[380] | 1 | expdef:
|
---|
[406] | 2 | name:Reproduction of benthic foraminifera
|
---|
[380] | 3 | info:~
|
---|
[434] | 4 | Basic information about this simulation:
|
---|
| 5 | www.framsticks.com/foraminifera
|
---|
| 6 |
|
---|
| 7 | Technical information:
|
---|
[476] | 8 | Genes and parameter values which control reproduction are stored in data->genes and data->lifeparams fields.
|
---|
[380] | 9 |
|
---|
[476] | 10 | genes:
|
---|
[402] | 11 | genes which are not encoded in Ff genotype:
|
---|
[422] | 12 | min_repro_energy - Minimum energy necessary for reproduction
|
---|
| 13 | hibernation - Defines foram behavior in the case of no nutrients
|
---|
[380] | 14 |
|
---|
[476] | 15 | lifeparams:
|
---|
[380] | 16 | Physiological parameters of foraminifera:
|
---|
[422] | 17 | max_energy_level - maximum energy level reached so far
|
---|
[380] | 18 | gen - generation: 0 haploid, 1 diploid
|
---|
[432] | 19 | species - species: 0 not hibernating 1 hibernating
|
---|
| 20 | hibernated - 0/1 foram is/isn't hibernated
|
---|
[422] | 21 | reproduce - 0/1 foram isn't/is ready for reproduction
|
---|
[380] | 22 | ~
|
---|
| 23 | code:~
|
---|
| 24 |
|
---|
[422] | 25 | global colors;
|
---|
[493] | 26 | global curColor;
|
---|
[479] | 27 | global max_chamber_volume;
|
---|
[474] | 28 | global movePerStep;
|
---|
[479] | 29 | global reprocounter;
|
---|
[481] | 30 | global changePeriod;
|
---|
| 31 | global phase;
|
---|
[493] | 32 | global nutrientSqrCm;
|
---|
[567] | 33 | global species_genes;
|
---|
| 34 | global max_chambers_def;
|
---|
| 35 | global foram_uid; //introduced because each replacement of a creature (while growing) would generate a new Creature.uid
|
---|
| 36 | global chamber_vis_denominator;
|
---|
| 37 | global curRadius;
|
---|
[590] | 38 | global nutrient_num_counter;
|
---|
| 39 | global wrldsizSquareMeters;
|
---|
[380] | 40 |
|
---|
[406] | 41 | @include "foraminifera.inc"
|
---|
[401] | 42 |
|
---|
[380] | 43 | // -------------------------------- experiment begin --------------------------------
|
---|
| 44 |
|
---|
| 45 | function onExpDefLoad()
|
---|
| 46 | {
|
---|
| 47 | // define genotype and creature groups
|
---|
| 48 | GenePools.clear();
|
---|
| 49 | Populations.clear();
|
---|
| 50 | GenePools[0].name = "Unused";
|
---|
| 51 |
|
---|
| 52 | var pop = Populations[0];
|
---|
[421] | 53 | pop.name = "Forams";
|
---|
[380] | 54 | pop.en_assim = 0;
|
---|
[404] | 55 | pop.nnsim = 0;
|
---|
[380] | 56 | pop.enableperf = 1;
|
---|
| 57 | pop.death = 1;
|
---|
| 58 | pop.energy = 1;
|
---|
[487] | 59 | pop.selfmask = 0;
|
---|
| 60 | pop.othermask = 0;
|
---|
[401] | 61 | //pop.selfmask = 0x20002; pop.othermask = 0x10002;
|
---|
[422] | 62 | pop.perfperiod = 25;
|
---|
[487] | 63 | pop.bodysim = 0;
|
---|
[380] | 64 |
|
---|
[421] | 65 | pop = Populations.addGroup("Nutrients");
|
---|
[380] | 66 | pop.nnsim = 0;
|
---|
| 67 | pop.enableperf = 0;
|
---|
| 68 | pop.death = 1;
|
---|
| 69 | pop.energy = 1;
|
---|
[487] | 70 | pop.selfmask = 0;
|
---|
| 71 | pop.othermask = 0;
|
---|
[422] | 72 | //pop.othermask = 0x10002;
|
---|
[487] | 73 | pop.bodysim = 0;
|
---|
[380] | 74 |
|
---|
[444] | 75 | pop = Populations.addGroup("ReticulopodiaNutrients");
|
---|
[430] | 76 | pop.nnsim = 0;
|
---|
| 77 | pop.enableperf = 0;
|
---|
| 78 | pop.death = 0;
|
---|
| 79 | pop.energy = 0;
|
---|
[487] | 80 | pop.selfmask = 0;
|
---|
| 81 | pop.othermask = 0;
|
---|
| 82 | pop.bodysim = 0;
|
---|
[444] | 83 |
|
---|
[422] | 84 | //world
|
---|
| 85 | SignalView.mode = 1;
|
---|
[496] | 86 | World.wrldwat = 200;
|
---|
[493] | 87 | World.wrldsiz = micronsToFrams(100000);
|
---|
[590] | 88 | wrldsizSquareMeters = Math.pow(framsToMicrons(World.wrldsiz)*0.000001,2);
|
---|
[422] | 89 | World.wrldbnd = 1;
|
---|
| 90 |
|
---|
[486] | 91 | //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
|
---|
[444] | 92 |
|
---|
[487] | 93 | //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files
|
---|
[493] | 94 | ExpProperties.logPref = "";
|
---|
[401] | 95 |
|
---|
[554] | 96 | //morphology
|
---|
[486] | 97 | ExpProperties.zone1_range = micronsToFrams(1000);
|
---|
| 98 | ExpProperties.zone2_range = micronsToFrams(3000);
|
---|
[567] | 99 | ExpProperties.chamber_proculus_haplo = micronsToFrams(20);
|
---|
| 100 | ExpProperties.chamber_proculus_diplo = micronsToFrams(10);
|
---|
[581] | 101 | colors = ["1.0,1.0,0.3","1.0,0.7,0.0"]; //yellow and orange
|
---|
[579] | 102 | curColor = colors[0];
|
---|
[567] | 103 | curRadius = ExpProperties.zone1_range;
|
---|
[479] | 104 |
|
---|
[422] | 105 | //nutrients
|
---|
[486] | 106 | ExpProperties.nutrientradius = micronsToFrams(10);
|
---|
[552] | 107 | ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
|
---|
[554] | 108 | nutrientSqrCm = 10;
|
---|
[493] | 109 | ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
|
---|
[554] | 110 |
|
---|
[380] | 111 | ExpState.totaltestedcr = 0;
|
---|
[421] | 112 | ExpState.nutrient = "";
|
---|
[567] | 113 |
|
---|
| 114 | max_chambers_def = 35;
|
---|
[569] | 115 | chamber_vis_denominator = 12;
|
---|
[493] | 116 | //addSpecies({"min_repro_energies" : [4,6]});
|
---|
| 117 | //addSpecies({"min_repro_energies" : [4,8]});
|
---|
[557] | 118 |
|
---|
[561] | 119 | //Simulator.print(create_genotype(0.2, 30, "1.0,1.0,0.0", 0.6)); //sample call
|
---|
| 120 | //Simulator.print(create_genotype(0.1, 40, "1.0,0.5,0.0", 0.1)); //sample call
|
---|
[380] | 121 | }
|
---|
| 122 |
|
---|
| 123 | @include "standard_placement.inc"
|
---|
| 124 |
|
---|
[567] | 125 | function onExpInit()
|
---|
[475] | 126 | {
|
---|
[568] | 127 | species_genes = [];
|
---|
[567] | 128 | foram_uid = 0;
|
---|
[568] | 129 | movePerStep = getMovePerStep();
|
---|
[475] | 130 |
|
---|
[567] | 131 | Populations[0].clear();
|
---|
| 132 | Populations[1].clear();
|
---|
| 133 | Populations[2].clear(); //reticulopodia and nutrients
|
---|
| 134 |
|
---|
