] | 83 |
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[422] | 84 | //world
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| 85 | SignalView.mode = 1;
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[496] | 86 | World.wrldwat = 200;
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[493] | 87 | World.wrldsiz = micronsToFrams(100000);
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[847] | 88 | wrldsizSquareMeters = Math.pow(framsToMicrons(World.wrldsiz) * 0.000001, 2);
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[422] | 89 | World.wrldbnd = 1;
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| 90 |
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[486] | 91 | //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
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[444] | 92 |
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[847] | 93 | //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files
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[493] | 94 | ExpProperties.logPref = "";
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[401] | 95 |
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[554] | 96 | //morphology
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[486] | 97 | ExpProperties.zone1_range = micronsToFrams(1000);
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| 98 | ExpProperties.zone2_range = micronsToFrams(3000);
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[567] | 99 | ExpProperties.chamber_proculus_haplo = micronsToFrams(20);
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| 100 | ExpProperties.chamber_proculus_diplo = micronsToFrams(10);
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[847] | 101 | colors = ["1.0,1.0,0.3", "1.0,0.7,0.0"]; //yellow and orange
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[579] | 102 | curColor = colors[0];
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[567] | 103 | curRadius = ExpProperties.zone1_range;
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[479] | 104 |
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[422] | 105 | //nutrients
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[486] | 106 | ExpProperties.nutrientradius = micronsToFrams(10);
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[847] | 107 | ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius, 1);
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[554] | 108 | nutrientSqrCm = 10;
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[847] | 109 | ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz) * 0.0001, 2) / nutrientSqrCm;
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[554] | 110 |
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[380] | 111 | ExpState.totaltestedcr = 0;
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[421] | 112 | ExpState.nutrient = "";
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[567] | 113 |
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| 114 | max_chambers_def = 35;
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[569] | 115 | chamber_vis_denominator = 12;
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[493] | 116 | //addSpecies({"min_repro_energies" : [4,6]});
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| 117 | //addSpecies({"min_repro_energies" : [4,8]});
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[847] | 118 |
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[561] | 119 | //Simulator.print(create_genotype(0.2, 30, "1.0,1.0,0.0", 0.6)); //sample call
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| 120 | //Simulator.print(create_genotype(0.1, 40, "1.0,0.5,0.0", 0.1)); //sample call
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[380] | 121 | }
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| 122 |
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| 123 | @include "standard_placement.inc"
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| 124 |
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[567] | 125 | function onExpInit()
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[475] | 126 | {
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[568] | 127 | species_genes = [];
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[567] | 128 | foram_uid = 0;
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[568] | 129 | movePerStep = getMovePerStep();
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[475] | 130 |
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[567] | 131 | Populations[0].clear();
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| 132 | Populations[1].clear();
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| 133 | Populations[2].clear(); //reticulopodia and nutrients
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| 134 |
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| 135 | if (ExpProperties.max_chamber_num_haplo == max_chambers_def && ExpProperties.max_chamber_num_diplo == max_chambers_def)
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[479] | 136 | {
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[847] | 137 | max_chamber_volume = [[30403.5869594578, 52812.2546633948, 79578.5148482541, 113588.815134453, 154620.677376218, 205094.322220826, 262572.712174265, 326078.453295303, 402342.518962956, 498133.985678766, 615066.864740109, 759500.497626816, 937064.025544282, 1155915.25563075, 1429139.14079748, 1762487.92940157, 2176286.62046069, 2685795.63187845, 3316190.12127043, 4096436.04462706, 5051343.25226193, 6231980.1061213, 7687880.79524734, 9485307.02904958, 11716968.9852569, 14459866.4934433, 17836388.9853663, 22004935.7247348, 27138607.2546045, 33482425.1582986, 41336775.1280297, 50997910.7842793, 62888631.7871037, 77563060.9243464, 95659468.591964]
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| 138 | , [3430.07716920763, 6159.93090353532, 9322.94192815286, 13462.9896597283, 18399.8550832969, 24558.9218126892, 31468.8148639192, 39189.4977865513, 48404.4292075836, 60185.8639086061, 74490.6048472854, 92117.8178412275, 113852.779747083, 140714.366929552, 174450.937643841, 215250.242147183, 266323.295274072, 328858.042352538, 406552.379957238, 503526.321155323, 621060.781025019, 767240.824049468, 947210.683224091, 1169506.19906112, 1447211.61255879, 1787155.29073739, 2205627.64766244, 2723413.2837305, 3360233.53738709, 4147771.02835393, 5126445.06973928, 6328060.3331703, 7805693.278958, 9631924.72156452, 11884287.1596814]];
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[479] | 139 | }
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| 140 |
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[567] | 141 | else
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[479] | 142 | {
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[567] | 143 | max_chamber_volume = [Vector.new(), Vector.new()];
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| 144 | var density = 100;
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[847] | 145 | for (var ploid = 0; ploid < 2; ploid++)
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[567] | 146 | {
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| 147 | var rad = getPloidRadius(ploid);
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[847] | 148 | for (var cham_num = 0; cham_num < getProperty(ploid, "max_chamber_num"); cham_num++)
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[567] | 149 | {
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[847] | 150 | max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num + 1, density));
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| 151 | }
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[567] | 152 | }
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[479] | 153 | }
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[422] | 154 |
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[487] | 155 | if (species_genes.size == 0)
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[380] | 156 | {
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[487] | 157 | addSpecies({}); //default
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[380] | 158 | }
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[487] | 159 |
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| 160 | for (var spec = 0; spec < species_genes.size; spec++)
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| 161 | {
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| 162 | for (var i = 0; i < ExpProperties.foramPop; i++)
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| 163 | {
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[847] | 164 | addInitialForam(spec, i);
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[487] | 165 | }
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| 166 | }
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[380] | 167 | ExpState.totaltestedcr = 0;
