source: experiments/frams/foraminifera/data/scripts/foraminifera.expdef @ 510

Last change on this file since 510 was 510, checked in by oriona, 8 years ago

Energy transfer changed for using tranferEnergyTo function. Dilpoid offspring number calculation changed.

File size: 27.6 KB
RevLine 
[380]1expdef:
[406]2name:Reproduction of benthic foraminifera
[380]3info:~
[434]4Basic information about this simulation:
5www.framsticks.com/foraminifera
6
7Technical information:
[476]8Genes and parameter values which control reproduction are stored in data->genes and data->lifeparams fields.
[380]9
[476]10genes:
[402]11genes which are not encoded in Ff genotype:
[422]12min_repro_energy - Minimum energy necessary for reproduction
13hibernation - Defines foram behavior in the case of no nutrients
[380]14
[476]15lifeparams:
[380]16Physiological parameters of foraminifera:
[422]17max_energy_level - maximum energy level reached so far
[380]18gen - generation: 0 haploid, 1 diploid
[432]19species - species: 0 not hibernating 1 hibernating
20hibernated - 0/1 foram is/isn't hibernated
[422]21reproduce - 0/1 foram isn't/is ready for reproduction
[380]22~
23code:~
24
[479]25global chambers;
[422]26global colors;
[493]27global retColors;
28global curColor;
29global dir_change_sec;
[479]30global max_chamber_volume;
[474]31global movePerStep;
[479]32global nutrientenergywaiting;
33global o;
34global reprocounter;
[481]35global changePeriod;
36global phase;
[493]37global nutrientSqrCm;
[487]38global species_genes;
[380]39
[406]40@include "foraminifera.inc"
[401]41
[380]42// -------------------------------- experiment begin --------------------------------
43
44function onExpDefLoad()
45{
46        // define genotype and creature groups
47        GenePools.clear();
48        Populations.clear();
49        GenePools[0].name = "Unused";
50
51        var pop = Populations[0];
[421]52        pop.name = "Forams";
[380]53        pop.en_assim = 0;
[404]54        pop.nnsim = 0;
[380]55        pop.enableperf = 1;
56        pop.death = 1;
57        pop.energy = 1;
[487]58        pop.selfmask = 0;
59        pop.othermask = 0;
[401]60        //pop.selfmask = 0x20002; pop.othermask = 0x10002;
[422]61        pop.perfperiod = 25;
[487]62        pop.bodysim = 0;
[380]63
[421]64        pop = Populations.addGroup("Nutrients");
[380]65        pop.nnsim = 0;
66        pop.enableperf = 0;
67        pop.death = 1;
68        pop.energy = 1;
[487]69        pop.selfmask = 0;
70        pop.othermask = 0;
[422]71        //pop.othermask = 0x10002;
[487]72        pop.bodysim = 0;
[380]73
[444]74        pop = Populations.addGroup("ReticulopodiaNutrients");
[430]75        pop.nnsim = 0;
76        pop.enableperf = 0;
77        pop.death = 0;
78        pop.energy = 0;
[487]79        pop.selfmask = 0;
80        pop.othermask = 0;
81        pop.bodysim = 0;
[444]82
[422]83        //world
84        SignalView.mode = 1;
[496]85        World.wrldwat = 200;
[493]86        World.wrldsiz = micronsToFrams(100000);
[422]87        World.wrldbnd = 1;
[486]88        ExpProperties.stress = 1;
89        ExpProperties.creath = -0.99; //just above the bottom
90        ExpProperties.autorestart = 0;
[422]91
[474]92        //time
[486]93        ExpProperties.secPerStep = 480;
94        ExpProperties.foramSpeedMmPerMin = 0.05;
[474]95        movePerStep = getMovePerStep();
96
[486]97        //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
[444]98
[487]99        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files   
[493]100        ExpProperties.logPref = "";
[401]101
[422]102        //reproduction
[486]103        ExpProperties.foramPop = 20;   
104        ExpProperties.crossprob = 0;
105        ExpProperties.mutationprob = 0;
106        ExpProperties.repro_time = 720;
[493]107        ExpProperties.gametoPeriod = 21600;
[486]108        ExpProperties.divisionCost = 15.6;
[422]109        reprocounter = 0;
[380]110
[487]111        species_genes = [];
112
[479]113        init_chambers();
114
[493]115        curColor = retColors[0];
[422]116        //morphology
[493]117        dir_change_sec = 30000;
[486]118        ExpProperties.zone1_range = micronsToFrams(1000);
119        ExpProperties.zone2_range = micronsToFrams(3000);