| 135 | if (ExpProperties.max_chamber_num_haplo == max_chambers_def && ExpProperties.max_chamber_num_diplo == max_chambers_def)
|
---|
[479] | 136 | {
|
---|
[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]
|
---|
| 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]];
|
---|
[479] | 139 | }
|
---|
| 140 |
|
---|
[567] | 141 | else
|
---|
[479] | 142 | {
|
---|
[567] | 143 | max_chamber_volume = [Vector.new(), Vector.new()];
|
---|
| 144 | var density = 100;
|
---|
| 145 | for (var ploid = 0; ploid < 2; ploid++)
|
---|
| 146 | {
|
---|
| 147 | var rad = getPloidRadius(ploid);
|
---|
| 148 | for (var cham_num = 0; cham_num < getProperty(ploid,"max_chamber_num"); cham_num++)
|
---|
| 149 | {
|
---|
| 150 | max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num+1, density));
|
---|
| 151 | }
|
---|
| 152 | }
|
---|
[479] | 153 | }
|
---|
[422] | 154 |
|
---|
[487] | 155 | if (species_genes.size == 0)
|
---|
[380] | 156 | {
|
---|
[487] | 157 | addSpecies({}); //default
|
---|
[380] | 158 | }
|
---|
[487] | 159 |
|
---|
| 160 | for (var spec = 0; spec < species_genes.size; spec++)
|
---|
| 161 | {
|
---|
| 162 | for (var i = 0; i < ExpProperties.foramPop; i++)
|
---|
| 163 | {
|
---|
| 164 | addInitialForam(spec, i);
|
---|
| 165 | }
|
---|
| 166 | }
|
---|
[380] | 167 | ExpState.totaltestedcr = 0;
|
---|
[554] | 168 |
|
---|
| 169 | reprocounter = 0;
|
---|
[590] | 170 | nutrient_num_counter = 0;
|
---|
[554] | 171 | changePeriod = 0;
|
---|
| 172 | phase = "low";
|
---|
[380] | 173 | }
|
---|
| 174 |
|
---|
| 175 | function onExpLoad()
|
---|
| 176 | {
|
---|
| 177 | for (var pop in Populations)
|
---|
| 178 | pop.clear();
|
---|
| 179 |
|
---|
| 180 | Loader.addClass(sim_params.*);
|
---|
| 181 | Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
|
---|
| 182 | Loader.run();
|
---|
| 183 |
|
---|
[421] | 184 | Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
|
---|
[380] | 185 | }
|
---|
| 186 |
|
---|
| 187 | function onExpLoad_Unknown()
|
---|
| 188 | {
|
---|
| 189 | if (Loader.objectName == "org") // saved by the old expdef
|
---|
| 190 | {
|
---|
| 191 | var g = Genotype.newFromString("");
|
---|
| 192 | Loader.currentObject = g;
|
---|
| 193 | Interface.makeFrom(g).setAllDefault();
|
---|
| 194 | Loader.loadObject();
|
---|
| 195 | var cr = Populations[0].add(g);
|
---|
| 196 | if (cr != null)
|
---|
| 197 | {
|
---|
[401] | 198 | //cr.rotate(0,0,Math.rnd01*Math.twopi);
|
---|
[476] | 199 | if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
|
---|
[401] | 200 | {
|
---|
| 201 | // [x,y,energy]
|
---|
[476] | 202 | cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
|
---|
| 203 | cr.energy = g.data->genes[2];
|
---|
[380] | 204 | }
|
---|
| 205 | else
|
---|
| 206 | {
|
---|
[401] | 207 | cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
|
---|
[380] | 208 | }
|
---|
| 209 | }
|
---|
| 210 | }
|
---|
| 211 | else if (Loader.objectName == "Creature")
|
---|
| 212 | {
|
---|
| 213 | Loader.currentObject = CreatureSnapshot.new();
|
---|
| 214 | Loader.loadObject();
|
---|
| 215 | Populations[0].add(Loader.currentObject);
|
---|
| 216 | }
|
---|
| 217 | }
|
---|
| 218 |
|
---|
| 219 | function onExpSave()
|
---|
| 220 | {
|
---|
| 221 | File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
|
---|
| 222 |
|
---|
[401] | 223 | var tmpvec = [], i;
|
---|
[380] | 224 |
|
---|
[401] | 225 | for(var cr in Populations[1])
|
---|
[380] | 226 | tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
|
---|
| 227 |
|
---|
[421] | 228 | ExpState.nutrient = tmpvec;
|
---|
[380] | 229 | File.writeObject(sim_params.*);
|
---|
[432] | 230 | ExpState.nutrient = null; //vectors are only created for saving and then discarded
|
---|
[380] | 231 |
|
---|
| 232 | for (var cr in Populations[0])
|
---|
| 233 | File.writeObject(cr);
|
---|
| 234 | }
|
---|
| 235 |
|
---|
| 236 | // -------------------------------- experiment end --------------------------------
|
---|
| 237 |
|
---|
[567] | 238 | function volumeFromGeno(morphotype, rad, chamber_num, density)
|
---|
| 239 | {
|
---|
| 240 | var geno = create_genotype(rad, chamber_num, colors[morphotype], 1);
|
---|
| 241 | var m=Model.newFromString(geno);
|
---|
| 242 | var mg=ModelGeometry.forModel(m);
|
---|
| 243 | mg.geom_density=density;
|
---|
| 244 | var volumeInFrams = mg.volume();
|
---|
| 245 |
|
---|
| 246 | return volumeInFrams/Math.pow(ExpProperties.scalingFactor,3);
|
---|
| 247 | }
|
---|
| 248 |
|
---|
| 249 | function secToSimSteps(value_in_sec){
|
---|
| 250 | return value_in_sec/ExpProperties.secPerStep;
|
---|
| 251 | }
|
---|
| 252 |
|
---|
| 253 | function volumeInMicrons(radiusInFrams)
|
---|
| 254 | {
|
---|
| 255 | return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
|
---|
| 256 | }
|
---|
| 257 |
|
---|
| 258 | function energyFromVolume(base, isRadiusInFrams)
|
---|
| 259 | {
|
---|
| 260 | if (isRadiusInFrams == 1) //radius in frams
|
---|
| 261 | {
|
---|
| 262 | return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
|
---|
| 263 | }
|
---|
| 264 | else //volume in microns
|
---|
| 265 | {
|
---|
| 266 | return ExpProperties.picoCarbonPerMikro * base;
|
---|
| 267 | }
|
---|
| 268 | }
|
---|
| 269 |
|
---|
| 270 | function getMovePerStep()
|
---|
| 271 | {
|
---|
| 272 | return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
|
---|
| 273 | }
|
---|
| 274 |
|
---|
| 275 | function micronsToFrams(micrometers)
|
---|
| 276 | {
|
---|
| 277 | return micrometers*ExpProperties.scalingFactor;
|
---|
| 278 | }
|
---|
| 279 |
|
---|
| 280 | function framsToMicrons(framsworldunits)
|
---|
| 281 | {
|
---|
| 282 | return framsworldunits/ExpProperties.scalingFactor;
|
---|
| 283 | }
|
---|
| 284 |
|
---|
| 285 | function getProperty(gen, prop_id)
|
---|
| 286 | {
|
---|
| 287 | var ploid = "haplo";
|
---|
| 288 | if (gen == 1) ploid = "diplo";
|
---|
| 289 | return ExpProperties.[prop_id + "_" + ploid];
|
---|
| 290 | }
|
---|
| 291 |
|
---|
| 292 | function getGene(cr, gen_id, gen_set)
|