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[554] | 168 |
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| 169 | reprocounter = 0;
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[590] | 170 | nutrient_num_counter = 0;
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[554] | 171 | changePeriod = 0;
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| 172 | phase = "low";
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[380] | 173 | }
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| 174 |
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| 175 | function onExpLoad()
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| 176 | {
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| 177 | for (var pop in Populations)
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| 178 | pop.clear();
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| 179 |
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| 180 | Loader.addClass(sim_params.*);
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| 181 | Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
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| 182 | Loader.run();
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| 183 |
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[421] | 184 | Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
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[380] | 185 | }
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| 186 |
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| 187 | function onExpLoad_Unknown()
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| 188 | {
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| 189 | if (Loader.objectName == "org") // saved by the old expdef
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| 190 | {
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| 191 | var g = Genotype.newFromString("");
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| 192 | Loader.currentObject = g;
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| 193 | Interface.makeFrom(g).setAllDefault();
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| 194 | Loader.loadObject();
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| 195 | var cr = Populations[0].add(g);
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| 196 | if (cr != null)
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| 197 | {
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[401] | 198 | //cr.rotate(0,0,Math.rnd01*Math.twopi);
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[476] | 199 | if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
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[401] | 200 | {
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| 201 | // [x,y,energy]
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[638] | 202 | cr.move(g.data->genes[0] - cr.bboxCenter.x, g.data->genes[1] - cr.bboxCenter.y, 0);
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[476] | 203 | cr.energy = g.data->genes[2];
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[380] | 204 | }
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| 205 | else
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| 206 | {
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[638] | 207 | cr.move(Math.rnd01 * World.wrldsiz - cr.bboxCenter.x, Math.rnd01 * World.wrldsiz - cr.bboxCenter.y, 0);
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[380] | 208 | }
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| 209 | }
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| 210 | }
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| 211 | else if (Loader.objectName == "Creature")
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| 212 | {
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| 213 | Loader.currentObject = CreatureSnapshot.new();
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| 214 | Loader.loadObject();
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| 215 | Populations[0].add(Loader.currentObject);
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| 216 | }
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| 217 | }
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| 218 |
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| 219 | function onExpSave()
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| 220 | {
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| 221 | File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
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| 222 |
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[401] | 223 | var tmpvec = [], i;
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[380] | 224 |
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[401] | 225 | for(var cr in Populations[1])
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[638] | 226 | tmpvec.add([cr.bboxCenter.x, cr.bboxCenter.y, cr.energy]);
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[380] | 227 |
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[421] | 228 | ExpState.nutrient = tmpvec;
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[380] | 229 | File.writeObject(sim_params.*);
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[432] | 230 | ExpState.nutrient = null; //vectors are only created for saving and then discarded
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[380] | 231 |
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| 232 | for (var cr in Populations[0])
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| 233 | File.writeObject(cr);
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| 234 | }
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| 235 |
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| 236 | // -------------------------------- experiment end --------------------------------
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| 237 |
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[567] | 238 | function volumeFromGeno(morphotype, rad, chamber_num, density)
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| 239 | {
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| 240 | var geno = create_genotype(rad, chamber_num, colors[morphotype], 1);
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[847] | 241 | var m = Model.newFromString(geno);
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| 242 | var mg = ModelGeometry.forModel(m);
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| 243 | mg.geom_density = density;
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[567] | 244 | var volumeInFrams = mg.volume();
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| 245 |
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[847] | 246 | return volumeInFrams / Math.pow(ExpProperties.scalingFactor, 3);
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[567] | 247 | }
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| 248 |
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[847] | 249 | function secToSimSteps(value_in_sec)
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| 250 | {
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| 251 | return value_in_sec / ExpProperties.secPerStep;
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[567] | 252 | }
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| 253 |
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| 254 | function volumeInMicrons(radiusInFrams)
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| 255 | {
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[847] | 256 | return 4.0 / 3.0 * Math.pi * Math.pow(framsToMicrons(radiusInFrams), 3);
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[567] | 257 | }
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| 258 |
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| 259 | function energyFromVolume(base, isRadiusInFrams)
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| 260 | {
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| 261 | if (isRadiusInFrams == 1) //radius in frams
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| 262 | {
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[847] | 263 | return ExpProperties.picoCarbonPerMikro * volumeInMicrons(base);
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[567] | 264 | }
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| 265 | else //volume in microns
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| 266 | {
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| 267 | return ExpProperties.picoCarbonPerMikro * base;
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| 268 | }
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| 269 | }
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| 270 |
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| 271 | function getMovePerStep()
