[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 retColors;
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| 27 | global curColor;
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[479] | 28 | global max_chamber_volume;
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[474] | 29 | global movePerStep;
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[479] | 30 | global nutrientenergywaiting;
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| 31 | global reprocounter;
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[481] | 32 | global changePeriod;
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| 33 | global phase;
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[493] | 34 | global nutrientSqrCm;
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[567] | 35 | global species_genes;
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| 36 | global max_chambers_def;
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| 37 | global foram_uid; //introduced because each replacement of a creature (while growing) would generate a new Creature.uid
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| 38 | global chamber_vis_denominator;
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| 39 | global curRadius;
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[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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[422] | 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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[422] | 88 | World.wrldbnd = 1;
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| 89 |
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[486] | 90 | //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
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[444] | 91 |
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[487] | 92 | //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files
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[493] | 93 | ExpProperties.logPref = "";
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[401] | 94 |
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[554] | 95 | //morphology
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[486] | 96 | ExpProperties.zone1_range = micronsToFrams(1000);
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| 97 | ExpProperties.zone2_range = micronsToFrams(3000);
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[567] | 98 | ExpProperties.chamber_proculus_haplo = micronsToFrams(20);
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| 99 | ExpProperties.chamber_proculus_diplo = micronsToFrams(10);
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| 100 | colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
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| 101 | retColors = ["1.0,1.0,1.0", "1.0,1.0,0.0"];
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| 102 | curColor = retColors[0];
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| 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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[552] | 107 | ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
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[554] | 108 | nutrientSqrCm = 10;
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[493] | 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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[557] | 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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[567] | 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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| 145 | for (var ploid = 0; ploid < 2; ploid++)
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| 146 | {
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| 147 | var rad = getPloidRadius(ploid);
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| 148 | for (var cham_num = 0; cham_num < getProperty(ploid,"max_chamber_num"); cham_num++)
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| 149 | {
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| 150 | max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num+1, density));
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| 151 | }
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| 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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| 164 | addInitialForam(spec, i);
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| 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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| 170 | nutrientenergywaiting = 0;
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| 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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[476] | 202 | cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
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| 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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[401] | 207 | cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_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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[380] | 226 | tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
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| 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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| 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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| 244 | var volumeInFrams = mg.volume();
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| 245 |
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| 246 | return volumeInFrams/Math.pow(ExpProperties.scalingFactor,3);
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| 247 | }
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| 248 |
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| 249 | function secToSimSteps(value_in_sec){
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| 250 | return value_in_sec/ExpProperties.secPerStep;
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| 251 | }
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| 252 |
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| 253 | function volumeInMicrons(radiusInFrams)
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| 254 | {
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| 255 | return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
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| 256 | }
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| 257 |
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| 258 | function energyFromVolume(base, isRadiusInFrams)