120        ExpProperties.chamber_growth_time = 720;
121        ExpProperties.chamberCostPerSec = 0.000001;
122        ExpProperties.chamber_proculus_haplo = micronsToFrams(50);
123        ExpProperties.chamber_difference_haplo = 0.0;
124        ExpProperties.chamber_proculus_diplo = micronsToFrams(20);
125        ExpProperties.chamber_difference_diplo = micronsToFrams(8);
[479]126
127        max_chamber_volume = [Vector.new(), Vector.new()];
[422]128        for (var j = 0; j < 2; j++)
129        {
130                for (var i = 0; i < chambers[0].size; i++)
131                {
[479]132                        max_chamber_volume[j].add(((volumeInMicrons(getProperty(j, "chamber_proculus")) + volumeInMicrons(getProperty(j, "chamber_proculus") + (i) * getProperty(j, "chamber_difference")))*(i+1))/2); 
[422]133                }                                 
134        }
135
136        //energetics
[486]137        ExpProperties.min_repro_energ_haplo = 4;
138        ExpProperties.min_repro_energ_diplo = 6;
[430]139
[486]140        ExpProperties.e_meta = 0.0000005;
141        ExpProperties.energy_hib = 0.0000001;
142        ExpProperties.energy_move = 0.0000005;
[430]143
[493]144        ExpProperties.energies0_haplo = 20;
145        ExpProperties.energies0_diplo = 1.25;
[486]146        ExpProperties.feedtrans = 0.001;
147        ExpProperties.e_repro_cost_haplo = 0.3;
148        ExpProperties.e_repro_cost_diplo = 0.2;
[422]149
[486]150        ExpProperties.e_death_level_haplo = 0.5;
151        ExpProperties.e_death_level_diplo = 0.5;
[479]152
[422]153        //nutrients
[481]154        changePeriod = 0;
[488]155        phase = "low";
[493]156        nutrientSqrCm = 10;
[502]157        ExpProperties.foodperiod = 19200;
158        ExpProperties.foodPeriodChange = 0;
[486]159        ExpProperties.nutrientradius = micronsToFrams(10);
[502]160        ExpProperties.energy_nut = 150 * energyFromVolume(ExpProperties.nutrientradius,1);
[493]161        ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
[486]162        ExpProperties.ingestion = 0.25;
[474]163        nutrientenergywaiting = 0;
[380]164        ExpState.totaltestedcr = 0;
[421]165        ExpState.nutrient = "";
[488]166       
[493]167        //addSpecies({"min_repro_energies" : [4,6]});
168        //addSpecies({"min_repro_energies" : [4,8]});
[380]169}
170
171@include "standard_placement.inc"
172
[479]173function volumeInMicrons(radiusInFrams)
[475]174{
[479]175        return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
[475]176}
177
[479]178function energyFromVolume(base, isRadiusInFrams)
179{
180        if (isRadiusInFrams == 1) //radius in frams
181        {
[486]182                return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
[479]183        }
184        else //volume in microns
185        {
[486]186                return ExpProperties.picoCarbonPerMikro * base;
[479]187        }
188}
189
[474]190function getMovePerStep()
191{
[486]192        return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
[474]193}
194
[447]195function micronsToFrams(micrometers)
[422]196{
[493]197        return micrometers*0.01;
[422]198}
199
[447]200function framsToMicrons(framsworldunits)
[445]201{
[493]202        return framsworldunits/0.01;
[445]203}
204
[422]205function getProperty(gen, prop_id)
206{
207        var ploid = "haplo";
208        if (gen == 1) ploid = "diplo";
[486]209        return ExpProperties.[prop_id + "_" + ploid];
[422]210}
211
[487]212function getGene(cr, gen_id, gen_set)
213{
214        if (cr.data->lifeparams->gen == 0)
215                return cr.data->genes[gen_id];
216        else
217                return cr.data->genes[gen_set][gen_id];
218}
219
[479]220function addForam(species, iter, chambernum, ploid)
[422]221{
[496]222        var geno = createForamMorphology(ploid, ploid, chambernum);
[493]223        curColor = retColors[ploid];
[422]224        var cr = Populations[0].add(geno);
[479]225        cr.name = "Initial creature" + species + "_" + iter;
[422]226        placeCreatureRandomly(cr, 0, 0);
[479]227        cr.energy0 = energyFromVolume(max_chamber_volume[ploid][chambernum],0);
[422]228        cr.energy = cr.energy0;