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| 272 | {
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[847] | 273 | return micronsToFrams((ExpProperties.foramSpeedMmPerMin / 60) * 1000) * ExpProperties.secPerStep;
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[567] | 274 | }
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| 275 |
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| 276 | function micronsToFrams(micrometers)
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| 277 | {
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[847] | 278 | return micrometers * ExpProperties.scalingFactor;
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[567] | 279 | }
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| 280 |
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| 281 | function framsToMicrons(framsworldunits)
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| 282 | {
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[847] | 283 | return framsworldunits / ExpProperties.scalingFactor;
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[567] | 284 | }
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| 285 |
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| 286 | function getProperty(gen, prop_id)
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| 287 | {
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| 288 | var ploid = "haplo";
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| 289 | if (gen == 1) ploid = "diplo";
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| 290 | return ExpProperties.[prop_id + "_" + ploid];
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| 291 | }
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| 292 |
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| 293 | function getGene(cr, gen_id, gen_set)
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| 294 | {
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[847] | 295 | if (cr.data->lifeparams->gen == 0)
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[567] | 296 | return cr.data->genes[gen_id];
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[847] | 297 | else
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[567] | 298 | return cr.data->genes[gen_set][gen_id];
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| 299 | }
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| 300 |
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| 301 | function getPloidRadius(ploid)
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| 302 | {
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| 303 | var radius = ExpProperties.chamber_proculus_haplo;
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[847] | 304 | if (ploid == 1)
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| 305 | {
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| 306 | radius = ExpProperties.chamber_proculus_diplo;
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| 307 | }
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[567] | 308 | return radius;
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| 309 | }
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| 310 |
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| 311 | function chamberNumFromEnergy(energy, ploid)
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| 312 | {
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| 313 | var chamber_num = max_chamber_volume[ploid].size;
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| 314 | for (var i = 0; i < chamber_num; i++)
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| 315 | {
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[847] | 316 | if (energy < energyFromVolume(max_chamber_volume[ploid][i], 0))
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[567] | 317 | {
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[847] | 318 | chamber_num = i + 1;
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[567] | 319 | break;
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[847] | 320 | }
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| 321 | }
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| 322 |
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[567] | 323 | return chamber_num;
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| 324 | }
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| 325 |
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[595] | 326 | function createAndRotate(geno, rotate_min, rotate_max, pop_num)
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| 327 | {
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| 328 | var cr = Populations[pop_num].add(geno);
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[847] | 329 | cr.rotate(0, 0, Math.rndUni(rotate_min, rotate_max));
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| 330 | return cr;
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[595] | 331 | }
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| 332 |
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| 333 | //TODO unifiy addForam, foramGrow and createOffspring
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[567] | 334 | function addForam(species, iter, start_energy, ploid)
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| 335 | {
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| 336 | var chambernum = chamberNumFromEnergy(start_energy, ploid);
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| 337 | var radius = getPloidRadius(ploid);
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| 338 | var geno = create_genotype(radius, chambernum, colors[ploid], 1);
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[579] | 339 | curColor = colors[ploid];
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[847] | 340 | var cr = createAndRotate(geno, 0, 2 * Math.pi, 0);
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[567] | 341 | cr.name = "Initial creature" + species + "_" + iter;
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[588] | 342 | placeRandomlyNotColliding(cr);
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[567] | 343 | cr.energy = start_energy;
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| 344 | setGenotype({"opt" : "birth", "cr" : cr, "gen" : ploid, "species" : species, "energy0" : cr.energy, "genes" : species_genes[species], "parentsuids" : ["c0"]});
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| 345 | if (ploid == 1)
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| 346 | {
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| 347 | cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
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| 348 | }
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| 349 | moveReticulopodia(cr);
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| 350 | }
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| 351 |
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| 352 | function addInitialForam(species, iter)
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| 353 | {
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| 354 | var ploid = 0;
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| 355 | if (Math.rnd01 > 0.5)
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| 356 | {
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| 357 | ploid = 1;
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[847] | 358 | }
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[567] | 359 | //add new foram with random energy bewtween starting energy and reproduction threshold
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| 360 | var repro_thr = species_genes[species]->min_repro_energies[ploid];
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[847] | 361 | var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid), 1), repro_thr - 0.25 * repro_thr);
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| 362 | addForam(species, iter, start_energy, ploid);
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[567] | 363 | }
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| 364 |
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| 365 | //new species can be added as a dictionary with parameter values that are different than default values
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| 366 | function addSpecies(new_genes)
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| 367 | {
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[847] | 368 | species_genes.add({"min_repro_energies" : [ExpProperties.min_repro_energ_haplo, ExpProperties.min_repro_energ_diplo], "energies0" : [ExpProperties.energies0_haplo, ExpProperties.energies0_diplo], "hibernation" : 0, "morphotype" : 0});
|
---|
[567] | 369 | for (var i = 0; i < new_genes.size; i++)
|
---|
| 370 | {
|
---|
| 371 | var key = new_genes.getKey(i);
|
---|
[847] | 372 | species_genes[species_genes.size - 1][key] = new_genes[key];