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| 259 | {
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| 260 | if (isRadiusInFrams == 1) //radius in frams
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| 261 | {
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| 262 | return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
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| 263 | }
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| 264 | else //volume in microns
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| 265 | {
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| 266 | return ExpProperties.picoCarbonPerMikro * base;
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| 267 | }
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| 268 | }
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| 269 |
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| 270 | function getMovePerStep()
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| 271 | {
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| 272 | return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
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| 273 | }
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| 274 |
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| 275 | function micronsToFrams(micrometers)
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| 276 | {
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| 277 | return micrometers*ExpProperties.scalingFactor;
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| 278 | }
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| 279 |
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| 280 | function framsToMicrons(framsworldunits)
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| 281 | {
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| 282 | return framsworldunits/ExpProperties.scalingFactor;
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| 283 | }
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| 284 |
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| 285 | function getProperty(gen, prop_id)
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| 286 | {
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| 287 | var ploid = "haplo";
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| 288 | if (gen == 1) ploid = "diplo";
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| 289 | return ExpProperties.[prop_id + "_" + ploid];
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| 290 | }
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| 291 |
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| 292 | function getGene(cr, gen_id, gen_set)
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| 293 | {
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| 294 | if (cr.data->lifeparams->gen == 0)
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| 295 | return cr.data->genes[gen_id];
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| 296 | else
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| 297 | return cr.data->genes[gen_set][gen_id];
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| 298 | }
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| 299 |
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| 300 | function getPloidRadius(ploid)
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| 301 | {
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| 302 | var radius = ExpProperties.chamber_proculus_haplo;
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| 303 | if (ploid == 1)
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| 304 | {
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| 305 | radius = ExpProperties.chamber_proculus_diplo;
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| 306 | }
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| 307 | return radius;
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| 308 | }
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| 309 |
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| 310 | function chamberNumFromEnergy(energy, ploid)
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| 311 | {
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| 312 | var chamber_num = max_chamber_volume[ploid].size;
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| 313 | for (var i = 0; i < chamber_num; i++)
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| 314 | {
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| 315 | if (energy < energyFromVolume(max_chamber_volume[ploid][i],0))
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| 316 | {
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| 317 | chamber_num = i+1;
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| 318 | break;
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| 319 | }
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| 320 | }
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| 321 |
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| 322 | return chamber_num;
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| 323 | }
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| 324 |
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| 325 | function addForam(species, iter, start_energy, ploid)
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| 326 | {
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| 327 | var chambernum = chamberNumFromEnergy(start_energy, ploid);
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| 328 | var radius = getPloidRadius(ploid);
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| 329 | var geno = create_genotype(radius, chambernum, colors[ploid], 1);
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| 330 | curColor = retColors[ploid];
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| 331 | var cr = Populations[0].add(geno);
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| 332 | cr.name = "Initial creature" + species + "_" + iter;
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| 333 | placeCreatureRandomly(cr, 0, 0);
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| 334 | cr.energy = start_energy;
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| 335 | setGenotype({"opt" : "birth", "cr" : cr, "gen" : ploid, "species" : species, "energy0" : cr.energy, "genes" : species_genes[species], "parentsuids" : ["c0"]});
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| 336 | if (ploid == 1)
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| 337 | {
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| 338 | cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