[487]229        setGenotype({"opt" : 0, "cr" : cr, "species" : species, "energy0" : cr.energy0, "genes" : species_genes[species]});
[479]230        if (ploid == 1)
231        {
232                cr.data->lifeparams->gen = 1;
233                cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
234        }
[422]235}
236
[479]237function addInitialForam(species, iter)
238{
239        var ploid = 0;
240        if (Math.rnd01 > 0.5)
241        {
242                ploid = 1;
243        }       
[493]244        //add new foram with random energy bewtween starting energy and reproduction threshold
[488]245        addForam(species, iter, int(Math.rndUni(0,species_genes[species]->min_repro_energies[ploid])),ploid);
[479]246}
247
[487]248//new species can be added as a dictionary with parameter values that are different than default values
249function addSpecies(new_genes)
250{
[493]251        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});
[487]252        for (var i = 0; i < new_genes.size; i++)
253        {
254                var key = new_genes.getKey(i);
255                species_genes[species_genes.size-1][key] = new_genes[key];
256        }
257}
258
[380]259function onExpInit()
260{
261        Populations[0].clear();
262        Populations[1].clear();
[444]263        Populations[2].clear(); //reticulopodia and nutrients
[380]264
[487]265        if (species_genes.size == 0)
[380]266        {
[487]267                addSpecies({}); //default
[380]268        }
[487]269
270        for (var spec = 0; spec < species_genes.size; spec++)
271        {
272                for (var i = 0; i < ExpProperties.foramPop; i++)
273                {
274                        addInitialForam(spec, i);       
275                }
276        }
[422]277        o = Populations[0][0].getMechPart(0).orient.clone();
[380]278        ExpState.totaltestedcr = 0;
279}
280
281function onExpLoad()
282{
283        for (var pop in Populations)
284                pop.clear();
285
286        Loader.addClass(sim_params.*);
287        Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
288        Loader.run();
289
[421]290        Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
[380]291}
292
293function onExpLoad_Unknown()
294{
295        if (Loader.objectName == "org") // saved by the old expdef
296        {
297                var g = Genotype.newFromString("");
298                Loader.currentObject = g;
299                Interface.makeFrom(g).setAllDefault();
300                Loader.loadObject();
301                var cr = Populations[0].add(g);
302                if (cr != null)
303                {
[401]304                        //cr.rotate(0,0,Math.rnd01*Math.twopi);
[476]305                        if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
[401]306                        {
307                                // [x,y,energy]
[476]308                                cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
309                                cr.energy = g.data->genes[2];
[380]310                        }
311                        else
312                        {
[401]313                                cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
[380]314                        }
315                }
316        }
317        else if (Loader.objectName == "Creature")
318        {
319                Loader.currentObject = CreatureSnapshot.new();
320                Loader.loadObject();
321                Populations[0].add(Loader.currentObject);
322        }
323}
324
325function onExpSave()
326{
327        File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
328
[401]329        var tmpvec = [], i;
[380]330
[401]331        for(var cr in Populations[1])
[380]332                tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
333
[421]334        ExpState.nutrient = tmpvec;
[380]335        File.writeObject(sim_params.*);
[432]336        ExpState.nutrient = null; //vectors are only created for saving and then discarded
[380]337
338        for (var cr in Populations[0])
339                File.writeObject(cr);
340}
341
342// -------------------------------- experiment end --------------------------------
343
[421]344// -------------------------------- foram begin -----------------------------------