|
---|
| 373 | }
|
---|
[567] | 374 | }
|
---|
| 375 |
|
---|
[421] | 376 | // -------------------------------- foram begin -----------------------------------
|
---|
[380] | 377 |
|
---|
[479] | 378 | function setForamMeta(cr)
|
---|
[430] | 379 | {
|
---|
[479] | 380 | //percent of current energy
|
---|
[847] | 381 | cr.idleen = (ExpProperties.e_meta * cr.energy) * ExpProperties.secPerStep;
|
---|
[430] | 382 | }
|
---|
| 383 |
|
---|
| 384 | function lastChamberNum(cr)
|
---|
| 385 | {
|
---|
[567] | 386 | return cr.numparts;
|
---|
[430] | 387 | }
|
---|
| 388 |
|
---|
[479] | 389 | function getZoneRange(cr, zone_num)
|
---|
| 390 | {
|
---|
[847] | 391 | return ExpProperties.["zone" + zone_num + "_range"];
|
---|
[479] | 392 | }
|
---|
| 393 |
|
---|
[567] | 394 | function addReticulopodia(cr, radius)
|
---|
| 395 | {
|
---|
[847] | 396 | if (reticulopodiaExists(cr))
|
---|
| 397 | {
|
---|
| 398 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
| 399 | }
|
---|
| 400 | var ret = Populations[2].add("//0\nm:Vstyle=reticulopodia\np:sh=1,sx=0.001,sy=0.001,sz=0.001\np:sh=3,sx=0.01,sy=" + radius + ",sz=" + radius + ",ry=1.57079633,vr=" + curColor + "\nj:0, 1, sh=1");
|
---|
| 401 | cr.data->reticulopodiacreature = ret;
|
---|
| 402 | ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
|
---|
| 403 | ret.locationSetBboxLow(cr.bboxCenter.x - radius, cr.bboxCenter.y - radius, cr.bboxCenter.z - radius);
|
---|
[567] | 404 | }
|
---|
| 405 |
|
---|
[421] | 406 | function onForamsBorn(cr)
|
---|
| 407 | {
|
---|
[479] | 408 | setForamMeta(cr);
|
---|
[486] | 409 | if (ExpProperties.visualize == 1)
|
---|
[430] | 410 | {
|
---|
[567] | 411 | addReticulopodia(cr, curRadius);
|
---|
[583] | 412 | moveReticulopodia(cr);
|
---|
[430] | 413 | }
|
---|
[380] | 414 | }
|
---|
| 415 |
|
---|
[401] | 416 | function placeRandomlyNotColliding(cr)
|
---|
| 417 | {
|
---|
| 418 | var retry = 100; //try 100 times
|
---|
| 419 | while (retry--)
|
---|
| 420 | {
|
---|
| 421 | placeCreatureRandomly(cr, 0, 0);
|
---|
| 422 | if (!cr.boundingBoxCollisions(0))
|
---|
[588] | 423 | {
|
---|
[847] | 424 | cr.locationSetBboxLow(cr.bboxLow.x, cr.bboxLow.y, -cr.getPart(cr.numparts - 1).sx); //place slightly under the bottom surface ("z" value depends on the size of the last=largest chamber)
|
---|
[401] | 425 | return cr;
|
---|
[588] | 426 | }
|
---|
[401] | 427 | }
|
---|
| 428 |
|
---|
| 429 | Populations[0].delete(cr);
|
---|
| 430 | }
|
---|
| 431 |
|
---|
[567] | 432 | function reticulopodiaExists(cr)
|
---|
[444] | 433 | {
|
---|
| 434 | var has_ret = 0;
|
---|
| 435 |
|
---|
[476] | 436 | if (cr.data->reticulopodiacreature != null)
|
---|
[444] | 437 | {
|
---|
[476] | 438 | if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
|
---|
[444] | 439 | {
|
---|
| 440 | has_ret = 1;
|
---|
| 441 | }
|
---|
| 442 | }
|
---|
| 443 |
|
---|
| 444 | return has_ret;
|
---|
| 445 | }
|
---|
| 446 |
|
---|
[567] | 447 | function visualization(cr)
|
---|
[380] | 448 | {
|
---|
[567] | 449 | return reticulopodiaExists(cr);
|
---|
| 450 | }
|
---|
| 451 |
|
---|
| 452 | function foramGrow(cr, chamber_num, lastchambergrowth)
|
---|
| 453 | {
|
---|
[847] | 454 | if ((chamber_num + 1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
|
---|
[474] | 455 | {
|
---|
[579] | 456 | curColor = colors[cr.data->lifeparams->gen];
|
---|
[567] | 457 | var ploid = cr.data->lifeparams->gen;
|
---|
[847] | 458 | var geno = create_genotype(getPloidRadius(ploid), chamber_num + 1, colors[ploid], lastchambergrowth);
|
---|
[595] | 459 | var cr2 = createAndRotate(geno, 0, 0, 0);
|
---|
[422] | 460 |
|
---|
[595] | 461 | cr2.orient.set(cr.orient);
|
---|
[474] | 462 | cr2.energy0 = cr.energy;
|
---|
| 463 | cr2.energy = cr2.energy0;
|
---|
[422] | 464 |
|
---|
[554] | 465 | setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
|
---|
[847] | 466 | cr2.locationSetBboxLow(cr.bboxLow.x, cr.bboxLow.y, cr.bboxLow.z);
|
---|
[479] | 467 | setForamMeta(cr2);
|
---|
[422] | 468 |
|
---|
[567] | 469 | if (reticulopodiaExists(cr))
|
---|
[474] | 470 | {
|
---|
[476] | 471 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[474] | 472 | }
|
---|
| 473 | Populations[0].delete(cr);
|
---|
[567] | 474 | return cr2;
|
---|
[430] | 475 | }
|
---|
[567] | 476 | return cr;
|
---|
[380] | 477 | }
|
---|
| 478 |
|
---|
[583] | 479 | function visualizeChamberGrowth(cr, chamber_time)
|
---|
| 480 | {
|
---|
| 481 | var total_time = secToSimSteps(ExpProperties.chamberGrowthSec);
|
---|
[847] | 482 | var ret_unit = total_time / chamber_vis_denominator;
|
---|
| 483 | var chamber_unit = total_time - ret_unit;
|
---|
[583] | 484 |
|
---|
| 485 | if (chamber_time < ret_unit || chamber_time >= chamber_unit)
|
---|
| 486 | {
|
---|
[847] | 487 | var new_rad = Math.min(Math.max((chamber_time % ret_unit) / ret_unit * getZoneRange(cr, 1), 0.01), getZoneRange(cr, 1));
|
---|
[583] | 488 |
|
---|
| 489 | if(chamber_time < ret_unit)
|
---|
| 490 | {
|
---|
[847] | 491 | new_rad = getZoneRange(cr, 1) - new_rad;
|
---|
[583] | 492 | }
|
---|
| 493 |
|
---|
| 494 | curColor = colors[cr.data->lifeparams->gen];
|
---|
[847] | 495 | addReticulopodia(cr, new_rad);
|
---|
[583] | 496 |
|
---|
| 497 | if (chamber_time == 0)//checking for end of chamber growth process
|
---|
| 498 | {
|
---|
[847] | 499 | cr.data->lifeparams->chamber_growth = -1;
|
---|
[583] | 500 | }
|
---|
| 501 | }
|
---|
| 502 | else
|
---|
| 503 | {
|
---|
[847] | 504 | var new_rad = 1 - Math.min(Math.max((chamber_time - ret_unit) / chamber_unit, 0.01), 1);
|
---|
[583] | 505 | curRadius = cr.data->reticulopodiacreature.getPart(1).sy;
|
---|
[847] | 506 |
|
---|
[583] | 507 | if (chamber_time == ret_unit)
|
---|
| 508 | {
|
---|
| 509 | new_rad = 1;
|
---|
| 510 | }
|
---|
| 511 |
|
---|
[847] | 512 | var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen) - 1, new_rad);
|
---|
| 513 | curRadius = getZoneRange(new_cr, 1);
|
---|
[583] | 514 | }
|
---|
| 515 | }
|
---|
| 516 |
|
---|
[435] | 517 | function stepToNearest(cr)
|
---|
[380] | 518 | {
|
---|
[638] | 519 | var p = XYZ.new(cr.bboxCenter.x, cr.bboxCenter.y, cr.bboxCenter.z);
|
---|
[847] | 520 | var n = cr.signals.receiveSet("nutrient", getZoneRange(cr, 2));
|
---|
[380] | 521 |
|
---|
[401] | 522 | //if signals are received find the source of the nearest
|
---|
[380] | 523 | if (n.size > 0)
|
---|
| 524 | {
|
---|
| 525 | var i;
|
---|
| 526 | var mp;
|
---|
| 527 | var distvec = XYZ.new(0, 0, 0);
|
---|
| 528 | var dist;
|
---|
[470] | 529 | var mindist = 100000000000.0;
|
---|
[380] | 530 | var mindistvec = null;
|
---|
[430] | 531 | var eating = 0;
|
---|
[380] | 532 |
|
---|
[401] | 533 | for (i = 0; i < n.size; i++)
|
---|
[380] | 534 | {
|
---|
[638] | 535 | mp = XYZ.new(n[i].value.bboxCenter.x, n[i].value.bboxCenter.y, n[i].value.bboxCenter.z);
|
---|
[595] | 536 | distvec.set(mp);
|
---|
| 537 | distvec.sub(p);
|
---|
[401] | 538 | dist = distvec.length;
|
---|
[847] | 539 | if (dist < getZoneRange(cr, 1))
|
---|
[380] | 540 | {
|
---|
[430] | 541 | if (n[i].value != null)
|
---|
| 542 | {
|
---|
| 543 | energyTransfer(cr, n[i].value);
|
---|
| 544 | eating = 1;
|
---|
| 545 | }
|
---|
| 546 | }
|
---|
[476] | 547 | else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
|
---|
[430] | 548 | {
|
---|
[401] | 549 | mindist = dist;
|
---|
| 550 | mindistvec = distvec.clone();
|
---|
[380] | 551 | }
|
---|
| 552 | }
|
---|
| 553 |
|
---|
[476] | 554 | if (!eating && cr.data->lifeparams->hibernated == 0)
|
---|
[430] | 555 | {
|
---|
[588] | 556 | mindistvec.z = 0;
|
---|
[430] | 557 | mindistvec.normalize();
|
---|
[595] | 558 | mindistvec.scale(movePerStep);
|
---|
| 559 | cr.drive = mindistvec;
|
---|
[430] | 560 | moveEnergyDec(cr);
|
---|
| 561 | }
|
---|
| 562 |
|
---|
[422] | 563 | return 1;
|
---|
[380] | 564 | }
|
---|
[847] | 565 |
|
---|
[422] | 566 | else
|
---|
[474] | 567 | {
|
---|
[422] | 568 | return 0;
|
---|
[474] | 569 | }
|
---|
[422] | 570 | }
|
---|
[401] | 571 |
|
---|
[422] | 572 | function moveEnergyDec(cr)
|
---|
| 573 | {
|
---|
[476] | 574 | if (cr.data->lifeparams->hibernated == 0)
|
---|
[422] | 575 | {
|
---|
[479] | 576 | //percent of maximal energy
|
---|
[847] | 577 | cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level) * ExpProperties.secPerStep;
|
---|
[422] | 578 | }
|
---|
[421] | 579 | }
|
---|
[380] | 580 |
|
---|
[584] | 581 | function fence(center, zone)
|
---|
[487] | 582 | {
|
---|
[847] | 583 | return Math.min(Math.max(0 + zone, center), World.wrldsiz - zone); //add and subtract zone from the world size to prevent reticulopodia from crossing the fence
|
---|
[487] | 584 | }
|
---|
| 585 |
|
---|
[422] | 586 | function foramMove(cr)
|
---|
[421] | 587 | {
|
---|
[430] | 588 | //are there any nutrients in zone 1 or 2?
|
---|
[401] | 589 | {
|
---|
[435] | 590 | var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