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| 339 | }
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| 340 | moveReticulopodia(cr);
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| 341 | }
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| 342 |
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| 343 | function addInitialForam(species, iter)
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| 344 | {
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| 345 | var ploid = 0;
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| 346 | if (Math.rnd01 > 0.5)
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| 347 | {
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| 348 | ploid = 1;
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| 349 | }
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| 350 | //add new foram with random energy bewtween starting energy and reproduction threshold
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| 351 | var repro_thr = species_genes[species]->min_repro_energies[ploid];
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| 352 | var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid),1),repro_thr-0.25*repro_thr);
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| 353 | addForam(species, iter, start_energy,ploid);
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| 354 | }
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| 355 |
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| 356 | //new species can be added as a dictionary with parameter values that are different than default values
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| 357 | function addSpecies(new_genes)
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| 358 | {
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| 359 | species_genes.add({"min_repro_energies" : [ExpProperties.min_repro_energ_haplo,ExpProperties.min_repro_energ_diplo], "energies0" : [ExpProperties.energies0_haplo, ExpProperties.energies0_diplo], "hibernation" : 0, "morphotype" : 0});
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| 360 | for (var i = 0; i < new_genes.size; i++)
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| 361 | {
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| 362 | var key = new_genes.getKey(i);
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| 363 | species_genes[species_genes.size-1][key] = new_genes[key];
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| 364 | }
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| 365 | }
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| 366 |
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[421] | 367 | // -------------------------------- foram begin -----------------------------------
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[380] | 368 |
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[479] | 369 | function setForamMeta(cr)
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[430] | 370 | {
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[479] | 371 | //percent of current energy
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[486] | 372 | cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
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[430] | 373 | }
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| 374 |
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| 375 | function lastChamberNum(cr)
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| 376 | {
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[567] | 377 | return cr.numparts;
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[430] | 378 | }
|
---|
| 379 |
|
---|
[479] | 380 | function getZoneRange(cr, zone_num)
|
---|
| 381 | {
|
---|
[486] | 382 | return ExpProperties.["zone"+zone_num+"_range"];
|
---|
[479] | 383 | }
|
---|
| 384 |
|
---|
[567] | 385 | function addReticulopodia(cr, radius)
|
---|
| 386 | {
|
---|
| 387 | if (reticulopodiaExists(cr))
|
---|
| 388 | {
|
---|
| 389 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
| 390 | }
|
---|
| 391 | 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");
|
---|
| 392 | cr.data->reticulopodiacreature = ret;
|
---|
| 393 | ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
|
---|
| 394 | ret.moveAbs(cr.center_x-radius, cr.center_y-radius, cr.center_z-radius);
|
---|
| 395 | }
|
---|
| 396 |
|
---|
[421] | 397 | function onForamsBorn(cr)
|
---|
| 398 | {
|
---|
[479] | 399 | setForamMeta(cr);
|
---|
[486] | 400 | if (ExpProperties.visualize == 1)
|
---|
[430] | 401 | {
|
---|
[567] | 402 | addReticulopodia(cr, curRadius);
|
---|
[430] | 403 | }
|
---|
[567] | 404 | moveReticulopodia(cr);
|
---|
[380] | 405 | }
|
---|
| 406 |
|
---|
[401] | 407 | function placeRandomlyNotColliding(cr)
|
---|
| 408 | {
|
---|
| 409 | var retry = 100; //try 100 times
|
---|
| 410 | while (retry--)
|
---|
| 411 | {
|
---|
| 412 | placeCreatureRandomly(cr, 0, 0);
|
---|
| 413 | if (!cr.boundingBoxCollisions(0))
|
---|
| 414 | return cr;
|
---|
| 415 | }
|
---|
| 416 |
|
---|
| 417 | Populations[0].delete(cr);
|
---|
| 418 | }
|
---|
| 419 |
|
---|
[567] | 420 | function reticulopodiaExists(cr)
|
---|
[444] | 421 | {
|
---|
| 422 | var has_ret = 0;
|
---|
| 423 |
|
---|
[476] | 424 | if (cr.data->reticulopodiacreature != null)
|
---|
[444] | 425 | {
|
---|
[476] | 426 | if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
|
---|
[444] | 427 | {
|
---|
| 428 | has_ret = 1;
|
---|
| 429 | }
|
---|
| 430 | }
|
---|
| 431 |
|
---|
| 432 | return has_ret;
|
---|
| 433 | }
|
---|
| 434 |
|
---|
[567] | 435 | function visualization(cr)
|
---|
[380] | 436 | {
|
---|
[567] | 437 | return reticulopodiaExists(cr);
|
---|
| 438 | }
|
---|
| 439 |
|
---|
| 440 | function foramGrow(cr, chamber_num, lastchambergrowth)
|
---|
| 441 | {
|
---|
| 442 | if ((chamber_num+1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
|
---|
[474] | 443 | {
|
---|
[493] | 444 | curColor = retColors[cr.data->lifeparams->gen];
|
---|
[567] | 445 | var ploid = cr.data->lifeparams->gen;
|
---|
| 446 | var geno = create_genotype(getPloidRadius(ploid), chamber_num+1, colors[ploid], lastchambergrowth);
|
---|
[474] | 447 | var cr2 = Populations[0].add(geno);
|
---|
[422] | 448 |
|
---|
[474] | 449 | cr2.energy0 = cr.energy;
|
---|
| 450 | cr2.energy = cr2.energy0;
|
---|
[422] | 451 |
|
---|
[554] | 452 | setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
|
---|
[567] | 453 | cr2.moveAbs(cr.pos_x, cr.pos_y,cr.pos_z);
|
---|
[479] | 454 | setForamMeta(cr2);
|
---|
[422] | 455 |
|
---|
[567] | 456 | if (reticulopodiaExists(cr))
|
---|
[474] | 457 | {
|
---|
[476] | 458 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[474] | 459 | }
|
---|
| 460 | Populations[0].delete(cr);