---|
| 293 | {
|
---|
| 294 | if (cr.data->lifeparams->gen == 0)
|
---|
| 295 | return cr.data->genes[gen_id];
|
---|
| 296 | else
|
---|
| 297 | return cr.data->genes[gen_set][gen_id];
|
---|
| 298 | }
|
---|
| 299 |
|
---|
| 300 | function getPloidRadius(ploid)
|
---|
| 301 | {
|
---|
| 302 | var radius = ExpProperties.chamber_proculus_haplo;
|
---|
| 303 | if (ploid == 1)
|
---|
| 304 | {
|
---|
| 305 | radius = ExpProperties.chamber_proculus_diplo;
|
---|
| 306 | }
|
---|
| 307 | return radius;
|
---|
| 308 | }
|
---|
| 309 |
|
---|
| 310 | function chamberNumFromEnergy(energy, ploid)
|
---|
| 311 | {
|
---|
| 312 | var chamber_num = max_chamber_volume[ploid].size;
|
---|
| 313 | for (var i = 0; i < chamber_num; i++)
|
---|
| 314 | {
|
---|
| 315 | if (energy < energyFromVolume(max_chamber_volume[ploid][i],0))
|
---|
| 316 | {
|
---|
| 317 | chamber_num = i+1;
|
---|
| 318 | break;
|
---|
| 319 | }
|
---|
| 320 | }
|
---|
| 321 |
|
---|
| 322 | return chamber_num;
|
---|
| 323 | }
|
---|
| 324 |
|
---|
[595] | 325 | function createAndRotate(geno, rotate_min, rotate_max, pop_num)
|
---|
| 326 | {
|
---|
| 327 | var cr = Populations[pop_num].add(geno);
|
---|
| 328 | cr.rotate(0,0,Math.rndUni(rotate_min, rotate_max));
|
---|
| 329 | return cr;
|
---|
| 330 | }
|
---|
| 331 |
|
---|
| 332 | //TODO unifiy addForam, foramGrow and createOffspring
|
---|
[567] | 333 | function addForam(species, iter, start_energy, ploid)
|
---|
| 334 | {
|
---|
| 335 | var chambernum = chamberNumFromEnergy(start_energy, ploid);
|
---|
| 336 | var radius = getPloidRadius(ploid);
|
---|
| 337 | var geno = create_genotype(radius, chambernum, colors[ploid], 1);
|
---|
[579] | 338 | curColor = colors[ploid];
|
---|
[595] | 339 | var cr = createAndRotate(geno, 0, 2*Math.pi, 0);
|
---|
[567] | 340 | cr.name = "Initial creature" + species + "_" + iter;
|
---|
[588] | 341 | placeRandomlyNotColliding(cr);
|
---|
[567] | 342 | cr.energy = start_energy;
|
---|
| 343 | setGenotype({"opt" : "birth", "cr" : cr, "gen" : ploid, "species" : species, "energy0" : cr.energy, "genes" : species_genes[species], "parentsuids" : ["c0"]});
|
---|
| 344 | if (ploid == 1)
|
---|
| 345 | {
|
---|
| 346 | cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
|
---|
| 347 | }
|
---|
| 348 | moveReticulopodia(cr);
|
---|
| 349 | }
|
---|
| 350 |
|
---|
| 351 | function addInitialForam(species, iter)
|
---|
| 352 | {
|
---|
| 353 | var ploid = 0;
|
---|
| 354 | if (Math.rnd01 > 0.5)
|
---|
| 355 | {
|
---|
| 356 | ploid = 1;
|
---|
| 357 | }
|
---|
| 358 | //add new foram with random energy bewtween starting energy and reproduction threshold
|
---|
| 359 | var repro_thr = species_genes[species]->min_repro_energies[ploid];
|
---|
| 360 | var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid),1),repro_thr-0.25*repro_thr);
|
---|
| 361 | addForam(species, iter, start_energy,ploid);
|
---|
| 362 | }
|
---|
| 363 |
|
---|
| 364 | //new species can be added as a dictionary with parameter values that are different than default values
|
---|
| 365 | function addSpecies(new_genes)
|
---|
| 366 | {
|
---|
| 367 | 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});
|
---|
| 368 | for (var i = 0; i < new_genes.size; i++)
|
---|
| 369 | {
|
---|
| 370 | var key = new_genes.getKey(i);
|
---|
| 371 | species_genes[species_genes.size-1][key] = new_genes[key];
|
---|
| 372 | }
|
---|
| 373 | }
|
---|
| 374 |
|
---|
[421] | 375 | // -------------------------------- foram begin -----------------------------------
|
---|
[380] | 376 |
|
---|
[479] | 377 | function setForamMeta(cr)
|
---|
[430] | 378 | {
|
---|
[479] | 379 | //percent of current energy
|
---|
[486] | 380 | cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
|
---|
[430] | 381 | }
|
---|
| 382 |
|
---|
| 383 | function lastChamberNum(cr)
|
---|
| 384 | {
|
---|
[567] | 385 | return cr.numparts;
|
---|
[430] | 386 | }
|
---|
| 387 |
|
---|
[479] | 388 | function getZoneRange(cr, zone_num)
|
---|
| 389 | {
|
---|
[486] | 390 | return ExpProperties.["zone"+zone_num+"_range"];
|
---|
[479] | 391 | }
|
---|
| 392 |
|
---|
[567] | 393 | function addReticulopodia(cr, radius)
|
---|
| 394 | {
|
---|
| 395 | if (reticulopodiaExists(cr))
|
---|
| 396 | {
|
---|
| 397 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
| 398 | }
|
---|
| 399 | 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");
|
---|
| 400 | cr.data->reticulopodiacreature = ret;
|
---|
| 401 | ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
|
---|
| 402 | ret.moveAbs(cr.center_x-radius, cr.center_y-radius, cr.center_z-radius);
|
---|
| 403 | }
|
---|
| 404 |
|
---|
[421] | 405 | function onForamsBorn(cr)
|
---|
| 406 | {
|
---|
[479] | 407 | setForamMeta(cr);
|
---|
[486] | 408 | if (ExpProperties.visualize == 1)
|
---|
[430] | 409 | {
|
---|
[567] | 410 | addReticulopodia(cr, curRadius);
|
---|
[583] | 411 | moveReticulopodia(cr);
|
---|
[430] | 412 | }
|
---|
[380] | 413 | }
|
---|
| 414 |
|
---|
[401] | 415 | function placeRandomlyNotColliding(cr)
|
---|
| 416 | {
|
---|
| 417 | var retry = 100; //try 100 times
|
---|
| 418 | while (retry--)
|
---|
| 419 | {
|
---|
| 420 | placeCreatureRandomly(cr, 0, 0);
|
---|
| 421 | if (!cr.boundingBoxCollisions(0))
|
---|
[588] | 422 | {
|
---|
| 423 | cr.moveAbs(cr.pos_x, cr.pos_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] | 424 | return cr;
|
---|
[588] | 425 | }
|
---|
[401] | 426 | }
|
---|
| 427 |
|
---|
| 428 | Populations[0].delete(cr);
|
---|
| 429 | }
|
---|
| 430 |
|
---|
[567] | 431 | function reticulopodiaExists(cr)
|
---|
[444] | 432 | {
|
---|
| 433 | var has_ret = 0;
|
---|
| 434 |
|
---|
[476] | 435 | if (cr.data->reticulopodiacreature != null)
|
---|
[444] | 436 | {
|
---|
[476] | 437 | if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
|
---|
[444] | 438 | {
|
---|
| 439 | has_ret = 1;
|
---|
| 440 | }
|
---|
| 441 | }
|
---|
| 442 |
|
---|
| 443 | return has_ret;
|
---|
| 444 | }
|
---|
| 445 |
|
---|