[380]345
[479]346function setForamMeta(cr)
[430]347{
[479]348        //percent of current energy
[486]349        cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
[430]350}
351
352function lastChamberNum(cr)
353{
354        return cr.numparts-1;
355}
356
[479]357function getZoneRange(cr, zone_num)
358{
[486]359        return ExpProperties.["zone"+zone_num+"_range"];
[479]360}
361
[421]362function onForamsBorn(cr)
363{
[479]364        setForamMeta(cr);
[486]365        if (ExpProperties.visualize == 1)
[430]366        {
[506]367                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="+getZoneRange(cr,1)+",sz="+getZoneRange(cr,1)+",ry=1.57079633,vr="+curColor+"\nj:0, 1, sh=1");
[476]368                cr.data->reticulopodiacreature = ret;
[506]369                ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
[496]370                ret.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
[430]371        }
[380]372}
373
[401]374function placeRandomlyNotColliding(cr)
375{
376        var retry = 100; //try 100 times
377        while (retry--)
378        {
379                placeCreatureRandomly(cr, 0, 0);
380                if (!cr.boundingBoxCollisions(0))
381                        return cr;
382        }
383
384        Populations[0].delete(cr);
385}
386
[444]387function visualization(cr)
388{
389        var has_ret = 0;
390
[476]391        if (cr.data->reticulopodiacreature != null)
[444]392        {
[476]393                if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
[444]394                {
395                        has_ret = 1;
396                }
397        }
398
399        return has_ret;
400}
401
[422]402function foramGrow(cr, chamber_num)
[380]403{
[476]404        if ((chamber_num+1) < chambers[cr.data->lifeparams->species].size)
[474]405        {
[493]406                curColor = retColors[cr.data->lifeparams->gen];
[496]407                var geno = createForamMorphology(cr.data->lifeparams->gen, cr.data->lifeparams->gen, chamber_num+1);
[474]408                var cr2 = Populations[0].add(geno);
[422]409
[474]410                cr2.energy0 = cr.energy;
411                cr2.energy = cr2.energy0;
[422]412
[487]413                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : 2, "energy0" : cr.energy0});
[474]414                cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
[479]415                setForamMeta(cr2);
[422]416
[474]417                if (visualization(cr))
418                {
[476]419                        Populations[2].delete(cr.data->reticulopodiacreature);
[474]420                }
421                Populations[0].delete(cr);
[430]422        }
[380]423}
424
[435]425function stepToNearest(cr)
[380]426{
427        var p = cr.getMechPart(0);
[479]428        var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
[380]429
[401]430        //if signals are received find the source of the nearest
[380]431        if (n.size > 0)
432        {
433                var i;
434                var mp;
435                var distvec = XYZ.new(0, 0, 0);
436                var dist;
[470]437                var mindist = 100000000000.0;
[380]438                var mindistvec = null;
[430]439                var eating = 0;
[380]440
[401]441                for (i = 0; i < n.size; i++)
[380]442                {
[430]443                        mp = n[i].value.getMechPart(0);
[401]444                        distvec.set(mp.pos);
445                        distvec.sub(p.pos);
446                        dist = distvec.length;
[479]447                        if (dist < getZoneRange(cr,1))
[380]448                        {
[430]449                                if (n[i].value != null)
450                                {
451                                        energyTransfer(cr, n[i].value);
452                                        eating = 1;
453                                }
454                        }
[476]455                        else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
[430]456                        {
[401]457                                mindist = dist;
458                                mindistvec = distvec.clone();