|
---|
[567] | 461 | return cr2;
|
---|
[430] | 462 | }
|
---|
[567] | 463 | return cr;
|
---|
[380] | 464 | }
|
---|
| 465 |
|
---|
[435] | 466 | function stepToNearest(cr)
|
---|
[380] | 467 | {
|
---|
| 468 | var p = cr.getMechPart(0);
|
---|
[479] | 469 | var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
|
---|
[380] | 470 |
|
---|
[401] | 471 | //if signals are received find the source of the nearest
|
---|
[380] | 472 | if (n.size > 0)
|
---|
| 473 | {
|
---|
| 474 | var i;
|
---|
| 475 | var mp;
|
---|
| 476 | var distvec = XYZ.new(0, 0, 0);
|
---|
| 477 | var dist;
|
---|
[470] | 478 | var mindist = 100000000000.0;
|
---|
[380] | 479 | var mindistvec = null;
|
---|
[430] | 480 | var eating = 0;
|
---|
[380] | 481 |
|
---|
[401] | 482 | for (i = 0; i < n.size; i++)
|
---|
[380] | 483 | {
|
---|
[430] | 484 | mp = n[i].value.getMechPart(0);
|
---|
[401] | 485 | distvec.set(mp.pos);
|
---|
| 486 | distvec.sub(p.pos);
|
---|
| 487 | dist = distvec.length;
|
---|
[479] | 488 | if (dist < getZoneRange(cr,1))
|
---|
[380] | 489 | {
|
---|
[430] | 490 | if (n[i].value != null)
|
---|
| 491 | {
|
---|
| 492 | energyTransfer(cr, n[i].value);
|
---|
| 493 | eating = 1;
|
---|
| 494 | }
|
---|
| 495 | }
|
---|
[476] | 496 | else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
|
---|
[430] | 497 | {
|
---|
[401] | 498 | mindist = dist;
|
---|
| 499 | mindistvec = distvec.clone();
|
---|
[380] | 500 | }
|
---|
| 501 | }
|
---|
| 502 |
|
---|
[476] | 503 | if (!eating && cr.data->lifeparams->hibernated == 0)
|
---|
[430] | 504 | {
|
---|
| 505 | mindistvec.normalize();
|
---|
[474] | 506 | mindistvec.scale(-1*movePerStep);
|
---|
[430] | 507 | cr.localDrive = mindistvec;
|
---|
| 508 | moveEnergyDec(cr);
|
---|
| 509 | }
|
---|
| 510 |
|
---|
[422] | 511 | return 1;
|
---|
[380] | 512 | }
|
---|
[422] | 513 |
|
---|
| 514 | else
|
---|
[474] | 515 | {
|
---|
[422] | 516 | return 0;
|
---|
[474] | 517 | }
|
---|
[422] | 518 | }
|
---|
[401] | 519 |
|
---|
[422] | 520 | function moveEnergyDec(cr)
|
---|
| 521 | {
|
---|
[476] | 522 | if (cr.data->lifeparams->hibernated == 0)
|
---|
[422] | 523 | {
|
---|
[479] | 524 | //percent of maximal energy
|
---|
[504] | 525 | cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
|
---|
[422] | 526 | }
|
---|
[421] | 527 | }
|
---|
[380] | 528 |
|
---|
[493] | 529 | function fence(pos, zone)
|
---|
[487] | 530 | {
|
---|
[496] | 531 | return Math.min(Math.max(0,pos),World.wrldsiz);
|
---|
[487] | 532 | }
|
---|
| 533 |
|
---|
[422] | 534 | function foramMove(cr)
|
---|
[421] | 535 | {
|
---|
[422] | 536 | //TODO moving inside sediment?
|
---|
[421] | 537 |
|
---|
[422] | 538 | //adjustment in z axis
|
---|
[554] | 539 | var change_direction = 0;
|
---|
| 540 | var new_x = fence(cr.pos_x, getZoneRange(cr, 1));
|
---|
| 541 | var new_y = fence(cr.pos_y,getZoneRange(cr, 1));
|
---|
[421] | 542 |
|
---|
[554] | 543 | if ((new_x != cr.pos_x) || (new_y != cr.pos_y) || (cr.data->lifeparams->dir_counter >= int(secToSimSteps(ExpProperties.dir_change_sec))))
|
---|
| 544 | {
|
---|
| 545 | change_direction = 1;
|
---|
| 546 | }
|
---|
| 547 |
|
---|
| 548 | cr.moveAbs(new_x, new_y, 0);
|
---|
| 549 |
|
---|
[430] | 550 | //are there any nutrients in zone 1 or 2?
|
---|
[401] | 551 | {
|
---|
[435] | 552 | var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
|
---|
[422] | 553 | if (moved==1)
|
---|
[430] | 554 | {
|
---|
[502] | 555 | moveReticulopodia(cr);
|
---|
[422] | 556 | return;
|
---|
| 557 | }
|
---|
[401] | 558 | }
|
---|
| 559 |
|
---|
[422] | 560 | //no nutrients in zone 2
|
---|
[487] | 561 | if (getGene(cr, "hibernation",0) == 1)
|
---|
[401] | 562 | {
|
---|
[430] | 563 | reverseHib(cr);
|
---|
[422] | 564 | cr.localDrive = XYZ.new(0,0,0);
|
---|
[380] | 565 | }
|
---|
[422] | 566 | //random move
|
---|
[554] | 567 | else if (change_direction == 1)
|
---|
[380] | 568 | {
|
---|
[476] | 569 | cr.data->lifeparams->dir = randomDir();
|
---|
[552] | 570 | cr.data->lifeparams->dir_counter = 0;
|
---|
[476] | 571 | cr.localDrive = cr.data->lifeparams->dir;
|
---|
[422] | 572 | moveEnergyDec(cr);
|
---|
| 573 | }
|
---|
[474] | 574 | else
|
---|
| 575 | {
|
---|
[476] | 576 | cr.localDrive = cr.data->lifeparams->dir;
|
---|
[474] | 577 | }
|
---|
[502] | 578 | moveReticulopodia(cr);
|
---|
[422] | 579 | }
|
---|
[401] | 580 |
|
---|
[502] | 581 | function moveReticulopodia(cr)
|
---|
| 582 | {
|
---|
| 583 | if (visualization(cr))
|
---|
| 584 | {
|
---|
| 585 | cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
|
---|
| 586 | cr.data->reticulopodiacreature.localDrive = cr.localDrive;
|
---|
| 587 | }
|
---|
| 588 | }
|
---|
| 589 |
|
---|
[474] | 590 | function randomDir()
|
---|
| 591 | {
|
---|
[486] | 592 | var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0);
|
---|
[474] | 593 | dir.normalize();
|
---|
| 594 | dir.scale(-1*movePerStep);
|
---|
| 595 | return dir;
|
---|
| 596 | }
|
---|
| 597 |
|
---|
[430] | 598 | function energyTransfer(cr1, cr2)
|
---|
[422] | 599 | {
|
---|
[430] | 600 | cr1.localDrive = XYZ.new(0,0,0);
|
---|
[510] | 601 | var e = ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
|
---|
[502] | 602 | //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
|
---|
[510] | 603 | var transferred = cr2.transferEnergyTo(cr1, e);
|
---|
| 604 | cr1.energy -= transferred*(1-ExpProperties.ingestion);
|
---|
[476] | 605 | if (cr1.data->lifeparams->hibernated == 1)
|
---|
[422] | 606 | {
|
---|
[430] | 607 | reverseHib(cr1);
|
---|
[422] | 608 | }
|
---|
| 609 | }
|
---|
[401] | 610 |
|
---|
[430] | 611 | function reverseHib(cr)
|
---|
| 612 | {
|
---|
[476] | 613 | if (cr.data->lifeparams->hibernated == 1)
|
---|
[430] | 614 | {
|
---|
[479] | 615 | setForamMeta(cr); //unhibernate
|
---|
[430] | 616 | }
|
---|
| 617 | else
|
---|
| 618 | {
|
---|
[486] | 619 | cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
|
---|
[430] | 620 | }
|
---|
[476] | 621 | cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
|
---|
[430] | 622 | }
|
---|
| 623 |
|
---|
[422] | 624 | function onForamsStep(cr)
|
---|
| 625 | {
|
---|
[479] | 626 | //checking for gametogenesis process
|
---|
| 627 | if (cr.data->lifeparams->division_time > 0)
|
---|
[444] | 628 | {
|
---|
[479] | 629 | cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
|
---|
[444] | 630 | }
|
---|
[479] | 631 | //checking for end of gametogenesis
|
---|
| 632 | else if (cr.data->lifeparams->division_time == 0)
|
---|
[422] | 633 | {
|
---|
[479] | 634 | //waiting for gamets fusion
|
---|
[422] | 635 | }
|
---|
[479] | 636 | //checking for chamber growth process
|
---|
| 637 | else if (cr.data->lifeparams->chamber_growth > 0)
|
---|
| 638 | {
|
---|