[567] | 446 | function visualization(cr)
|
---|
[380] | 447 | {
|
---|
[567] | 448 | return reticulopodiaExists(cr);
|
---|
| 449 | }
|
---|
| 450 |
|
---|
| 451 | function foramGrow(cr, chamber_num, lastchambergrowth)
|
---|
| 452 | {
|
---|
| 453 | if ((chamber_num+1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
|
---|
[474] | 454 | {
|
---|
[579] | 455 | curColor = colors[cr.data->lifeparams->gen];
|
---|
[567] | 456 | var ploid = cr.data->lifeparams->gen;
|
---|
| 457 | var geno = create_genotype(getPloidRadius(ploid), chamber_num+1, colors[ploid], lastchambergrowth);
|
---|
[595] | 458 | var cr2 = createAndRotate(geno, 0, 0, 0);
|
---|
[422] | 459 |
|
---|
[595] | 460 | cr2.orient.set(cr.orient);
|
---|
[474] | 461 | cr2.energy0 = cr.energy;
|
---|
| 462 | cr2.energy = cr2.energy0;
|
---|
[422] | 463 |
|
---|
[554] | 464 | setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
|
---|
[567] | 465 | cr2.moveAbs(cr.pos_x, cr.pos_y,cr.pos_z);
|
---|
[479] | 466 | setForamMeta(cr2);
|
---|
[422] | 467 |
|
---|
[567] | 468 | if (reticulopodiaExists(cr))
|
---|
[474] | 469 | {
|
---|
[476] | 470 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[474] | 471 | }
|
---|
| 472 | Populations[0].delete(cr);
|
---|
[567] | 473 | return cr2;
|
---|
[430] | 474 | }
|
---|
[567] | 475 | return cr;
|
---|
[380] | 476 | }
|
---|
| 477 |
|
---|
[583] | 478 | function visualizeChamberGrowth(cr, chamber_time)
|
---|
| 479 | {
|
---|
| 480 | var total_time = secToSimSteps(ExpProperties.chamberGrowthSec);
|
---|
| 481 | var ret_unit = total_time/chamber_vis_denominator;
|
---|
| 482 | var chamber_unit = total_time-ret_unit;
|
---|
| 483 |
|
---|
| 484 | if (chamber_time < ret_unit || chamber_time >= chamber_unit)
|
---|
| 485 | {
|
---|
| 486 | var new_rad = Math.min(Math.max((chamber_time%ret_unit)/ret_unit*getZoneRange(cr,1),0.01),getZoneRange(cr,1));
|
---|
| 487 |
|
---|
| 488 | if(chamber_time < ret_unit)
|
---|
| 489 | {
|
---|
| 490 | new_rad = getZoneRange(cr,1)-new_rad;
|
---|
| 491 | }
|
---|
| 492 |
|
---|
| 493 | curColor = colors[cr.data->lifeparams->gen];
|
---|
| 494 | addReticulopodia(cr,new_rad);
|
---|
| 495 |
|
---|
| 496 | if (chamber_time == 0)//checking for end of chamber growth process
|
---|
| 497 | {
|
---|
| 498 | cr.data->lifeparams->chamber_growth = -1;
|
---|
| 499 | }
|
---|
| 500 | }
|
---|
| 501 | else
|
---|
| 502 | {
|
---|
| 503 | var new_rad = 1 - Math.min(Math.max((chamber_time-ret_unit)/chamber_unit,0.01),1);
|
---|
| 504 | curRadius = cr.data->reticulopodiacreature.getPart(1).sy;
|
---|
| 505 |
|
---|
| 506 | if (chamber_time == ret_unit)
|
---|
| 507 | {
|
---|
| 508 | new_rad = 1;
|
---|
| 509 | }
|
---|
| 510 |
|
---|
| 511 | var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen)-1, new_rad);
|
---|
| 512 | curRadius = getZoneRange(new_cr,1);
|
---|
| 513 | }
|
---|
| 514 | }
|
---|
| 515 |
|
---|
[435] | 516 | function stepToNearest(cr)
|
---|
[380] | 517 | {
|
---|
[595] | 518 | var p = XYZ.new(cr.center_x, cr.center_y, cr.center_z);
|
---|
[479] | 519 | var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
|
---|
[380] | 520 |
|
---|
[401] | 521 | //if signals are received find the source of the nearest
|
---|
[380] | 522 | if (n.size > 0)
|
---|
| 523 | {
|
---|
| 524 | var i;
|
---|
| 525 | var mp;
|
---|
| 526 | var distvec = XYZ.new(0, 0, 0);
|
---|
| 527 | var dist;
|
---|
[470] | 528 | var mindist = 100000000000.0;
|
---|
[380] | 529 | var mindistvec = null;
|
---|
[430] | 530 | var eating = 0;
|
---|
[380] | 531 |
|
---|
[401] | 532 | for (i = 0; i < n.size; i++)
|
---|
[380] | 533 | {
|
---|
[595] | 534 | mp = XYZ.new(n[i].value.center_x, n[i].value.center_y, n[i].value.center_z);
|
---|
| 535 | distvec.set(mp);
|
---|
| 536 | distvec.sub(p);
|
---|
[401] | 537 | dist = distvec.length;
|
---|
[479] | 538 | if (dist < getZoneRange(cr,1))
|
---|
[380] | 539 | {
|
---|
[430] | 540 | if (n[i].value != null)
|
---|
| 541 | {
|
---|
| 542 | energyTransfer(cr, n[i].value);
|
---|
| 543 | eating = 1;
|
---|
| 544 | }
|
---|
| 545 | }
|
---|
[476] | 546 | else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
|
---|
[430] | 547 | {
|
---|
[401] | 548 | mindist = dist;
|
---|
| 549 | mindistvec = distvec.clone();
|
---|
[380] | 550 | }
|
---|
| 551 | }
|
---|
| 552 |
|
---|
[476] | 553 | if (!eating && cr.data->lifeparams->hibernated == 0)
|
---|
[430] | 554 | {
|
---|
[588] | 555 | mindistvec.z = 0;
|
---|
[430] | 556 | mindistvec.normalize();
|
---|
[595] | 557 | mindistvec.scale(movePerStep);
|
---|
| 558 | cr.drive = mindistvec;
|
---|
[430] | 559 | moveEnergyDec(cr);
|
---|
| 560 | }
|
---|
| 561 |
|
---|
[422] | 562 | return 1;
|
---|
[380] | 563 | }
|
---|
[422] | 564 |
|
---|
| 565 | else
|
---|
[474] | 566 | {
|
---|
[422] | 567 | return 0;
|
---|
[474] | 568 | }
|
---|
[422] | 569 | }
|
---|
[401] | 570 |
|
---|
[422] | 571 | function moveEnergyDec(cr)
|
---|
| 572 | {
|
---|
[476] | 573 | if (cr.data->lifeparams->hibernated == 0)
|
---|
[422] | 574 | {
|
---|
[479] | 575 | //percent of maximal energy
|
---|
[504] | 576 | cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
|
---|
[422] | 577 | }
|
---|
[421] | 578 | }
|
---|
[380] | 579 |
|
---|
[584] | 580 | function fence(center, zone)
|
---|
[487] | 581 | {
|
---|
[584] | 582 | 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] | 583 | }
|
---|
| 584 |
|
---|
[422] | 585 | function foramMove(cr)
|
---|
[421] | 586 | {
|
---|
[430] | 587 | //are there any nutrients in zone 1 or 2?
|
---|
[401] | 588 | {
|
---|
[435] | 589 | var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
|
---|
[422] | 590 | if (moved==1)
|
---|
[430] | 591 | {
|
---|
[502] | 592 | moveReticulopodia(cr);
|
---|
[422] | 593 | return;
|
---|
| 594 | }
|
---|
[401] | 595 | }
|
---|
| 596 |
|
---|
[584] | 597 | //Prevents forams from crossing the world border. In the case of touching the border with the reticulopodia direction of the movement should be changed.