|
---|
[847] | 591 | if (moved == 1)
|
---|
| 592 | {
|
---|
[502] | 593 | moveReticulopodia(cr);
|
---|
[422] | 594 | return;
|
---|
| 595 | }
|
---|
[401] | 596 | }
|
---|
| 597 |
|
---|
[847] | 598 | //Prevents forams from crossing the world border. In the case of touching the border with the reticulopodia direction of the movement should be changed.
|
---|
[584] | 599 | var change_direction = 0;
|
---|
[638] | 600 | var new_x = fence(cr.bboxCenter.x, getZoneRange(cr, 1));
|
---|
| 601 | var new_y = fence(cr.bboxCenter.y, getZoneRange(cr, 1));
|
---|
[584] | 602 |
|
---|
[638] | 603 | if ((new_x != cr.bboxCenter.x) || (new_y != cr.bboxCenter.y) || (cr.data->lifeparams->dir_counter >= int(secToSimSteps(ExpProperties.dir_change_sec))))
|
---|
[584] | 604 | {
|
---|
| 605 | change_direction = 1;
|
---|
[847] | 606 | cr.locationSetBboxLow(new_x - cr.bboxSize.x / 2, new_y - cr.bboxSize.y / 2, -cr.getPart(cr.numparts - 1).sx); //place slightly under the bottom surface ("z" value depends on the size of the last=largest chamber)
|
---|
[584] | 607 | }
|
---|
| 608 |
|
---|
[422] | 609 | //no nutrients in zone 2
|
---|
[847] | 610 | if (getGene(cr, "hibernation", 0) == 1)
|
---|
[401] | 611 | {
|
---|
[430] | 612 | reverseHib(cr);
|
---|
[847] | 613 | cr.drive = XYZ.new(0, 0, 0);
|
---|
[380] | 614 | }
|
---|
[422] | 615 | //random move
|
---|
[554] | 616 | else if (change_direction == 1)
|
---|
[380] | 617 | {
|
---|
[476] | 618 | cr.data->lifeparams->dir = randomDir();
|
---|
[552] | 619 | cr.data->lifeparams->dir_counter = 0;
|
---|
[595] | 620 | cr.drive = cr.data->lifeparams->dir;
|
---|
[422] | 621 | moveEnergyDec(cr);
|
---|
| 622 | }
|
---|
[474] | 623 | else
|
---|
| 624 | {
|
---|
[595] | 625 | cr.drive = cr.data->lifeparams->dir;
|
---|
[474] | 626 | }
|
---|
[502] | 627 | moveReticulopodia(cr);
|
---|
[422] | 628 | }
|
---|
[401] | 629 |
|
---|
[502] | 630 | function moveReticulopodia(cr)
|
---|
| 631 | {
|
---|
| 632 | if (visualization(cr))
|
---|
| 633 | {
|
---|
[847] | 634 | cr.data->reticulopodiacreature.locationSetBboxLow(cr.bboxCenter.x - getZoneRange(cr, 1), cr.bboxCenter.y - getZoneRange(cr, 1), cr.bboxCenter.z - getZoneRange(cr, 1));
|
---|
[595] | 635 | cr.data->reticulopodiacreature.drive = cr.drive;
|
---|
[502] | 636 | }
|
---|
| 637 | }
|
---|
| 638 |
|
---|
[474] | 639 | function randomDir()
|
---|
| 640 | {
|
---|
[847] | 641 | var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0);
|
---|
[474] | 642 | dir.normalize();
|
---|
[847] | 643 | dir.scale(-1 * movePerStep);
|
---|
[474] | 644 | return dir;
|
---|
| 645 | }
|
---|
| 646 |
|
---|
[430] | 647 | function energyTransfer(cr1, cr2)
|
---|
[422] | 648 | {
|
---|
[847] | 649 | cr1.drive = XYZ.new(0, 0, 0);
|
---|
| 650 | var e = ExpProperties.feedtrans * cr1.energy * ExpProperties.secPerStep; //TODO efficiency dependent on age
|
---|
[502] | 651 | //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
|
---|
[510] | 652 | var transferred = cr2.transferEnergyTo(cr1, e);
|
---|
[847] | 653 | cr1.energy -= transferred * (1 - ExpProperties.ingestion);
|
---|
[476] | 654 | if (cr1.data->lifeparams->hibernated == 1)
|
---|
[422] | 655 | {
|
---|
[430] | 656 | reverseHib(cr1);
|
---|
[422] | 657 | }
|
---|
| 658 | }
|
---|
[401] | 659 |
|
---|
[430] | 660 | function reverseHib(cr)
|
---|
| 661 | {
|
---|
[476] | 662 | if (cr.data->lifeparams->hibernated == 1)
|
---|
[430] | 663 | {
|
---|
[479] | 664 | setForamMeta(cr); //unhibernate
|
---|
[847] | 665 | }
|
---|
[430] | 666 | else
|
---|
| 667 | {
|
---|
[847] | 668 | cr.idleen = (ExpProperties.energy_hib * cr.energy) * ExpProperties.secPerStep; //hibernate
|
---|
[430] | 669 | }
|
---|
[476] | 670 | cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
|
---|
[430] | 671 | }
|
---|
| 672 |
|
---|
[422] | 673 | function onForamsStep(cr)
|
---|
| 674 | {
|
---|
[479] | 675 | //checking for gametogenesis process
|
---|
| 676 | if (cr.data->lifeparams->division_time > 0)
|
---|
[444] | 677 | {
|
---|
[847] | 678 | cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time - 1, 0);
|
---|
[444] | 679 | }
|
---|
[479] | 680 | //checking for end of gametogenesis
|
---|
| 681 | else if (cr.data->lifeparams->division_time == 0)
|
---|
[422] | 682 | {
|
---|
[479] | 683 | //waiting for gamets fusion
|
---|
[422] | 684 | }
|
---|
[479] | 685 | //checking for chamber growth process
|
---|
| 686 | else if (cr.data->lifeparams->chamber_growth > 0)
|
---|
| 687 | {
|
---|
[847] | 688 | var chamber_time = Math.max(cr.data->lifeparams->chamber_growth - 1, 0);
|
---|
[567] | 689 | cr.data->lifeparams->chamber_growth = chamber_time;
|
---|
[504] | 690 | cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
|
---|
[422] | 691 |
|
---|
[567] | 692 | if (visualization(cr))
|
---|
| 693 | {
|
---|
[583] | 694 | visualizeChamberGrowth(cr, chamber_time);
|
---|
[567] | 695 | }
|
---|
[479] | 696 | }
|
---|
[583] | 697 | //checking for end of the chamber growth process
|
---|
[847] | 698 | else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr) == 0)
|
---|
| 699 | {
|
---|
| 700 | foramGrow(cr, lastChamberNum(cr), 1);
|
---|
[479] | 701 | cr.data->lifeparams->chamber_growth = -1;
|
---|
| 702 | //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
|
---|
[430] | 703 | }
|
---|
[479] | 704 | else
|
---|
[422] | 705 | {
|
---|
[479] | 706 | //update of metabolism rate
|
---|
| 707 | if (cr.data->lifeparams->hibernated == 0)
|
---|
[401] | 708 | {
|
---|
[479] | 709 | setForamMeta(cr);
|
---|
| 710 | }
|
---|
| 711 |
|
---|
| 712 | if (deathConditions(cr) == 1)
|
---|
| 713 | {
|
---|
[493] | 714 | if (ExpProperties.logging == 1)
|
---|
| 715 | {
|
---|
[847] | 716 | log(createLogVector(cr, cr.data->lifeparams->max_energy_level), ExpProperties.logPref + "fossil_log.txt");
|
---|
| 717 | log(createLogVector(cr, cr.lifespan), ExpProperties.logPref + "lifespan_log.txt");
|
---|
| 718 | }
|
---|
[479] | 719 | Populations[0].kill(cr);
|
---|
| 720 | return;
|
---|
| 721 | }
|
---|
| 722 |
|
---|
[552] | 723 | //update direction change counter
|
---|
| 724 | cr.data->lifeparams->dir_counter += 1;
|
---|
| 725 |
|
---|
[479] | 726 | foramMove(cr);
|
---|
| 727 |
|
---|
| 728 | var repro = foramReproduce(cr);
|
---|
| 729 | if (repro == 1)
|
---|
| 730 | {
|
---|
| 731 | return;
|
---|
| 732 | }
|
---|
| 733 |
|
---|
| 734 | cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
|
---|
| 735 |
|
---|
| 736 | //cheking conditions of chamber growth process start
|
---|
[567] | 737 | if (lastChamberNum(cr) < max_chamber_volume[cr.data->lifeparams->gen].size)
|
---|
[479] | 738 | {
|
---|
[847] | 739 | if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr) - 1], 0)))
|
---|
[479] | 740 | {
|
---|
[554] | 741 | cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
|
---|
[847] | 742 | }
|
---|
[479] | 743 | }
|
---|
[847] | 744 | }
|
---|
[380] | 745 | }
|
---|
| 746 |
|
---|
[422] | 747 | function deathConditions(cr)
|
---|
| 748 | {
|
---|
[847] | 749 | if ((cr.energy <= getProperty(cr.data->lifeparams->gen, "e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
|
---|
[479] | 750 | {
|
---|
[422] | 751 | return 1;
|
---|
[479] | 752 | }
|
---|
[422] | 753 | else
|
---|
| 754 | return 0;
|
---|
| 755 | }
|
---|
| 756 |
|
---|
[421] | 757 | function onForamsDied(cr)
|
---|
[380] | 758 | {
|
---|
[444] | 759 | if (visualization(cr))
|
---|
[430] | 760 | {
|
---|
[476] | 761 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[430] | 762 | }
|
---|
[380] | 763 | //fossilization
|
---|
| 764 | var geno = GenePools[0].add(cr.genotype);
|
---|
[476] | 765 | geno.data->genes = cr.data->genes;
|
---|
| 766 | geno.data->lifeparams = cr.data->lifeparams;
|
---|
[486] | 767 | if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
|
---|
[380] | 768 | ExpState.totaltestedcr++;
|
---|
| 769 | }
|
---|
| 770 |
|
---|
[421] | 771 | // --------------------------------foram end -------------------------------------
|
---|
[380] | 772 |
|
---|
[421] | 773 | // -------------------------------- nutrient begin --------------------------------
|
---|
[380] | 774 |
|
---|
[479] | 775 | function createNutrientGenotype(nutrientradius)
|
---|
[422] | 776 | {
|
---|
[847] | 777 | return "//0\nm:Vstyle=nutrient\np:sh=3,sx=" + nutrientradius + ",sy=" + nutrientradius + ",sz=" + nutrientradius + ",ry=1.57,vr=0.0,1.0,0.0";
|
---|
[422] | 778 | }
|
---|
| 779 |
|
---|
[421] | 780 | function onNutrientsStep(cr)
|
---|
[380] | 781 | {
|
---|
[638] | 782 | cr.locationSetBboxLow(cr.bboxLow.x % World.wrldsiz, cr.bboxLow.y % World.wrldsiz, 0.5);
|
---|
[380] | 783 | }
|
---|
| 784 |
|
---|
[421] | 785 | function addNutrient()
|
---|
[380] | 786 | {
|
---|
[486] | 787 | var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
|
---|
[380] | 788 |
|
---|
[421] | 789 | cr.name = "Nutrients";
|
---|
[380] | 790 | cr.idleen = 0;
|
---|
[486] | 791 | cr.energy0 = ExpProperties.energy_nut;