[567] | 639 | var chamber_time = Math.max(cr.data->lifeparams->chamber_growth-1,0);
|
---|
| 640 | cr.data->lifeparams->chamber_growth = chamber_time;
|
---|
[504] | 641 | cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
|
---|
[422] | 642 |
|
---|
[567] | 643 | if (visualization(cr))
|
---|
| 644 | {
|
---|
| 645 | var total_time = secToSimSteps(ExpProperties.chamberGrowthSec);
|
---|
| 646 | var ret_unit = total_time/chamber_vis_denominator;
|
---|
| 647 | var chamber_unit = total_time-ret_unit;
|
---|
| 648 |
|
---|
| 649 | if (chamber_time < ret_unit || chamber_time >= chamber_unit)
|
---|
| 650 | {
|
---|
| 651 | var new_rad = Math.min(Math.max((chamber_time%ret_unit)/ret_unit*getZoneRange(cr,1),0.01),getZoneRange(cr,1));
|
---|
| 652 |
|
---|
| 653 | if(chamber_time < ret_unit)
|
---|
| 654 | new_rad = getZoneRange(cr,1)-new_rad;
|
---|
| 655 |
|
---|
| 656 | addReticulopodia(cr,new_rad);
|
---|
| 657 | }
|
---|
| 658 | else
|
---|
| 659 | {
|
---|
| 660 | var new_rad = 1 - Math.min(Math.max((chamber_time-ret_unit)/chamber_unit,0.01),1);
|
---|
| 661 | curRadius = cr.data->reticulopodiacreature.getPart(1).sy;
|
---|
| 662 |
|
---|
| 663 | if (chamber_time == ret_unit){
|
---|
| 664 | new_rad == 1;
|
---|
| 665 | }
|
---|
| 666 |
|
---|
| 667 | var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen)-1, new_rad);
|
---|
| 668 | curRadius = getZoneRange(new_cr,1);
|
---|
| 669 |
|
---|
| 670 | if (chamber_time == 0)//checking for end of chamber growth process
|
---|
| 671 | {
|
---|
| 672 | new_cr.data->lifeparams->chamber_growth = -1;
|
---|
| 673 | }
|
---|
| 674 | }
|
---|
| 675 | }
|
---|
[479] | 676 | }
|
---|
| 677 | //checking for end of chamber growth process
|
---|
[567] | 678 | else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr)==0)
|
---|
| 679 | {
|
---|
| 680 | foramGrow(cr, lastChamberNum(cr), 1);
|
---|
[479] | 681 | cr.data->lifeparams->chamber_growth = -1;
|
---|
| 682 | //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
|
---|
[430] | 683 | }
|
---|
[479] | 684 | else
|
---|
[422] | 685 | {
|
---|
[479] | 686 | //update of metabolism rate
|
---|
| 687 | if (cr.data->lifeparams->hibernated == 0)
|
---|
[401] | 688 | {
|
---|
[479] | 689 | setForamMeta(cr);
|
---|
| 690 | }
|
---|
| 691 |
|
---|
| 692 | if (deathConditions(cr) == 1)
|
---|
| 693 | {
|
---|
[493] | 694 | if (ExpProperties.logging == 1)
|
---|
| 695 | {
|
---|
| 696 | log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
|
---|
[552] | 697 | log(createLogVector(cr, cr.lifespan),ExpProperties.logPref+"lifespan_log.txt");
|
---|
[493] | 698 | }
|
---|
[479] | 699 | Populations[0].kill(cr);
|
---|
| 700 | return;
|
---|
| 701 | }
|
---|
| 702 |
|
---|
[552] | 703 | //update direction change counter
|
---|
| 704 | cr.data->lifeparams->dir_counter += 1;
|
---|
| 705 |
|
---|
[479] | 706 | foramMove(cr);
|
---|
| 707 |
|
---|
| 708 | var repro = foramReproduce(cr);
|
---|
| 709 | if (repro == 1)
|
---|
| 710 | {
|
---|
| 711 | return;
|
---|
| 712 | }
|
---|
| 713 |
|
---|
| 714 | cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
|
---|
| 715 |
|
---|
| 716 | //cheking conditions of chamber growth process start
|
---|
[567] | 717 | if (lastChamberNum(cr) < max_chamber_volume[cr.data->lifeparams->gen].size)
|
---|
[479] | 718 | {
|
---|
[567] | 719 | if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)-1],0)))
|
---|
[479] | 720 | {
|
---|
[554] | 721 | cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
|
---|
[479] | 722 | }
|
---|
| 723 | }
|
---|
[430] | 724 | }
|
---|
[380] | 725 | }
|
---|
| 726 |
|
---|
[422] | 727 | function deathConditions(cr)
|
---|
| 728 | {
|
---|
[486] | 729 | if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
|
---|
[479] | 730 | {
|
---|
[422] | 731 | return 1;
|
---|
[479] | 732 | }
|
---|
[422] | 733 | else
|
---|
| 734 | return 0;
|
---|
| 735 | }
|
---|
| 736 |
|
---|
[421] | 737 | function onForamsDied(cr)
|
---|
[380] | 738 | {
|
---|
[444] | 739 | if (visualization(cr))
|
---|
[430] | 740 | {
|
---|
[476] | 741 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[430] | 742 | }
|
---|
[380] | 743 | //fossilization
|
---|
| 744 | var geno = GenePools[0].add(cr.genotype);
|
---|
[476] | 745 | geno.data->genes = cr.data->genes;
|
---|
| 746 | geno.data->lifeparams = cr.data->lifeparams;
|
---|
[486] | 747 | if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
|
---|
[380] | 748 | ExpState.totaltestedcr++;
|
---|
| 749 | }
|
---|
| 750 |
|
---|
[421] | 751 | // --------------------------------foram end -------------------------------------
|
---|
[380] | 752 |
|
---|
[421] | 753 | // -------------------------------- nutrient begin --------------------------------
|
---|
[380] | 754 |
|
---|
[479] | 755 | function createNutrientGenotype(nutrientradius)
|
---|
[422] | 756 | {
|
---|
[524] | 757 | 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] | 758 | }
|
---|
| 759 |
|
---|
[421] | 760 | function onNutrientsStep(cr)
|
---|
[380] | 761 | {
|
---|
[444] | 762 | cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
|
---|
[380] | 763 | }
|
---|
| 764 |
|
---|
[421] | 765 | function addNutrient()
|
---|
[380] | 766 | {
|
---|
[486] | 767 | var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
|
---|
[380] | 768 |
|
---|
[421] | 769 | cr.name = "Nutrients";
|
---|
[380] | 770 | cr.idleen = 0;
|
---|
[486] | 771 | cr.energy0 = ExpProperties.energy_nut;
|
---|
[416] | 772 | cr.energy = cr.energy0;
|
---|
[421] | 773 | cr.signals.add("nutrient");
|
---|
[380] | 774 |
|
---|
[430] | 775 | cr.signals[0].value = cr;
|
---|
[380] | 776 |
|
---|
[422] | 777 | placeCreatureRandomly(cr, 0, 0);
|
---|
[486] | 778 | if (ExpProperties.visualize == 1)
|
---|
[444] | 779 | {
|
---|
[486] | 780 | var nutsize = ExpProperties.nutrientradius*10;
|
---|
[555] | 781 | 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] | 782 | cr.data->reticulopodiacreature = nut;
|
---|
[444] | 783 | nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
|
---|
| 784 | }
|
---|
[380] | 785 | }
|
---|
| 786 |
|
---|
[444] | 787 | function onNutrientsDied(cr)
|
---|
| 788 | {
|
---|
| 789 | if (visualization(cr))
|
---|
| 790 | {
|
---|
[476] | 791 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[444] | 792 | }
|
---|
| 793 | }
|
---|
| 794 |
|
---|
[422] | 795 | function nutrientGrowth()
|
---|
[380] | 796 | {
|
---|
[486] | 797 | if (ExpProperties.foodPeriodChange > 0)
|
---|
[481] | 798 | {
|
---|
| 799 | changePeriod += 1;
|
---|
[554] | 800 | if (phase=="low" && changePeriod >= secToSimSteps(23328000)) //9 months
|
---|
[481] | 801 | {
|
---|
[486] | 802 | ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
|
---|
[481] | 803 | phase = "high";
|
---|
| 804 | changePeriod = 0;
|
---|
| 805 | }
|
---|
| 806 |
|
---|