|
---|
| 598 | var change_direction = 0;
|
---|
| 599 | var new_x = fence(cr.center_x, getZoneRange(cr, 1));
|
---|
| 600 | var new_y = fence(cr.center_y, getZoneRange(cr, 1));
|
---|
| 601 |
|
---|
| 602 | if ((new_x != cr.center_x) || (new_y != cr.center_y) || (cr.data->lifeparams->dir_counter >= int(secToSimSteps(ExpProperties.dir_change_sec))))
|
---|
| 603 | {
|
---|
| 604 | change_direction = 1;
|
---|
[587] | 605 | cr.moveAbs(new_x-cr.size_x/2, new_y-cr.size_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] | 606 | }
|
---|
| 607 |
|
---|
[422] | 608 | //no nutrients in zone 2
|
---|
[487] | 609 | if (getGene(cr, "hibernation",0) == 1)
|
---|
[401] | 610 | {
|
---|
[430] | 611 | reverseHib(cr);
|
---|
[595] | 612 | cr.drive = XYZ.new(0,0,0);
|
---|
[380] | 613 | }
|
---|
[422] | 614 | //random move
|
---|
[554] | 615 | else if (change_direction == 1)
|
---|
[380] | 616 | {
|
---|
[476] | 617 | cr.data->lifeparams->dir = randomDir();
|
---|
[552] | 618 | cr.data->lifeparams->dir_counter = 0;
|
---|
[595] | 619 | cr.drive = cr.data->lifeparams->dir;
|
---|
[422] | 620 | moveEnergyDec(cr);
|
---|
| 621 | }
|
---|
[474] | 622 | else
|
---|
| 623 | {
|
---|
[595] | 624 | cr.drive = cr.data->lifeparams->dir;
|
---|
[474] | 625 | }
|
---|
[502] | 626 | moveReticulopodia(cr);
|
---|
[422] | 627 | }
|
---|
[401] | 628 |
|
---|
[502] | 629 | function moveReticulopodia(cr)
|
---|
| 630 | {
|
---|
| 631 | if (visualization(cr))
|
---|
| 632 | {
|
---|
| 633 | cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
|
---|
[595] | 634 | cr.data->reticulopodiacreature.drive = cr.drive;
|
---|
[502] | 635 | }
|
---|
| 636 | }
|
---|
| 637 |
|
---|
[474] | 638 | function randomDir()
|
---|
| 639 | {
|
---|
[486] | 640 | var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0);
|
---|
[474] | 641 | dir.normalize();
|
---|
| 642 | dir.scale(-1*movePerStep);
|
---|
| 643 | return dir;
|
---|
| 644 | }
|
---|
| 645 |
|
---|
[430] | 646 | function energyTransfer(cr1, cr2)
|
---|
[422] | 647 | {
|
---|
[595] | 648 | cr1.drive = XYZ.new(0,0,0);
|
---|
[510] | 649 | var e = ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
|
---|
[502] | 650 | //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
|
---|
[510] | 651 | var transferred = cr2.transferEnergyTo(cr1, e);
|
---|
| 652 | cr1.energy -= transferred*(1-ExpProperties.ingestion);
|
---|
[476] | 653 | if (cr1.data->lifeparams->hibernated == 1)
|
---|
[422] | 654 | {
|
---|
[430] | 655 | reverseHib(cr1);
|
---|
[422] | 656 | }
|
---|
| 657 | }
|
---|
[401] | 658 |
|
---|
[430] | 659 | function reverseHib(cr)
|
---|
| 660 | {
|
---|
[476] | 661 | if (cr.data->lifeparams->hibernated == 1)
|
---|
[430] | 662 | {
|
---|
[479] | 663 | setForamMeta(cr); //unhibernate
|
---|
[430] | 664 | }
|
---|
| 665 | else
|
---|
| 666 | {
|
---|
[486] | 667 | cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
|
---|
[430] | 668 | }
|
---|
[476] | 669 | cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
|
---|
[430] | 670 | }
|
---|
| 671 |
|
---|
[422] | 672 | function onForamsStep(cr)
|
---|
| 673 | {
|
---|
[479] | 674 | //checking for gametogenesis process
|
---|
| 675 | if (cr.data->lifeparams->division_time > 0)
|
---|
[444] | 676 | {
|
---|
[479] | 677 | cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
|
---|
[444] | 678 | }
|
---|
[479] | 679 | //checking for end of gametogenesis
|
---|
| 680 | else if (cr.data->lifeparams->division_time == 0)
|
---|
[422] | 681 | {
|
---|
[479] | 682 | //waiting for gamets fusion
|
---|
[422] | 683 | }
|
---|
[479] | 684 | //checking for chamber growth process
|
---|
| 685 | else if (cr.data->lifeparams->chamber_growth > 0)
|
---|
| 686 | {
|
---|
[567] | 687 | var chamber_time = Math.max(cr.data->lifeparams->chamber_growth-1,0);
|
---|
| 688 | cr.data->lifeparams->chamber_growth = chamber_time;
|
---|
[504] | 689 | cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
|
---|
[422] | 690 |
|
---|
[567] | 691 | if (visualization(cr))
|
---|
| 692 | {
|
---|
[583] | 693 | visualizeChamberGrowth(cr, chamber_time);
|
---|
[567] | 694 | }
|
---|
[479] | 695 | }
|
---|
[583] | 696 | //checking for end of the chamber growth process
|
---|
[567] | 697 | else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr)==0)
|
---|
| 698 | {
|
---|
| 699 | foramGrow(cr, lastChamberNum(cr), 1);
|
---|
[479] | 700 | cr.data->lifeparams->chamber_growth = -1;
|
---|
| 701 | //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
|
---|
[430] | 702 | }
|
---|
[479] | 703 | else
|
---|
[422] | 704 | {
|
---|
[479] | 705 | //update of metabolism rate
|
---|
| 706 | if (cr.data->lifeparams->hibernated == 0)
|
---|
[401] | 707 | {
|
---|
[479] | 708 | setForamMeta(cr);
|
---|
| 709 | }
|
---|
| 710 |
|
---|
| 711 | if (deathConditions(cr) == 1)
|
---|
| 712 | {
|
---|
[493] | 713 | if (ExpProperties.logging == 1)
|
---|
| 714 | {
|
---|
| 715 | log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
|
---|
[552] | 716 | log(createLogVector(cr, cr.lifespan),ExpProperties.logPref+"lifespan_log.txt");
|
---|
[493] | 717 | }
|
---|
[479] | 718 | Populations[0].kill(cr);
|
---|
| 719 | return;
|
---|
| 720 | }
|
---|
| 721 |
|
---|
[552] | 722 | //update direction change counter
|
---|
| 723 | cr.data->lifeparams->dir_counter += 1;
|
---|
| 724 |
|
---|
[479] | 725 | foramMove(cr);
|
---|
| 726 |
|
---|
| 727 | var repro = foramReproduce(cr);
|
---|
| 728 | if (repro == 1)
|
---|
| 729 | {
|
---|
| 730 | return;
|
---|
| 731 | }
|
---|
| 732 |
|
---|
| 733 | cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
|
---|
| 734 |
|
---|
| 735 | //cheking conditions of chamber growth process start
|
---|
[567] | 736 | if (lastChamberNum(cr) < max_chamber_volume[cr.data->lifeparams->gen].size)
|
---|
[479] | 737 | {
|
---|
[567] | 738 | if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)-1],0)))
|
---|
[479] | 739 | {
|
---|
[554] | 740 | cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
|
---|
[479] | 741 | }
|
---|
| 742 | }
|
---|
[430] | 743 | }
|
---|
[380] | 744 | }
|
---|
| 745 |
|
---|
[422] | 746 | function deathConditions(cr)
|
---|
| 747 | {
|
---|
[486] | 748 | if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
|
---|
[479] | 749 | {
|
---|
[422] | 750 | return 1;
|
---|
[479] | 751 | }
|
---|
[422] | 752 | else
|
---|
| 753 | return 0;
|
---|
| 754 | }
|
---|
| 755 |
|
---|
[421] | 756 | function onForamsDied(cr)
|
---|
[380] | 757 | {
|
---|
[444] | 758 | if (visualization(cr))
|
---|
[430] | 759 | {
|
---|
[476] | 760 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[430] | 761 | }
|
---|