|
---|
[416] | 792 | cr.energy = cr.energy0;
|
---|
[421] | 793 | cr.signals.add("nutrient");
|
---|
[380] | 794 |
|
---|
[430] | 795 | cr.signals[0].value = cr;
|
---|
[380] | 796 |
|
---|
[422] | 797 | placeCreatureRandomly(cr, 0, 0);
|
---|
[486] | 798 | if (ExpProperties.visualize == 1)
|
---|
[444] | 799 | {
|
---|
[847] | 800 | var nutsize = ExpProperties.nutrientradius * 10;
|
---|
| 801 | var nut = Populations[2].add("//0\nm:Vstyle=nutrient_visual\np:sh=2,sx=" + nutsize + ",sy=" + nutsize + ",sz=" + nutsize + ",ry=1.5,vr=0.0,1.0,0.0");
|
---|
[476] | 802 | cr.data->reticulopodiacreature = nut;
|
---|
[847] | 803 | nut.locationSetBboxLow( cr.bboxLow.x + cr.bboxSize.x / 2 - nut.bboxSize.x / 2, cr.bboxLow.y + cr.bboxSize.y / 2 - nut.bboxSize.y / 2, -nutsize);
|
---|
[444] | 804 | }
|
---|
[380] | 805 | }
|
---|
| 806 |
|
---|
[444] | 807 | function onNutrientsDied(cr)
|
---|
| 808 | {
|
---|
| 809 | if (visualization(cr))
|
---|
| 810 | {
|
---|
[476] | 811 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[444] | 812 | }
|
---|
| 813 | }
|
---|
| 814 |
|
---|
[592] | 815 | function getNumberCounter(counter, increase, unitsize) //increase counter and then deduct and return an integer (=discrete) number of "full" units
|
---|
[590] | 816 | {
|
---|
| 817 | counter += increase;
|
---|
[847] | 818 | var unitcount = int(counter / unitsize);
|
---|
| 819 | counter -= unitcount * unitsize;
|
---|
[592] | 820 | return {"counter" : counter, "number" : unitcount};
|
---|
[590] | 821 | }
|
---|
| 822 |
|
---|
[422] | 823 | function nutrientGrowth()
|
---|
[380] | 824 | {
|
---|
[590] | 825 | if (ExpProperties.foodfluxChange > 0)
|
---|
[481] | 826 | {
|
---|
[847] | 827 | changePeriod += 1;
|
---|
| 828 | if (phase == "low" && changePeriod >= secToSimSteps(23328000)) //9 months
|
---|
| 829 | {
|
---|
| 830 | ExpProperties.foodflux = ExpProperties.foodflux / ExpProperties.foodfluxChange;
|
---|
| 831 | phase = "high";
|
---|
| 832 | changePeriod = 0;
|
---|
| 833 | }
|
---|
| 834 |
|
---|
| 835 | else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
|
---|
| 836 | {
|
---|
| 837 | ExpProperties.foodflux = ExpProperties.foodflux * ExpProperties.foodfluxChange;
|
---|
| 838 | phase = "low";
|
---|
| 839 | changePeriod = 0;
|
---|
| 840 | }
|
---|
[481] | 841 | }
|
---|
[422] | 842 |
|
---|
[847] | 843 | var nutrientNum = getNumberCounter(nutrient_num_counter, ExpProperties.foodflux * wrldsizSquareMeters * ExpProperties.secPerStep, ExpProperties.energy_nut * 0.000000000001);
|
---|
[493] | 844 |
|
---|
[590] | 845 | nutrient_num_counter = nutrientNum["counter"];
|
---|
| 846 |
|
---|
| 847 | for (var i = 0; i < nutrientNum["number"]; i++)
|
---|
[847] | 848 | {
|
---|
[590] | 849 | addNutrient();
|
---|
[380] | 850 | }
|
---|
[493] | 851 |
|
---|
[590] | 852 | if (ExpProperties.logging == 1 && nutrientNum["number"] > 0)
|
---|
| 853 | {
|
---|
[847] | 854 | log([nutrientNum["number"]], ExpProperties.logPref + "nutrients_log.txt");
|
---|
[590] | 855 | }
|
---|
| 856 |
|
---|
[380] | 857 | }
|
---|
| 858 |
|
---|
[421] | 859 | // -------------------------------- nutrient end --------------------------------
|
---|
[380] | 860 |
|
---|
[422] | 861 | // -------------------------------- step begin --------------------------------
|
---|
[380] | 862 |
|
---|
[422] | 863 | function onStep()
|
---|
| 864 | {
|
---|
[432] | 865 |
|
---|
| 866 | nutrientGrowth();
|
---|
[486] | 867 | if (ExpProperties.logging == 1)
|
---|
[422] | 868 | {
|
---|
| 869 | createStatistics();
|
---|
| 870 | }
|
---|
| 871 |
|
---|
| 872 | //reproduction --------------------------------------------
|
---|
| 873 | reprocounter += 1;
|
---|
[554] | 874 | if (reprocounter > secToSimSteps(ExpProperties.reproTimeSec))
|
---|
[422] | 875 | {
|
---|
| 876 | reprocounter = 0;
|
---|
[567] | 877 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 878 | {
|
---|
| 879 | reproduce_parents(s);
|
---|
| 880 | }
|
---|
[847] | 881 |
|
---|
[422] | 882 | }
|
---|
| 883 |
|
---|
| 884 | //check for extinction -----------------------------------------------
|
---|
| 885 | if (Populations[0].size == 0)
|
---|
| 886 | {
|
---|
[486] | 887 | if (ExpProperties.autorestart)
|
---|
[422] | 888 | {
|
---|
| 889 | Simulator.print("no more creatures, restarting...");
|
---|
| 890 | onExpInit();
|
---|
| 891 | }
|
---|
| 892 | else
|
---|
| 893 | {
|
---|
| 894 | Simulator.print("no more creatures, stopped.");
|
---|
| 895 | Simulator.stop();
|
---|
| 896 | }
|
---|
| 897 | }
|
---|
[486] | 898 | if (ExpProperties.maxSteps > 0)
|
---|
[432] | 899 | {
|
---|
[486] | 900 | if (Simulator.stepNumber >= ExpProperties.maxSteps)
|
---|
[432] | 901 | Simulator.stop();
|
---|
| 902 | }
|
---|
[422] | 903 | }
|
---|
| 904 |
|
---|
| 905 | function createStatistics()
|
---|
[847] | 906 | {
|
---|
[487] | 907 | var number = [];
|
---|
| 908 | var e_inc = [];
|
---|
[422] | 909 | var e_nut = 0.0;
|
---|
| 910 |
|
---|
[487] | 911 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 912 | {
|
---|
[847] | 913 | number.add([0, 0]); // [haplo][diplo]
|
---|
| 914 | e_inc.add([0, 0]);
|
---|
[487] | 915 | }
|
---|
| 916 |
|
---|
[422] | 917 | for (var i = 0; i < Populations[0].size; i++)
|
---|
| 918 | {
|
---|
| 919 | var cr = Populations[0].get(i);
|
---|
[476] | 920 | var gen = cr.data->lifeparams->gen;
|
---|
| 921 | var species = cr.data->lifeparams->species;
|
---|
[430] | 922 |
|
---|
[847] | 923 | number[species][gen] = number[species][gen] + 1;
|
---|
[430] | 924 | e_inc[species][gen] = e_inc[species][gen] + cr.energy;
|
---|
[422] | 925 | }
|
---|
| 926 |
|
---|
| 927 | for (var i = 0; i < Populations[1].size; i++)
|
---|
| 928 | {
|
---|
| 929 | var cr = Populations[1].get(i);
|
---|
| 930 | e_nut += cr.energy;
|
---|
| 931 | }
|
---|
| 932 |
|
---|
[487] | 933 | var log_numbers = [];
|
---|
| 934 | var log_energies = [];
|
---|
[422] | 935 |
|
---|
[487] | 936 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 937 | {
|
---|
| 938 | for (var p = 0; p < 2; p++)
|
---|
| 939 | {
|
---|
| 940 | log_numbers.add(number[s][p]);
|
---|
| 941 | log_energies.add(e_inc[s][p]);
|
---|
| 942 | }
|
---|
| 943 | }
|
---|
[847] | 944 |
|
---|
[487] | 945 | log_numbers.add(Populations[1].size);
|
---|
| 946 | log_energies.add(e_nut);
|
---|
| 947 |
|
---|
[847] | 948 | log(log_numbers, ExpProperties.logPref + "forams_log.txt");
|
---|
| 949 | log(log_energies, ExpProperties.logPref + "energies_log.txt");
|
---|
[422] | 950 | }
|
---|
| 951 |
|
---|
[380] | 952 | function log(tolog, fname)
|
---|
| 953 | {
|
---|
[847] | 954 | var f = File.appendDirect(fname, "forams data");
|
---|
[380] | 955 | f.writeString("" + Simulator.stepNumber);
|
---|
[401] | 956 | for (var i = 0; i < tolog.size; i++)
|
---|
[380] | 957 | {
|
---|
| 958 | f.writeString(";" + tolog[i]);
|
---|
| 959 | }
|
---|
| 960 | f.writeString("\n");
|
---|
| 961 | f.close();
|
---|
| 962 | }
|
---|
| 963 |
|
---|
[567] | 964 | function createLogVector(cr, value)
|
---|
| 965 | {
|
---|
| 966 | var vec = Vector.new();
|
---|
| 967 | for (var i = 0; i < species_genes.size; i++)
|
---|
| 968 | {
|
---|
| 969 | for (var j = 0; j < 2; j++)
|
---|
| 970 | {
|
---|
| 971 | vec.add(0);
|
---|
| 972 | }
|
---|
| 973 | if (cr.data->lifeparams->species == i)
|
---|
| 974 | {
|
---|
[847] | 975 | vec[i * 2 + cr.data->lifeparams->gen] = value;
|
---|
[567] | 976 | }
|
---|
| 977 | }
|
---|
| 978 | return vec;
|
---|
| 979 | }
|
---|
| 980 |
|
---|
| 981 |
|
---|
[422] | 982 | // -------------------------------- step end --------------------------------
|
---|
[479] | 983 | //TODO default params values in frams instead of microns/seconds
|
---|
[380] | 984 |
|
---|
[401] | 985 | @include "standard_events.inc"
|
---|
[380] | 986 |
|
---|
[401] | 987 | ~
|
---|
[380] | 988 |
|
---|
[486] | 989 | property:
|
---|
[444] | 990 | id:visualize
|
---|
| 991 | name:Show reticulopodia and nutrients
|
---|
[430] | 992 | type:d 0 1 0
|
---|
[554] | 993 | group:
|
---|
[430] | 994 |
|
---|
[486] | 995 | property:
|
---|
[434] | 996 | id:maxSteps
|
---|
[554] | 997 | name:Maximum number of steps
|
---|
[552] | 998 | type:d 0 10000000 0
|
---|
[554] | 999 | group:
|
---|
[432] | 1000 |
|
---|
[486] | 1001 | property:
|
---|
[567] | 1002 | id:scalingFactor
|
---|
| 1003 | name:Scaling factor for micrometers
|
---|
| 1004 | type:f 0 -1 0.01
|
---|
| 1005 | group:
|
---|
| 1006 |
|
---|
| 1007 | property:
|
---|
[554] | 1008 | id:logging
|
---|
| 1009 | name:Log statistics to file
|
---|
| 1010 | type:d 0 1 0
|
---|
| 1011 | group:
|
---|
| 1012 |
|
---|
| 1013 | property:
|
---|
[493] | 1014 | id:logPref
|
---|
| 1015 | name:Log prefix
|
---|
| 1016 | type:s
|
---|
| 1017 |
|
---|
| 1018 | property:
|
---|
[554] | 1019 | id:secPerStep
|
---|
| 1020 | name:Seconds per simulation step
|
---|
[568] | 1021 | help:~
|
---|
[570] | 1022 | Number of seconds of foraminifera time per simulation step.