[554] | 807 | else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
|
---|
[481] | 808 | {
|
---|
[486] | 809 | ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
|
---|
[481] | 810 | phase = "low";
|
---|
| 811 | changePeriod = 0;
|
---|
| 812 | }
|
---|
| 813 | }
|
---|
[474] | 814 | nutrientenergywaiting = nutrientenergywaiting + 1;
|
---|
[554] | 815 | if (nutrientenergywaiting >= secToSimSteps(ExpProperties.foodperiod))
|
---|
[380] | 816 | {
|
---|
[493] | 817 | for (var i = 0; i < ExpProperties.nutrient_pop; i++)
|
---|
[432] | 818 | {
|
---|
[422] | 819 | addNutrient();
|
---|
| 820 | }
|
---|
| 821 |
|
---|
| 822 | nutrientenergywaiting = 0.0;
|
---|
| 823 | Simulator.checkpoint();
|
---|
[493] | 824 |
|
---|
| 825 | if (ExpProperties.logging == 1)
|
---|
| 826 | {
|
---|
| 827 | log([ExpProperties.nutrient_pop],ExpProperties.logPref+"nutrients_log.txt");
|
---|
| 828 | }
|
---|
[380] | 829 | }
|
---|
[493] | 830 |
|
---|
[380] | 831 | }
|
---|
| 832 |
|
---|
[421] | 833 | // -------------------------------- nutrient end --------------------------------
|
---|
[380] | 834 |
|
---|
[422] | 835 | // -------------------------------- step begin --------------------------------
|
---|
[380] | 836 |
|
---|
[422] | 837 | function onStep()
|
---|
| 838 | {
|
---|
[432] | 839 |
|
---|
| 840 | nutrientGrowth();
|
---|
[486] | 841 | if (ExpProperties.logging == 1)
|
---|
[422] | 842 | {
|
---|
| 843 | createStatistics();
|
---|
| 844 | }
|
---|
| 845 |
|
---|
| 846 | //reproduction --------------------------------------------
|
---|
| 847 | reprocounter += 1;
|
---|
[554] | 848 | if (reprocounter > secToSimSteps(ExpProperties.reproTimeSec))
|
---|
[422] | 849 | {
|
---|
| 850 | reprocounter = 0;
|
---|
[567] | 851 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 852 | {
|
---|
| 853 | reproduce_parents(s);
|
---|
| 854 | }
|
---|
| 855 |
|
---|
[422] | 856 | }
|
---|
| 857 |
|
---|
| 858 | //check for extinction -----------------------------------------------
|
---|
| 859 | if (Populations[0].size == 0)
|
---|
| 860 | {
|
---|
[486] | 861 | if (ExpProperties.autorestart)
|
---|
[422] | 862 | {
|
---|
| 863 | Simulator.print("no more creatures, restarting...");
|
---|
| 864 | onExpInit();
|
---|
| 865 | }
|
---|
| 866 | else
|
---|
| 867 | {
|
---|
| 868 | Simulator.print("no more creatures, stopped.");
|
---|
| 869 | Simulator.stop();
|
---|
| 870 | }
|
---|
| 871 | }
|
---|
[486] | 872 | if (ExpProperties.maxSteps > 0)
|
---|
[432] | 873 | {
|
---|
[486] | 874 | if (Simulator.stepNumber >= ExpProperties.maxSteps)
|
---|
[432] | 875 | Simulator.stop();
|
---|
| 876 | }
|
---|
[422] | 877 | }
|
---|
| 878 |
|
---|
| 879 | function createStatistics()
|
---|
| 880 | {
|
---|
[487] | 881 | var number = [];
|
---|
| 882 | var e_inc = [];
|
---|
[422] | 883 | var e_nut = 0.0;
|
---|
| 884 |
|
---|
[487] | 885 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 886 | {
|
---|
| 887 | number.add([0,0]);// [haplo][diplo]
|
---|
| 888 | e_inc.add([0,0]);
|
---|
| 889 | }
|
---|
| 890 |
|
---|
[422] | 891 | for (var i = 0; i < Populations[0].size; i++)
|
---|
| 892 | {
|
---|
| 893 | var cr = Populations[0].get(i);
|
---|
[476] | 894 | var gen = cr.data->lifeparams->gen;
|
---|
| 895 | var species = cr.data->lifeparams->species;
|
---|
[430] | 896 |
|
---|
| 897 | number[species][gen] = number[species][gen] + 1;
|
---|
| 898 | e_inc[species][gen] = e_inc[species][gen] + cr.energy;
|
---|
[422] | 899 | }
|
---|
| 900 |
|
---|
| 901 | for (var i = 0; i < Populations[1].size; i++)
|
---|
| 902 | {
|
---|
| 903 | var cr = Populations[1].get(i);
|
---|
| 904 | e_nut += cr.energy;
|
---|
| 905 | }
|
---|
| 906 |
|
---|
[487] | 907 | var log_numbers = [];
|
---|
| 908 | var log_energies = [];
|
---|
[422] | 909 |
|
---|
[487] | 910 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 911 | {
|
---|
| 912 | for (var p = 0; p < 2; p++)
|
---|
| 913 | {
|
---|
| 914 | log_numbers.add(number[s][p]);
|
---|
| 915 | log_energies.add(e_inc[s][p]);
|
---|
| 916 | }
|
---|
| 917 | }
|
---|
| 918 |
|
---|
| 919 | log_numbers.add(Populations[1].size);
|
---|
| 920 | log_energies.add(e_nut);
|
---|
| 921 |
|
---|
[493] | 922 | log(log_numbers, ExpProperties.logPref+"forams_log.txt");
|
---|
| 923 | log(log_energies, ExpProperties.logPref+"energies_log.txt");
|
---|
[422] | 924 | }
|
---|
| 925 |
|
---|
[380] | 926 | function log(tolog, fname)
|
---|
| 927 | {
|
---|
[430] | 928 | var f = File.appendDirect(fname, "forams data");
|
---|
[380] | 929 | f.writeString("" + Simulator.stepNumber);
|
---|
[401] | 930 | for (var i = 0; i < tolog.size; i++)
|
---|
[380] | 931 | {
|
---|
| 932 | f.writeString(";" + tolog[i]);
|
---|
| 933 | }
|
---|
| 934 | f.writeString("\n");
|
---|
| 935 | f.close();
|
---|
| 936 | }
|
---|
| 937 |
|
---|
[567] | 938 | function createLogVector(cr, value)
|
---|
| 939 | {
|
---|
| 940 | var vec = Vector.new();
|
---|
| 941 | for (var i = 0; i < species_genes.size; i++)
|
---|
| 942 | {
|
---|
| 943 | for (var j = 0; j < 2; j++)
|
---|
| 944 | {
|
---|
| 945 | vec.add(0);
|
---|
| 946 | }
|
---|
| 947 | if (cr.data->lifeparams->species == i)
|
---|
| 948 | {
|
---|
| 949 | vec[i*2+cr.data->lifeparams->gen] = value;
|
---|
| 950 | }
|
---|
| 951 | }
|
---|
| 952 | return vec;
|
---|
| 953 | }
|
---|
| 954 |
|
---|
| 955 |
|
---|
[422] | 956 | // -------------------------------- step end --------------------------------
|
---|
[479] | 957 | //TODO default params values in frams instead of microns/seconds
|
---|
[380] | 958 |
|
---|
[401] | 959 | @include "standard_events.inc"
|
---|
[380] | 960 |
|
---|
[401] | 961 | ~
|
---|
[380] | 962 |
|
---|
[486] | 963 | property:
|
---|
[444] | 964 | id:visualize
|
---|
| 965 | name:Show reticulopodia and nutrients
|
---|
[430] | 966 | type:d 0 1 0
|
---|
[554] | 967 | group:
|
---|
[430] | 968 |
|
---|
[486] | 969 | property:
|
---|
[434] | 970 | id:maxSteps
|
---|
[554] | 971 | name:Maximum number of steps
|
---|
[552] | 972 | type:d 0 10000000 0
|
---|
[554] | 973 | group:
|
---|
[432] | 974 |
|
---|
[486] | 975 | property:
|
---|
[567] | 976 | id:scalingFactor
|
---|
| 977 | name:Scaling factor for micrometers
|
---|
| 978 | type:f 0 -1 0.01
|
---|
| 979 | group:
|
---|
| 980 |
|
---|
| 981 | property:
|
---|
[554] | 982 | id:logging
|
---|
| 983 | name:Log statistics to file
|
---|
| 984 | type:d 0 1 0
|
---|
| 985 | group:
|
---|
| 986 |
|
---|
| 987 | property:
|
---|
[493] | 988 | id:logPref
|
---|
| 989 | name:Log prefix
|
---|
| 990 | type:s
|
---|
| 991 |
|
---|
| 992 | property:
|
---|
[554] | 993 | id:secPerStep
|
---|
| 994 | name:Seconds per simulation step
|
---|
[568] | 995 | help:~
|
---|
[570] | 996 | Number of seconds of foraminifera time per simulation step.