[380] | 762 | //fossilization
|
---|
| 763 | var geno = GenePools[0].add(cr.genotype);
|
---|
[476] | 764 | geno.data->genes = cr.data->genes;
|
---|
| 765 | geno.data->lifeparams = cr.data->lifeparams;
|
---|
[486] | 766 | if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
|
---|
[380] | 767 | ExpState.totaltestedcr++;
|
---|
| 768 | }
|
---|
| 769 |
|
---|
[421] | 770 | // --------------------------------foram end -------------------------------------
|
---|
[380] | 771 |
|
---|
[421] | 772 | // -------------------------------- nutrient begin --------------------------------
|
---|
[380] | 773 |
|
---|
[479] | 774 | function createNutrientGenotype(nutrientradius)
|
---|
[422] | 775 | {
|
---|
[524] | 776 | 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] | 777 | }
|
---|
| 778 |
|
---|
[421] | 779 | function onNutrientsStep(cr)
|
---|
[380] | 780 | {
|
---|
[444] | 781 | cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
|
---|
[380] | 782 | }
|
---|
| 783 |
|
---|
[421] | 784 | function addNutrient()
|
---|
[380] | 785 | {
|
---|
[486] | 786 | var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
|
---|
[380] | 787 |
|
---|
[421] | 788 | cr.name = "Nutrients";
|
---|
[380] | 789 | cr.idleen = 0;
|
---|
[486] | 790 | cr.energy0 = ExpProperties.energy_nut;
|
---|
[416] | 791 | cr.energy = cr.energy0;
|
---|
[421] | 792 | cr.signals.add("nutrient");
|
---|
[380] | 793 |
|
---|
[430] | 794 | cr.signals[0].value = cr;
|
---|
[380] | 795 |
|
---|
[422] | 796 | placeCreatureRandomly(cr, 0, 0);
|
---|
[486] | 797 | if (ExpProperties.visualize == 1)
|
---|
[444] | 798 | {
|
---|
[486] | 799 | var nutsize = ExpProperties.nutrientradius*10;
|
---|
[555] | 800 | 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] | 801 | cr.data->reticulopodiacreature = nut;
|
---|
[587] | 802 | nut.moveAbs( cr.pos_x+cr.size_x/2-nut.size_x/2, cr.pos_y+cr.size_y/2-nut.size_y/2, -nutsize);
|
---|
[444] | 803 | }
|
---|
[380] | 804 | }
|
---|
| 805 |
|
---|
[444] | 806 | function onNutrientsDied(cr)
|
---|
| 807 | {
|
---|
| 808 | if (visualization(cr))
|
---|
| 809 | {
|
---|
[476] | 810 | Populations[2].delete(cr.data->reticulopodiacreature);
|
---|
[444] | 811 | }
|
---|
| 812 | }
|
---|
| 813 |
|
---|
[592] | 814 | function getNumberCounter(counter, increase, unitsize) //increase counter and then deduct and return an integer (=discrete) number of "full" units
|
---|
[590] | 815 | {
|
---|
| 816 | counter += increase;
|
---|
[592] | 817 | var unitcount = int(counter/unitsize);
|
---|
| 818 | counter -= unitcount*unitsize;
|
---|
| 819 | return {"counter" : counter, "number" : unitcount};
|
---|
[590] | 820 | }
|
---|
| 821 |
|
---|
[422] | 822 | function nutrientGrowth()
|
---|
[380] | 823 | {
|
---|
[590] | 824 | if (ExpProperties.foodfluxChange > 0)
|
---|
[481] | 825 | {
|
---|
| 826 | changePeriod += 1;
|
---|
[554] | 827 | if (phase=="low" && changePeriod >= secToSimSteps(23328000)) //9 months
|
---|
[481] | 828 | {
|
---|
[590] | 829 | ExpProperties.foodflux = ExpProperties.foodflux/ExpProperties.foodfluxChange;
|
---|
[481] | 830 | phase = "high";
|
---|
| 831 | changePeriod = 0;
|
---|
| 832 | }
|
---|
| 833 |
|
---|
[554] | 834 | else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
|
---|
[481] | 835 | {
|
---|
[590] | 836 | ExpProperties.foodflux = ExpProperties.foodflux*ExpProperties.foodfluxChange;
|
---|
[481] | 837 | phase = "low";
|
---|
| 838 | changePeriod = 0;
|
---|
| 839 | }
|
---|
| 840 | }
|
---|
[422] | 841 |
|
---|
[590] | 842 | var nutrientNum = getNumberCounter(nutrient_num_counter, ExpProperties.foodflux*wrldsizSquareMeters*ExpProperties.secPerStep,ExpProperties.energy_nut*0.000000000001);
|
---|
[493] | 843 |
|
---|
[590] | 844 | nutrient_num_counter = nutrientNum["counter"];
|
---|
| 845 |
|
---|
| 846 | for (var i = 0; i < nutrientNum["number"]; i++)
|
---|
| 847 | {
|
---|
| 848 | addNutrient();
|
---|
[380] | 849 | }
|
---|
[493] | 850 |
|
---|
[590] | 851 | if (ExpProperties.logging == 1 && nutrientNum["number"] > 0)
|
---|
| 852 | {
|
---|
| 853 | log([nutrientNum["number"]],ExpProperties.logPref+"nutrients_log.txt");
|
---|
| 854 | }
|
---|
| 855 |
|
---|
[380] | 856 | }
|
---|
| 857 |
|
---|
[421] | 858 | // -------------------------------- nutrient end --------------------------------
|
---|
[380] | 859 |
|
---|
[422] | 860 | // -------------------------------- step begin --------------------------------
|
---|
[380] | 861 |
|
---|
[422] | 862 | function onStep()
|
---|
| 863 | {
|
---|
[432] | 864 |
|
---|
| 865 | nutrientGrowth();
|
---|
[486] | 866 | if (ExpProperties.logging == 1)
|
---|
[422] | 867 | {
|
---|
| 868 | createStatistics();
|
---|
| 869 | }
|
---|
| 870 |
|
---|
| 871 | //reproduction --------------------------------------------
|
---|
| 872 | reprocounter += 1;
|
---|
[554] | 873 | if (reprocounter > secToSimSteps(ExpProperties.reproTimeSec))
|
---|
[422] | 874 | {
|
---|
| 875 | reprocounter = 0;
|
---|
[567] | 876 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 877 | {
|
---|
| 878 | reproduce_parents(s);
|
---|
| 879 | }
|
---|
| 880 |
|
---|
[422] | 881 | }
|
---|
| 882 |
|
---|
| 883 | //check for extinction -----------------------------------------------
|
---|
| 884 | if (Populations[0].size == 0)
|
---|
| 885 | {
|
---|
[486] | 886 | if (ExpProperties.autorestart)
|
---|
[422] | 887 | {
|
---|
| 888 | Simulator.print("no more creatures, restarting...");
|
---|
| 889 | onExpInit();
|
---|
| 890 | }
|
---|
| 891 | else
|
---|
| 892 | {
|
---|
| 893 | Simulator.print("no more creatures, stopped.");
|
---|
| 894 | Simulator.stop();
|
---|
| 895 | }
|
---|
| 896 | }
|
---|
[486] | 897 | if (ExpProperties.maxSteps > 0)
|
---|
[432] | 898 | {
|
---|
[486] | 899 | if (Simulator.stepNumber >= ExpProperties.maxSteps)
|
---|
[432] | 900 | Simulator.stop();
|
---|
| 901 | }
|
---|
[422] | 902 | }
|
---|
| 903 |
|
---|
| 904 | function createStatistics()
|
---|
| 905 | {
|
---|
[487] | 906 | var number = [];
|
---|
| 907 | var e_inc = [];
|
---|
[422] | 908 | var e_nut = 0.0;
|
---|
| 909 |
|
---|
[487] | 910 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 911 | {
|
---|
| 912 | number.add([0,0]);// [haplo][diplo]
|
---|
| 913 | e_inc.add([0,0]);
|
---|
| 914 | }
|
---|
| 915 |
|
---|
[422] | 916 | for (var i = 0; i < Populations[0].size; i++)
|
---|
| 917 | {
|
---|
| 918 | var cr = Populations[0].get(i);
|
---|
[476] | 919 | var gen = cr.data->lifeparams->gen;
|
---|
| 920 | var species = cr.data->lifeparams->species;
|
---|
[430] | 921 |
|
---|
| 922 | number[species][gen] = number[species][gen] + 1;
|
---|