|
---|
| 1023 | Lower values mean smoother animation.~
|
---|
[554] | 1024 | type:f 1 480 300
|
---|
| 1025 | flags: 16
|
---|
| 1026 | group:
|
---|
| 1027 |
|
---|
| 1028 | property:
|
---|
[474] | 1029 | id:foramSpeedMmPerMin
|
---|
| 1030 | name:Speed of foraminfera in mm/min
|
---|
[554] | 1031 | type:f 0.01 0.1 0.05
|
---|
[474] | 1032 | flags: 16
|
---|
| 1033 | group:Foraminifera
|
---|
| 1034 |
|
---|
[486] | 1035 | property:
|
---|
[554] | 1036 | id:dir_change_sec
|
---|
| 1037 | name:Number of seconds before direction change
|
---|
| 1038 | type:d 300 300000 6000
|
---|
[479] | 1039 | group:Foraminifera
|
---|
| 1040 |
|
---|
[486] | 1041 | property:
|
---|
[554] | 1042 | id:foramPop
|
---|
| 1043 | name:Initial forams population size
|
---|
| 1044 | type:d 1 1000 20
|
---|
[552] | 1045 | group:Foraminifera
|
---|
| 1046 |
|
---|
| 1047 | property:
|
---|
[554] | 1048 | id:gametoPeriodSec
|
---|
[479] | 1049 | name:Time of gametogenesis
|
---|
[554] | 1050 | type:f 300 300000 21600
|
---|
| 1051 | group:Reproduction
|
---|
[479] | 1052 |
|
---|
[486] | 1053 | property:
|
---|
[554] | 1054 | id:gametSuccessRate
|
---|
| 1055 | name:Ratio of successful gamets
|
---|
| 1056 | type:f 0.0001 0.01 0.001
|
---|
| 1057 | group:Reproduction
|
---|
[479] | 1058 |
|
---|
[486] | 1059 | property:
|
---|
[554] | 1060 | id:divisionCost
|
---|
| 1061 | name:Cost of division in pG
|
---|
| 1062 | type:f 15 25 20
|
---|
| 1063 | group:Reproduction
|
---|
[474] | 1064 |
|
---|
[486] | 1065 | property:
|
---|
[554] | 1066 | id:min_repro_energ_haplo
|
---|
[567] | 1067 | name:Min reproduction energy of haploid in pg
|
---|
| 1068 | type:f 0 -1 350000
|
---|
[554] | 1069 | group:Energy
|
---|
[380] | 1070 |
|
---|
[486] | 1071 | property:
|
---|
[554] | 1072 | id:min_repro_energ_diplo
|
---|
[567] | 1073 | name:Min reproduction energy of diploid in pg
|
---|
| 1074 | type:f 0 -1 600000
|
---|
[554] | 1075 | group:Energy
|
---|
[479] | 1076 |
|
---|
[486] | 1077 | property:
|
---|
[554] | 1078 | id:repro_prob
|
---|
| 1079 | name:Probability of reproduction
|
---|
| 1080 | type:f 0 1 0.8
|
---|
| 1081 | group:Reproduction
|
---|
[380] | 1082 |
|
---|
[486] | 1083 | property:
|
---|
[554] | 1084 | id:energies0_haplo
|
---|
| 1085 | name:Energy of offspring from diploid forams
|
---|
| 1086 | type:f 0 -1 20
|
---|
| 1087 | group:Energy
|
---|
[479] | 1088 |
|
---|
[486] | 1089 | property:
|
---|
[554] | 1090 | id:energies0_diplo
|
---|
| 1091 | name:Energy of offspring from diploid forams
|
---|
| 1092 | type:f 0 -1 1.25
|
---|
| 1093 | group:Energy
|
---|
| 1094 |
|
---|
| 1095 | property:
|
---|
[567] | 1096 | id:max_chamber_num_haplo
|
---|
| 1097 | name:Maximum number of haploid chambers
|
---|
| 1098 | type:f 1 50 35
|
---|
| 1099 | group:Energy
|
---|
| 1100 |
|
---|
| 1101 | property:
|
---|
| 1102 | id:max_chamber_num_diplo
|
---|
| 1103 | name:Maximum number of diploid chambers
|
---|
| 1104 | type:f 1 50 35
|
---|
| 1105 | group:Energy
|
---|
| 1106 |
|
---|
| 1107 | property:
|
---|
[554] | 1108 | id:crossprob
|
---|
| 1109 | name:Crossover probability
|
---|
| 1110 | type:f 0 1 0
|
---|
| 1111 | group:Reproduction
|
---|
| 1112 |
|
---|
| 1113 | property:
|
---|
| 1114 | id:mutationprob
|
---|
| 1115 | name:Mutation probability
|
---|
| 1116 | type:f 0 1 0
|
---|
| 1117 | group:Reproduction
|
---|
| 1118 |
|
---|
| 1119 | property:
|
---|
| 1120 | id:reproTimeSec
|
---|
| 1121 | name:Time before reproduction
|
---|
| 1122 | type:d 0 10000 720
|
---|
| 1123 | group:Reproduction
|
---|
| 1124 |
|
---|
| 1125 | property:
|
---|
| 1126 | id:chamberGrowthSec
|
---|
| 1127 | name:Time of the chamber growth in seconds
|
---|
[567] | 1128 | type:f 720 43200 43200
|
---|
[479] | 1129 | group:Foraminifera
|
---|
| 1130 |
|
---|
[486] | 1131 | property:
|
---|
[422] | 1132 | id:chamber_proculus_haplo
|
---|
[423] | 1133 | name:Size of proculus
|
---|
[422] | 1134 | type:f
|
---|
[421] | 1135 | group:Foraminifera
|
---|
[380] | 1136 |
|
---|
[486] | 1137 | property:
|
---|
[422] | 1138 | id:chamber_proculus_diplo
|
---|
[423] | 1139 | name:Size of proculus
|
---|
[422] | 1140 | type:f
|
---|
[380] | 1141 | group:Foraminifera
|
---|
| 1142 |
|
---|
[486] | 1143 | property:
|
---|
[422] | 1144 | id:hunted_prob
|
---|
| 1145 | name:Probability of being hunted
|
---|
| 1146 | type:f 0 1 0
|
---|
[554] | 1147 | group:Foraminifera
|
---|
[380] | 1148 |
|
---|
[486] | 1149 | property:
|
---|
[557] | 1150 | id:zone1_range
|
---|
[556] | 1151 | name:Zone 1 range in frams units
|
---|
[554] | 1152 | type:f 0 200 10
|
---|
[422] | 1153 | group:Foraminifera
|
---|
[380] | 1154 |
|
---|
[486] | 1155 | property:
|
---|
[422] | 1156 | id:zone2_range
|
---|
[556] | 1157 | name:Zone 2 range in frams units
|
---|
[554] | 1158 | type:f 0 3000 30
|
---|
[421] | 1159 | group:Foraminifera
|
---|
[380] | 1160 |
|
---|
[486] | 1161 | property:
|
---|