[380]459                        }
460                }
461
[476]462                if (!eating && cr.data->lifeparams->hibernated == 0)
[430]463                {
464                        mindistvec.normalize();
[474]465                        mindistvec.scale(-1*movePerStep);
[430]466                        cr.localDrive = mindistvec;
467                        moveEnergyDec(cr);
468                }
469
[422]470                return 1;
[380]471        }
[422]472       
473        else
[474]474        {
[422]475                return 0;
[474]476        }
[422]477}
[401]478
[422]479function moveEnergyDec(cr)
480{
[476]481        if (cr.data->lifeparams->hibernated == 0)
[422]482        {
[479]483                //percent of maximal energy
[504]484                cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
[422]485        }
[421]486}
[380]487
[493]488function fence(pos, zone)
[487]489{
[496]490        return Math.min(Math.max(0,pos),World.wrldsiz);
[487]491}
492
[422]493function foramMove(cr)
[421]494{
[422]495        //TODO moving inside sediment?
[421]496
[422]497        //adjustment in z axis
[493]498        cr.moveAbs(fence(cr.pos_x, getZoneRange(cr, 1)), fence(cr.pos_y,getZoneRange(cr, 1)), 0);
[421]499
[430]500        //are there any nutrients in zone 1 or 2?
[401]501        {
[435]502                var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
[422]503                if (moved==1)
[430]504                {
[502]505                        moveReticulopodia(cr);
[422]506                        return;
507                }
[401]508        }
509
[422]510        //no nutrients in zone 2
[487]511        if (getGene(cr, "hibernation",0) == 1)
[401]512        {
[430]513                reverseHib(cr);
[422]514                cr.localDrive = XYZ.new(0,0,0);
[380]515        }
[422]516        //random move
[493]517        else if (Simulator.stepNumber%int(dir_change_sec/ExpProperties.secPerStep) == 0)
[380]518        {
[476]519                cr.data->lifeparams->dir = randomDir();
520                cr.localDrive = cr.data->lifeparams->dir;
[422]521                moveEnergyDec(cr);
522        }
[474]523        else
524        {
[476]525                cr.localDrive = cr.data->lifeparams->dir;
[474]526        }
[502]527        moveReticulopodia(cr);
[422]528}
[401]529
[502]530function moveReticulopodia(cr)
531{
532        if (visualization(cr))
533        {
534                cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
535                cr.data->reticulopodiacreature.localDrive = cr.localDrive;
536        }
537}
538
[474]539function randomDir()
540{
[486]541        var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0); 
[474]542        dir.normalize();
543        dir.scale(-1*movePerStep);
544        return dir;
545}
546
[430]547function energyTransfer(cr1, cr2)
[422]548{
[430]549        cr1.localDrive = XYZ.new(0,0,0);
[510]550        var e =  ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
[502]551        //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
[510]552        var transferred = cr2.transferEnergyTo(cr1, e);
553        cr1.energy -= transferred*(1-ExpProperties.ingestion);
[476]554        if (cr1.data->lifeparams->hibernated == 1)
[422]555        {
[430]556                reverseHib(cr1);
[422]557        }
558}
[401]559
[430]560function reverseHib(cr)
561{
[476]562        if (cr.data->lifeparams->hibernated == 1)
[430]563        {
[479]564                setForamMeta(cr); //unhibernate
[430]565        }
566        else
567        {
[486]568                cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
[430]569        }
[476]570        cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
[430]571}
572
[493]573function createLogVector(cr, value)
574{
575        var vec = Vector.new();
576        for (var i = 0; i < species_genes.size; i++)
577        {
578                for (var j = 0; j < 2; j++)
579                {
580                        vec.add(0);
581                }
582                if (cr.data->lifeparams->species == i)
583                {
584                        vec[i*2+cr.data->lifeparams->gen] = value;             
585                }
586        }
587        return vec;
588}