| 923 | e_inc[species][gen] = e_inc[species][gen] + cr.energy;
|
---|
[422] | 924 | }
|
---|
| 925 |
|
---|
| 926 | for (var i = 0; i < Populations[1].size; i++)
|
---|
| 927 | {
|
---|
| 928 | var cr = Populations[1].get(i);
|
---|
| 929 | e_nut += cr.energy;
|
---|
| 930 | }
|
---|
| 931 |
|
---|
[487] | 932 | var log_numbers = [];
|
---|
| 933 | var log_energies = [];
|
---|
[422] | 934 |
|
---|
[487] | 935 | for (var s = 0; s < species_genes.size; s++)
|
---|
| 936 | {
|
---|
| 937 | for (var p = 0; p < 2; p++)
|
---|
| 938 | {
|
---|
| 939 | log_numbers.add(number[s][p]);
|
---|
| 940 | log_energies.add(e_inc[s][p]);
|
---|
| 941 | }
|
---|
| 942 | }
|
---|
| 943 |
|
---|
| 944 | log_numbers.add(Populations[1].size);
|
---|
| 945 | log_energies.add(e_nut);
|
---|
| 946 |
|
---|
[493] | 947 | log(log_numbers, ExpProperties.logPref+"forams_log.txt");
|
---|
| 948 | log(log_energies, ExpProperties.logPref+"energies_log.txt");
|
---|
[422] | 949 | }
|
---|
| 950 |
|
---|
[380] | 951 | function log(tolog, fname)
|
---|
| 952 | {
|
---|
[430] | 953 | var f = File.appendDirect(fname, "forams data");
|
---|
[380] | 954 | f.writeString("" + Simulator.stepNumber);
|
---|
[401] | 955 | for (var i = 0; i < tolog.size; i++)
|
---|
[380] | 956 | {
|
---|
| 957 | f.writeString(";" + tolog[i]);
|
---|
| 958 | }
|
---|
| 959 | f.writeString("\n");
|
---|
| 960 | f.close();
|
---|
| 961 | }
|
---|
| 962 |
|
---|
[567] | 963 | function createLogVector(cr, value)
|
---|
| 964 | {
|
---|
| 965 | var vec = Vector.new();
|
---|
| 966 | for (var i = 0; i < species_genes.size; i++)
|
---|
| 967 | {
|
---|
| 968 | for (var j = 0; j < 2; j++)
|
---|
| 969 | {
|
---|
| 970 | vec.add(0);
|
---|
| 971 | }
|
---|
| 972 | if (cr.data->lifeparams->species == i)
|
---|
| 973 | {
|
---|
| 974 | vec[i*2+cr.data->lifeparams->gen] = value;
|
---|
| 975 | }
|
---|
| 976 | }
|
---|
| 977 | return vec;
|
---|
| 978 | }
|
---|
| 979 |
|
---|
| 980 |
|
---|
[422] | 981 | // -------------------------------- step end --------------------------------
|
---|
[479] | 982 | //TODO default params values in frams instead of microns/seconds
|
---|
[380] | 983 |
|
---|
[401] | 984 | @include "standard_events.inc"
|
---|
[380] | 985 |
|
---|
[401] | 986 | ~
|
---|
[380] | 987 |
|
---|
[486] | 988 | property:
|
---|
[444] | 989 | id:visualize
|
---|
| 990 | name:Show reticulopodia and nutrients
|
---|
[430] | 991 | type:d 0 1 0
|
---|
[554] | 992 | group:
|
---|
[430] | 993 |
|
---|
[486] | 994 | property:
|
---|
[434] | 995 | id:maxSteps
|
---|
[554] | 996 | name:Maximum number of steps
|
---|
[552] | 997 | type:d 0 10000000 0
|
---|
[554] | 998 | group:
|
---|
[432] | 999 |
|
---|
[486] | 1000 | property:
|
---|
[567] | 1001 | id:scalingFactor
|
---|
| 1002 | name:Scaling factor for micrometers
|
---|
| 1003 | type:f 0 -1 0.01
|
---|
| 1004 | group:
|
---|
| 1005 |
|
---|
| 1006 | property:
|
---|
[554] | 1007 | id:logging
|
---|
| 1008 | name:Log statistics to file
|
---|
| 1009 | type:d 0 1 0
|
---|
| 1010 | group:
|
---|
| 1011 |
|
---|
| 1012 | property:
|
---|
[493] | 1013 | id:logPref
|
---|
| 1014 | name:Log prefix
|
---|
| 1015 | type:s
|
---|
| 1016 |
|
---|
| 1017 | property:
|
---|
[554] | 1018 | id:secPerStep
|
---|
| 1019 | name:Seconds per simulation step
|
---|
[568] | 1020 | help:~
|
---|
[570] | 1021 | Number of seconds of foraminifera time per simulation step.
|
---|
| 1022 | Lower values mean smoother animation.~
|
---|
[554] | 1023 | type:f 1 480 300
|
---|
| 1024 | flags: 16
|
---|
| 1025 | group:
|
---|
| 1026 |
|
---|
| 1027 | property:
|
---|
[474] | 1028 | id:foramSpeedMmPerMin
|
---|
| 1029 | name:Speed of foraminfera in mm/min
|
---|
[554] | 1030 | type:f 0.01 0.1 0.05
|
---|
[474] | 1031 | flags: 16
|
---|
| 1032 | group:Foraminifera
|
---|
| 1033 |
|
---|
[486] | 1034 | property:
|
---|
[554] | 1035 | id:dir_change_sec
|
---|
| 1036 | name:Number of seconds before direction change
|
---|
| 1037 | type:d 300 300000 6000
|
---|
[479] | 1038 | group:Foraminifera
|
---|
| 1039 |
|
---|
[486] | 1040 | property:
|
---|
[554] | 1041 | id:foramPop
|
---|
| 1042 | name:Initial forams population size
|
---|
| 1043 | type:d 1 1000 20
|
---|
[552] | 1044 | group:Foraminifera
|
---|
| 1045 |
|
---|
| 1046 | property:
|
---|
[554] | 1047 | id:gametoPeriodSec
|
---|
[479] | 1048 | name:Time of gametogenesis
|
---|
[554] | 1049 | type:f 300 300000 21600
|
---|
| 1050 | group:Reproduction
|
---|
[479] | 1051 |
|
---|
[486] | 1052 | property:
|
---|
[554] | 1053 | id:gametSuccessRate
|
---|
| 1054 | name:Ratio of successful gamets
|
---|
| 1055 | type:f 0.0001 0.01 0.001
|
---|
| 1056 | group:Reproduction
|
---|
[479] | 1057 |
|
---|
[486] | 1058 | property:
|
---|
[554] | 1059 | id:divisionCost
|
---|
| 1060 | name:Cost of division in pG
|
---|
| 1061 | type:f 15 25 20
|
---|
| 1062 | group:Reproduction
|
---|
[474] | 1063 |
|
---|
[486] | 1064 | property:
|
---|
[554] | 1065 | id:min_repro_energ_haplo
|
---|
[567] | 1066 | name:Min reproduction energy of haploid in pg
|
---|
| 1067 | type:f 0 -1 350000
|
---|
[554] | 1068 | group:Energy
|
---|
[380] | 1069 |
|
---|
[486] | 1070 | property:
|
---|
[554] | 1071 | id:min_repro_energ_diplo
|
---|
[567] | 1072 | name:Min reproduction energy of diploid in pg
|
---|
| 1073 | type:f 0 -1 600000
|
---|
[554] | 1074 | group:Energy
|
---|
[479] | 1075 |
|
---|
[486] | 1076 | property:
|
---|
[554] | 1077 | id:repro_prob
|
---|
| 1078 | name:Probability of reproduction
|
---|
| 1079 | type:f 0 1 0.8
|
---|
| 1080 | group:Reproduction
|
---|
[380] | 1081 |
|
---|
[486] | 1082 | property:
|
---|
[554] | 1083 | id:energies0_haplo
|
---|
| 1084 | name:Energy of offspring from diploid forams
|
---|
| 1085 | type:f 0 -1 20
|
---|
| 1086 | group:Energy
|
---|
[479] | 1087 |
|
---|
[486] | 1088 | property:
|
---|
[554] | 1089 | id:energies0_diplo
|
---|
| 1090 | name:Energy of offspring from diploid forams
|
---|
| 1091 | type:f 0 -1 1.25
|
---|
| 1092 | group:Energy
|
---|
| 1093 |
|
---|
| 1094 | property:
|
---|
[567] | 1095 | id:max_chamber_num_haplo
|
---|
| 1096 | name:Maximum number of haploid chambers
|
---|
| 1097 | type:f 1 50 35
|
---|
| 1098 | group:Energy
|
---|
| 1099 |
|
---|
| 1100 | property:
|
---|
| 1101 | id:max_chamber_num_diplo
|
---|
| 1102 | name:Maximum number of diploid chambers
|
---|
| 1103 | type:f 1 50 35
|
---|
| 1104 | group:Energy
|
---|
| 1105 |
|
---|
| 1106 | property:
|
---|
[554] | 1107 | id:crossprob
|
---|
| 1108 | name:Crossover probability
|
---|
| 1109 | type:f 0 1 0
|
---|
| 1110 | group:Reproduction
|
---|
| 1111 |
|
---|
| 1112 | property:
|
---|
| 1113 | id:mutationprob
|
---|
| 1114 | name:Mutation probability
|
---|
| 1115 | type:f 0 1 0
|
---|
| 1116 | group:Reproduction
|
---|
| 1117 |
|
---|
| 1118 | property:
|
---|
| 1119 | id:reproTimeSec
|
---|
| 1120 | name:Time before reproduction
|
---|
| 1121 | type:d 0 10000 720
|
---|
| 1122 | group:Reproduction
|
---|
| 1123 |
|
---|
| 1124 | property:
|
---|
| 1125 | id:chamberGrowthSec
|
---|
| 1126 | name:Time of the chamber growth in seconds
|
---|
[567] | 1127 | type:f 720 43200 43200
|
---|
[479] | 1128 | group:Foraminifera
|
---|
| 1129 |
|
---|
[486] | 1130 | property:
|
---|
[422] | 1131 | id:chamber_proculus_haplo
|
---|
[423] | 1132 | name:Size of proculus
|
---|
[422] | 1133 | type:f
|
---|
[421] | 1134 | group:Foraminifera
|
---|
[380] | 1135 |
|
---|
[486] | 1136 | property:
|
---|
[422] | 1137 | id:chamber_proculus_diplo
|
---|
[423] | 1138 | name:Size of proculus
|
---|
[422] | 1139 | type:f
|
---|
[380] | 1140 | group:Foraminifera
|
---|
| 1141 |
|
---|
[486] | 1142 | property:
|
---|
[422] | 1143 | id:hunted_prob
|
---|
| 1144 | name:Probability of being hunted
|
---|
| 1145 | type:f 0 1 0
|
---|
[554] | 1146 | group:Foraminifera
|
---|
[380] | 1147 |
|
---|
[486] | 1148 | property:
|
---|
[557] | 1149 | id:zone1_range
|
---|
[556] | 1150 | name:Zone 1 range in frams units
|
---|
[554] | 1151 | type:f 0 200 10
|
---|
[422] | 1152 | group:Foraminifera
|
---|
[380] | 1153 |
|
---|
[486] | 1154 | property:
|
---|
[422] | 1155 | id:zone2_range
|
---|
[556] | 1156 | name:Zone 2 range in frams units
|
---|
[554] | 1157 | type:f 0 3000 30
|
---|
[421] | 1158 | group:Foraminifera
|
---|
[380] | 1159 |
|
---|
[486] | 1160 | property:
|
---|
[554] | 1161 | id:chamberCostPerSec
|
---|
| 1162 | name:Cost of growning chamber per second
|
---|
| 1163 | type:f 0 1 0.000001
|
---|
| 1164 | group:Energy
|
---|
[380] | 1165 |
|
---|
[486] | 1166 | property:
|
---|
[475] | 1167 | id:e_death_level_haplo
|
---|
| 1168 | name:Minimal level of energy to sustain life of haploid
|
---|
[554] | 1169 | type:f 0 1 0.5
|
---|
| 1170 | group:Energy
|
---|
[475] | 1171 |
|
---|
[486] | 1172 | property:
|
---|
[475] | 1173 | id:e_death_level_diplo
|
---|
| 1174 | name:Minimal level of energy to sustain life of diploid
|
---|
[554] | 1175 | type:f 0 1 0.5
|
---|
| 1176 | group:Energy
|
---|
[475] | 1177 |
|
---|
[486] | 1178 | property:
|
---|
[422] | 1179 | id:energy_hib
|
---|
| 1180 | name:Energy used for hibernation during one step
|
---|
[554] | 1181 | type:f 0 1 0.0000001
|
---|
| 1182 | group:Energy
|
---|
[422] | 1183 |
|
---|
[486] | 1184 | property:
|
---|
[422] | 1185 | id:energy_move
|
---|
| 1186 | name:Energy used for movement during one step
|
---|
[554] | 1187 | type:f 0 1 0.0000005
|
---|
| 1188 | group:Energy
|
---|
[422] | 1189 |
|
---|
[486] | 1190 | property:
|
---|
[380] | 1191 | id:e_meta
|
---|
| 1192 | name:Idle metabolism
|
---|
[554] | 1193 | type:f 0 1 0.0000005
|
---|
[380] | 1194 | group:Energy
|
---|
[556] | 1195 | help:Foraminifera consumes this proportion of its energy in one time step
|
---|
[380] | 1196 |
|
---|
[486] | 1197 | property:
|
---|
[554] | 1198 | id:ingestion
|
---|
| 1199 | name:Ingestion rate
|
---|
| 1200 | type:f 0 -1 0.25
|
---|
| 1201 | group:Energy
|
---|
| 1202 |
|
---|
| 1203 | property:
|
---|
[493] | 1204 | id:nutrient_pop
|
---|
[554] | 1205 | name:Nutrient population
|
---|
[474] | 1206 | type:f 0 1000000
|
---|
[380] | 1207 | group:Energy
|
---|
| 1208 | help:How fast energy is created in the world
|
---|
| 1209 |
|
---|
[486] | 1210 | property:
|
---|
[554] | 1211 | id:energy_nut
|
---|
| 1212 | name:Nutrient energy
|
---|
| 1213 | type:f 0 10000000
|
---|
[481] | 1214 | group:Energy
|
---|
| 1215 |
|
---|
[486] | 1216 | property:
|
---|
[554] | 1217 | id:nutrientradius
|
---|
| 1218 | name:Nutrient size
|
---|
| 1219 | type:f 0.001 0.9 0.1
|
---|
[479] | 1220 | group:Energy
|
---|
| 1221 |
|
---|
[486] | 1222 | property:
|
---|
[554] | 1223 | id:picoCarbonPerMikro
|
---|
[556] | 1224 | name:Picograms of carbon in cubic micrometer
|
---|
[554] | 1225 | type:f 0 -1 0.13
|
---|
[380] | 1226 | group:Energy
|
---|
| 1227 |
|
---|
[486] | 1228 | property:
|
---|
[380] | 1229 | id:feedtrans
|
---|
[479] | 1230 | name:Energy transfer per second
|
---|
[554] | 1231 | type:f 0 1 0.001
|
---|
[380] | 1232 | group:Energy
|
---|
[422] | 1233 |
|
---|
[486] | 1234 | property:
|
---|
[590] | 1235 | id:foodflux
|
---|
| 1236 | name:POM flux in grams per second per square meter
|
---|
| 1237 | type:f 0 1 0.0000000075631
|
---|
[422] | 1238 | group:Energy
|
---|
| 1239 |
|
---|
[486] | 1240 | property:
|
---|
[590] | 1241 | id:foodfluxChange
|
---|
[554] | 1242 | name:Set variable feed rate
|
---|
| 1243 | type:f 0 -1 0
|
---|
[421] | 1244 | group:Energy
|
---|
| 1245 |
|
---|
[486] | 1246 | property:
|
---|
[422] | 1247 | id:stress
|
---|
| 1248 | name:Environmental stress
|
---|
| 1249 | type:d 0 1 1
|
---|
[554] | 1250 | group:
|
---|
[422] | 1251 |
|
---|
[486] | 1252 | property:
|
---|
[422] | 1253 | id:repro_trigger
|
---|
| 1254 | name:Reproduction trigger
|
---|
| 1255 | type:d 0 1 1
|
---|
[554] | 1256 | group:Reproduction
|
---|
[422] | 1257 |
|
---|
[486] | 1258 | property:
|
---|
[422] | 1259 | id:creath
|
---|
| 1260 | name:Creation height
|
---|
[554] | 1261 | type:f -1 50 -0.99
|
---|
[422] | 1262 | help:~
|
---|
| 1263 | Vertical position (above the surface) where new Forams are revived.
|
---|
| 1264 | Negative values are only used in the water area:
|
---|
| 1265 | 0 = at the surface
|
---|
| 1266 | -0.5 = half depth
|
---|
| 1267 | -1 = just above the bottom~
|
---|
| 1268 |
|
---|
[554] | 1269 | property:
|
---|
| 1270 | id:autorestart
|
---|
| 1271 | name:Restart after extinction
|
---|
| 1272 | help:Restart automatically this experiment after the last creature has died?
|
---|
| 1273 | type:d 0 1 0
|
---|
| 1274 |
|
---|
[421] | 1275 | state:
|
---|
| 1276 | id:nutrient
|
---|
[428] | 1277 | name:Nutrient locations
|
---|
[421] | 1278 | help:vector of vectors [x,y,energy]
|
---|
| 1279 | type:x
|
---|
| 1280 | flags:32
|
---|
| 1281 |
|
---|
[380] | 1282 | state:
|
---|
| 1283 | id:notes
|
---|
| 1284 | name:Notes
|
---|
| 1285 | type:s 1
|
---|
| 1286 | help:~
|
---|
| 1287 | You can write anything here
|
---|
| 1288 | (it will be saved to the experiment file)~
|
---|
| 1289 |
|
---|
| 1290 | state:
|
---|
| 1291 | id:totaltestedcr
|
---|
[421] | 1292 | name:Evaluated Forams
|
---|
| 1293 | help:Total number of the Forams evaluated in the experiment
|
---|
[380] | 1294 | type:d
|
---|
| 1295 | flags:16
|
---|