[554] | 1162 | id:chamberCostPerSec
|
---|
| 1163 | name:Cost of growning chamber per second
|
---|
| 1164 | type:f 0 1 0.000001
|
---|
| 1165 | group:Energy
|
---|
[380] | 1166 |
|
---|
[486] | 1167 | property:
|
---|
[475] | 1168 | id:e_death_level_haplo
|
---|
| 1169 | name:Minimal level of energy to sustain life of haploid
|
---|
[554] | 1170 | type:f 0 1 0.5
|
---|
| 1171 | group:Energy
|
---|
[475] | 1172 |
|
---|
[486] | 1173 | property:
|
---|
[475] | 1174 | id:e_death_level_diplo
|
---|
| 1175 | name:Minimal level of energy to sustain life of diploid
|
---|
[554] | 1176 | type:f 0 1 0.5
|
---|
| 1177 | group:Energy
|
---|
[475] | 1178 |
|
---|
[486] | 1179 | property:
|
---|
[422] | 1180 | id:energy_hib
|
---|
| 1181 | name:Energy used for hibernation during one step
|
---|
[554] | 1182 | type:f 0 1 0.0000001
|
---|
| 1183 | group:Energy
|
---|
[422] | 1184 |
|
---|
[486] | 1185 | property:
|
---|
[422] | 1186 | id:energy_move
|
---|
| 1187 | name:Energy used for movement during one step
|
---|
[554] | 1188 | type:f 0 1 0.0000005
|
---|
| 1189 | group:Energy
|
---|
[422] | 1190 |
|
---|
[486] | 1191 | property:
|
---|
[380] | 1192 | id:e_meta
|
---|
| 1193 | name:Idle metabolism
|
---|
[554] | 1194 | type:f 0 1 0.0000005
|
---|
[380] | 1195 | group:Energy
|
---|
[556] | 1196 | help:Foraminifera consumes this proportion of its energy in one time step
|
---|
[380] | 1197 |
|
---|
[486] | 1198 | property:
|
---|
[554] | 1199 | id:ingestion
|
---|
| 1200 | name:Ingestion rate
|
---|
| 1201 | type:f 0 -1 0.25
|
---|
| 1202 | group:Energy
|
---|
| 1203 |
|
---|
| 1204 | property:
|
---|
[493] | 1205 | id:nutrient_pop
|
---|
[554] | 1206 | name:Nutrient population
|
---|
[474] | 1207 | type:f 0 1000000
|
---|
[380] | 1208 | group:Energy
|
---|
| 1209 | help:How fast energy is created in the world
|
---|
| 1210 |
|
---|
[486] | 1211 | property:
|
---|
[554] | 1212 | id:energy_nut
|
---|
| 1213 | name:Nutrient energy
|
---|
| 1214 | type:f 0 10000000
|
---|
[481] | 1215 | group:Energy
|
---|
| 1216 |
|
---|
[486] | 1217 | property:
|
---|
[554] | 1218 | id:nutrientradius
|
---|
| 1219 | name:Nutrient size
|
---|
| 1220 | type:f 0.001 0.9 0.1
|
---|
[479] | 1221 | group:Energy
|
---|
| 1222 |
|
---|
[486] | 1223 | property:
|
---|
[554] | 1224 | id:picoCarbonPerMikro
|
---|
[556] | 1225 | name:Picograms of carbon in cubic micrometer
|
---|
[554] | 1226 | type:f 0 -1 0.13
|
---|
[380] | 1227 | group:Energy
|
---|
| 1228 |
|
---|
[486] | 1229 | property:
|
---|
[380] | 1230 | id:feedtrans
|
---|
[479] | 1231 | name:Energy transfer per second
|
---|
[554] | 1232 | type:f 0 1 0.001
|
---|
[380] | 1233 | group:Energy
|
---|
[422] | 1234 |
|
---|
[486] | 1235 | property:
|
---|
[590] | 1236 | id:foodflux
|
---|
| 1237 | name:POM flux in grams per second per square meter
|
---|
| 1238 | type:f 0 1 0.0000000075631
|
---|
[422] | 1239 | group:Energy
|
---|
| 1240 |
|
---|
[486] | 1241 | property:
|
---|
[590] | 1242 | id:foodfluxChange
|
---|
[554] | 1243 | name:Set variable feed rate
|
---|
| 1244 | type:f 0 -1 0
|
---|
[421] | 1245 | group:Energy
|
---|
| 1246 |
|
---|
[486] | 1247 | property:
|
---|
[422] | 1248 | id:stress
|
---|
| 1249 | name:Environmental stress
|
---|
| 1250 | type:d 0 1 1
|
---|
[554] | 1251 | group:
|
---|
[422] | 1252 |
|
---|
[486] | 1253 | property:
|
---|
[422] | 1254 | id:repro_trigger
|
---|
| 1255 | name:Reproduction trigger
|
---|
| 1256 | type:d 0 1 1
|
---|
[554] | 1257 | group:Reproduction
|
---|
[422] | 1258 |
|
---|
[486] | 1259 | property:
|
---|
[422] | 1260 | id:creath
|
---|
| 1261 | name:Creation height
|
---|
[554] | 1262 | type:f -1 50 -0.99
|
---|
[422] | 1263 | help:~
|
---|
| 1264 | Vertical position (above the surface) where new Forams are revived.
|
---|
| 1265 | Negative values are only used in the water area:
|
---|
| 1266 | 0 = at the surface
|
---|
| 1267 | -0.5 = half depth
|
---|
| 1268 | -1 = just above the bottom~
|
---|
| 1269 |
|
---|
[554] | 1270 | property:
|
---|
| 1271 | id:autorestart
|
---|
| 1272 | name:Restart after extinction
|
---|
| 1273 | help:Restart automatically this experiment after the last creature has died?
|
---|
| 1274 | type:d 0 1 0
|
---|
| 1275 |
|
---|
[421] | 1276 | state:
|
---|
| 1277 | id:nutrient
|
---|
[428] | 1278 | name:Nutrient locations
|
---|
[421] | 1279 | help:vector of vectors [x,y,energy]
|
---|
| 1280 | type:x
|
---|
| 1281 | flags:32
|
---|
| 1282 |
|
---|
[380] | 1283 | state:
|
---|
| 1284 | id:notes
|
---|
| 1285 | name:Notes
|
---|
| 1286 | type:s 1
|
---|
| 1287 | help:~
|
---|
| 1288 | You can write anything here
|
---|
| 1289 | (it will be saved to the experiment file)~
|
---|
| 1290 |
|
---|
| 1291 | state:
|
---|
| 1292 | id:totaltestedcr
|
---|
[421] | 1293 | name:Evaluated Forams
|
---|
| 1294 | help:Total number of the Forams evaluated in the experiment
|
---|
[380] | 1295 | type:d
|
---|
| 1296 | flags:16
|
---|