|
---|
| 997 | Lower values mean smoother animation.~
|
---|
[554] | 998 | type:f 1 480 300
|
---|
| 999 | flags: 16
|
---|
| 1000 | group:
|
---|
| 1001 |
|
---|
| 1002 | property:
|
---|
[474] | 1003 | id:foramSpeedMmPerMin
|
---|
| 1004 | name:Speed of foraminfera in mm/min
|
---|
[554] | 1005 | type:f 0.01 0.1 0.05
|
---|
[474] | 1006 | flags: 16
|
---|
| 1007 | group:Foraminifera
|
---|
| 1008 |
|
---|
[486] | 1009 | property:
|
---|
[554] | 1010 | id:dir_change_sec
|
---|
| 1011 | name:Number of seconds before direction change
|
---|
| 1012 | type:d 300 300000 6000
|
---|
[479] | 1013 | group:Foraminifera
|
---|
| 1014 |
|
---|
[486] | 1015 | property:
|
---|
[554] | 1016 | id:foramPop
|
---|
| 1017 | name:Initial forams population size
|
---|
| 1018 | type:d 1 1000 20
|
---|
[552] | 1019 | group:Foraminifera
|
---|
| 1020 |
|
---|
| 1021 | property:
|
---|
[554] | 1022 | id:gametoPeriodSec
|
---|
[479] | 1023 | name:Time of gametogenesis
|
---|
[554] | 1024 | type:f 300 300000 21600
|
---|
| 1025 | group:Reproduction
|
---|
[479] | 1026 |
|
---|
[486] | 1027 | property:
|
---|
[554] | 1028 | id:gametSuccessRate
|
---|
| 1029 | name:Ratio of successful gamets
|
---|
| 1030 | type:f 0.0001 0.01 0.001
|
---|
| 1031 | group:Reproduction
|
---|
[479] | 1032 |
|
---|
[486] | 1033 | property:
|
---|
[554] | 1034 | id:divisionCost
|
---|
| 1035 | name:Cost of division in pG
|
---|
| 1036 | type:f 15 25 20
|
---|
| 1037 | group:Reproduction
|
---|
[474] | 1038 |
|
---|
[486] | 1039 | property:
|
---|
[554] | 1040 | id:min_repro_energ_haplo
|
---|
[567] | 1041 | name:Min reproduction energy of haploid in pg
|
---|
| 1042 | type:f 0 -1 350000
|
---|
[554] | 1043 | group:Energy
|
---|
[380] | 1044 |
|
---|
[486] | 1045 | property:
|
---|
[554] | 1046 | id:min_repro_energ_diplo
|
---|
[567] | 1047 | name:Min reproduction energy of diploid in pg
|
---|
| 1048 | type:f 0 -1 600000
|
---|
[554] | 1049 | group:Energy
|
---|
[479] | 1050 |
|
---|
[486] | 1051 | property:
|
---|
[554] | 1052 | id:repro_prob
|
---|
| 1053 | name:Probability of reproduction
|
---|
| 1054 | type:f 0 1 0.8
|
---|
| 1055 | group:Reproduction
|
---|
[380] | 1056 |
|
---|
[486] | 1057 | property:
|
---|
[554] | 1058 | id:energies0_haplo
|
---|
| 1059 | name:Energy of offspring from diploid forams
|
---|
| 1060 | type:f 0 -1 20
|
---|
| 1061 | group:Energy
|
---|
[479] | 1062 |
|
---|
[486] | 1063 | property:
|
---|
[554] | 1064 | id:energies0_diplo
|
---|
| 1065 | name:Energy of offspring from diploid forams
|
---|
| 1066 | type:f 0 -1 1.25
|
---|
| 1067 | group:Energy
|
---|
| 1068 |
|
---|
| 1069 | property:
|
---|
[567] | 1070 | id:max_chamber_num_haplo
|
---|
| 1071 | name:Maximum number of haploid chambers
|
---|
| 1072 | type:f 1 50 35
|
---|
| 1073 | group:Energy
|
---|
| 1074 |
|
---|
| 1075 | property:
|
---|
| 1076 | id:max_chamber_num_diplo
|
---|
| 1077 | name:Maximum number of diploid chambers
|
---|
| 1078 | type:f 1 50 35
|
---|
| 1079 | group:Energy
|
---|
| 1080 |
|
---|
| 1081 |
|
---|
| 1082 | property:
|
---|
[554] | 1083 | id:crossprob
|
---|
| 1084 | name:Crossover probability
|
---|
| 1085 | type:f 0 1 0
|
---|
| 1086 | group:Reproduction
|
---|
| 1087 |
|
---|
| 1088 | property:
|
---|
| 1089 | id:mutationprob
|
---|
| 1090 | name:Mutation probability
|
---|
| 1091 | type:f 0 1 0
|
---|
| 1092 | group:Reproduction
|
---|
| 1093 |
|
---|
| 1094 | property:
|
---|
| 1095 | id:reproTimeSec
|
---|
| 1096 | name:Time before reproduction
|
---|
| 1097 | type:d 0 10000 720
|
---|
| 1098 | group:Reproduction
|
---|
| 1099 |
|
---|
| 1100 | property:
|
---|
| 1101 | id:chamberGrowthSec
|
---|
| 1102 | name:Time of the chamber growth in seconds
|
---|
[567] | 1103 | type:f 720 43200 43200
|
---|
[479] | 1104 | group:Foraminifera
|
---|
| 1105 |
|
---|
[486] | 1106 | property:
|
---|
[422] | 1107 | id:chamber_proculus_haplo
|
---|
[423] | 1108 | name:Size of proculus
|
---|
[422] | 1109 | type:f
|
---|
[421] | 1110 | group:Foraminifera
|
---|
[380] | 1111 |
|
---|
[486] | 1112 | property:
|
---|
[422] | 1113 | id:chamber_proculus_diplo
|
---|
[423] | 1114 | name:Size of proculus
|
---|
[422] | 1115 | type:f
|
---|
[380] | 1116 | group:Foraminifera
|
---|
| 1117 |
|
---|
[486] | 1118 | property:
|
---|
[422] | 1119 | id:hunted_prob
|
---|
| 1120 | name:Probability of being hunted
|
---|
| 1121 | type:f 0 1 0
|
---|
[554] | 1122 | group:Foraminifera
|
---|
[380] | 1123 |
|
---|
[486] | 1124 | property:
|
---|
[557] | 1125 | id:zone1_range
|
---|
[556] | 1126 | name:Zone 1 range in frams units
|
---|
[554] | 1127 | type:f 0 200 10
|
---|
[422] | 1128 | group:Foraminifera
|
---|
[380] | 1129 |
|
---|
[486] | 1130 | property:
|
---|
[422] | 1131 | id:zone2_range
|
---|
[556] | 1132 | name:Zone 2 range in frams units
|
---|
[554] | 1133 | type:f 0 3000 30
|
---|
[421] | 1134 | group:Foraminifera
|
---|
[380] | 1135 |
|
---|
[486] | 1136 | property:
|
---|
[554] | 1137 | id:chamberCostPerSec
|
---|
| 1138 | name:Cost of growning chamber per second
|
---|
| 1139 | type:f 0 1 0.000001
|
---|
| 1140 | group:Energy
|
---|
[380] | 1141 |
|
---|
[486] | 1142 | property:
|
---|
[475] | 1143 | id:e_death_level_haplo
|
---|
| 1144 | name:Minimal level of energy to sustain life of haploid
|
---|
[554] | 1145 | type:f 0 1 0.5
|
---|
| 1146 | group:Energy
|
---|
[475] | 1147 |
|
---|
[486] | 1148 | property:
|
---|
[475] | 1149 | id:e_death_level_diplo
|
---|
| 1150 | name:Minimal level of energy to sustain life of diploid
|
---|
[554] | 1151 | type:f 0 1 0.5
|
---|
| 1152 | group:Energy
|
---|
[475] | 1153 |
|
---|
[486] | 1154 | property:
|
---|
[422] | 1155 | id:energy_hib
|
---|
| 1156 | name:Energy used for hibernation during one step
|
---|
[554] | 1157 | type:f 0 1 0.0000001
|
---|
| 1158 | group:Energy
|
---|
[422] | 1159 |
|
---|
[486] | 1160 | property:
|
---|
[422] | 1161 | id:energy_move
|
---|
| 1162 | name:Energy used for movement during one step
|
---|
[554] | 1163 | type:f 0 1 0.0000005
|
---|
| 1164 | group:Energy
|
---|
[422] | 1165 |
|
---|
[486] | 1166 | property:
|
---|
[380] | 1167 | id:e_meta
|
---|
| 1168 | name:Idle metabolism
|
---|
[554] | 1169 | type:f 0 1 0.0000005
|
---|
[380] | 1170 | group:Energy
|
---|
[556] | 1171 | help:Foraminifera consumes this proportion of its energy in one time step
|
---|
[380] | 1172 |
|
---|
[486] | 1173 | property:
|
---|
[554] | 1174 | id:ingestion
|
---|
| 1175 | name:Ingestion rate
|
---|
| 1176 | type:f 0 -1 0.25
|
---|
| 1177 | group:Energy
|
---|
| 1178 |
|
---|
| 1179 | property:
|
---|
[493] | 1180 | id:nutrient_pop
|
---|
[554] | 1181 | name:Nutrient population
|
---|
[474] | 1182 | type:f 0 1000000
|
---|
[380] | 1183 | group:Energy
|
---|
| 1184 | help:How fast energy is created in the world
|
---|
| 1185 |
|
---|
[486] | 1186 | property:
|
---|
[554] | 1187 | id:energy_nut
|
---|
| 1188 | name:Nutrient energy
|
---|
| 1189 | type:f 0 10000000
|
---|
[481] | 1190 | group:Energy
|
---|
| 1191 |
|
---|
[486] | 1192 | property:
|
---|
[554] | 1193 | id:nutrientradius
|
---|
| 1194 | name:Nutrient size
|
---|
| 1195 | type:f 0.001 0.9 0.1
|
---|
[479] | 1196 | group:Energy
|
---|
| 1197 |
|
---|
[486] | 1198 | property:
|
---|
[554] | 1199 | id:picoCarbonPerMikro
|
---|
[556] | 1200 | name:Picograms of carbon in cubic micrometer
|
---|
[554] | 1201 | type:f 0 -1 0.13
|
---|
[380] | 1202 | group:Energy
|
---|
| 1203 |
|
---|
[486] | 1204 | property:
|
---|
[380] | 1205 | id:feedtrans
|
---|
[479] | 1206 | name:Energy transfer per second
|
---|
[554] | 1207 | type:f 0 1 0.001
|
---|
[380] | 1208 | group:Energy
|
---|
[422] | 1209 |
|
---|
[486] | 1210 | property:
|
---|
[479] | 1211 | id:foodperiod
|
---|
| 1212 | name:Time between food occurrences
|
---|
[554] | 1213 | type:f 0 1000000 14400
|
---|
[422] | 1214 | group:Energy
|
---|
| 1215 |
|
---|
[486] | 1216 | property:
|
---|
[554] | 1217 | id:foodPeriodChange
|
---|
| 1218 | name:Set variable feed rate
|
---|
| 1219 | type:f 0 -1 0
|
---|
[421] | 1220 | group:Energy
|
---|
| 1221 |
|
---|
[486] | 1222 | property:
|
---|
[422] | 1223 | id:stress
|
---|
| 1224 | name:Environmental stress
|
---|
| 1225 | type:d 0 1 1
|
---|
[554] | 1226 | group:
|
---|
[422] | 1227 |
|
---|
[486] | 1228 | property:
|
---|
[422] | 1229 | id:repro_trigger
|
---|
| 1230 | name:Reproduction trigger
|
---|
| 1231 | type:d 0 1 1
|
---|
[554] | 1232 | group:Reproduction
|
---|
[422] | 1233 |
|
---|
[486] | 1234 | property:
|
---|
[422] | 1235 | id:creath
|
---|
| 1236 | name:Creation height
|
---|
[554] | 1237 | type:f -1 50 -0.99
|
---|
[422] | 1238 | help:~
|
---|
| 1239 | Vertical position (above the surface) where new Forams are revived.
|
---|
| 1240 | Negative values are only used in the water area:
|
---|
| 1241 | 0 = at the surface
|
---|
| 1242 | -0.5 = half depth
|
---|
| 1243 | -1 = just above the bottom~
|
---|
| 1244 |
|
---|
[554] | 1245 | property:
|
---|
| 1246 | id:autorestart
|
---|
| 1247 | name:Restart after extinction
|
---|
| 1248 | help:Restart automatically this experiment after the last creature has died?
|
---|
| 1249 | type:d 0 1 0
|
---|
| 1250 |
|
---|
[421] | 1251 | state:
|
---|
| 1252 | id:nutrient
|
---|
[428] | 1253 | name:Nutrient locations
|
---|
[421] | 1254 | help:vector of vectors [x,y,energy]
|
---|
| 1255 | type:x
|
---|
| 1256 | flags:32
|
---|
| 1257 |
|
---|
[380] | 1258 | state:
|
---|
| 1259 | id:notes
|
---|
| 1260 | name:Notes
|
---|
| 1261 | type:s 1
|
---|
| 1262 | help:~
|
---|
| 1263 | You can write anything here
|
---|
| 1264 | (it will be saved to the experiment file)~
|
---|
| 1265 |
|
---|
| 1266 | state:
|
---|
| 1267 | id:totaltestedcr
|
---|
[421] | 1268 | name:Evaluated Forams
|
---|
| 1269 | help:Total number of the Forams evaluated in the experiment
|
---|
[380] | 1270 | type:d
|
---|
| 1271 | flags:16
|
---|