[479]589
[422]590function onForamsStep(cr)
591{
[479]592        //checking for gametogenesis process
593        if (cr.data->lifeparams->division_time > 0)
[444]594        {
[479]595                cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
[444]596        }
[479]597        //checking for end of gametogenesis
598        else if (cr.data->lifeparams->division_time == 0)
[422]599        {
[479]600                //waiting for gamets fusion
[422]601        }
[479]602        //checking for chamber growth process
603        else if (cr.data->lifeparams->chamber_growth > 0)
604        {
605                cr.data->lifeparams->chamber_growth = Math.max(cr.data->lifeparams->chamber_growth-1,0);
[486]606                //Simulator.print("chamber growing, time left = " + cr.data->lifeparams->chamber_growth*ExpProperties.secPerStep);
[504]607                cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
[422]608
[479]609                //Simulator.print("energy " + cr2.energy + " subtracting " + growth_cost);
610        }
611        //checking for end of chamber growth process
612        else if (cr.data->lifeparams->chamber_growth == 0)
[430]613        {
[479]614                foramGrow(cr, lastChamberNum(cr));
615                cr.data->lifeparams->chamber_growth = -1;
616                //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
[430]617        }
[479]618        else
[422]619        {
[479]620                //update of metabolism rate
621                if (cr.data->lifeparams->hibernated == 0)
[401]622                {
[479]623                        setForamMeta(cr);
624                }
625
626                cr.getMechPart(0).orient.set(o);
627
628                if (deathConditions(cr) == 1)
629                {
[493]630                        if (ExpProperties.logging == 1)
631                        {
632                                log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
633                        }                       
[479]634                        Populations[0].kill(cr);
635                        return;
636                }
637
638                foramMove(cr);
639
640                var repro = foramReproduce(cr);
641                if (repro == 1)
642                {
643                        return;
644                }
645
646                cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
647
648                //cheking conditions of chamber growth process start
649                if  (lastChamberNum(cr) != chambers[0].size-1)
650                {
651                        if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)],0)))   
652                        {
[486]653                                cr.data->lifeparams->chamber_growth = int(ExpProperties.chamber_growth_time/ExpProperties.secPerStep);
[479]654                        }       
655                }
[430]656        }       
[380]657}
658
[422]659function deathConditions(cr)
660{
[486]661        if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
[479]662        {
[422]663                return 1;
[479]664        }
[422]665        else
666                return 0;
667}
668
[421]669function onForamsDied(cr)
[380]670{
[444]671        if (visualization(cr))
[430]672        {
[476]673                Populations[2].delete(cr.data->reticulopodiacreature);
[430]674        }
[380]675        //fossilization
676        var geno = GenePools[0].add(cr.genotype);
[476]677        geno.data->genes = cr.data->genes;
678        geno.data->lifeparams = cr.data->lifeparams;
[486]679        if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
[380]680        ExpState.totaltestedcr++;
681}
682
[421]683// --------------------------------foram end -------------------------------------
[380]684
[421]685// -------------------------------- nutrient begin --------------------------------
[380]686
[479]687function createNutrientGenotype(nutrientradius)
[422]688{
[502]689        return "//0\np:sh=3,sx="+nutrientradius+",sy="+nutrientradius+",sz="+nutrientradius+",ry=1.57,vr=0.0,1.0,0.0";
[422]690}
691
[421]692function onNutrientsStep(cr)
[380]693{
[444]694        cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
[380]695}
696
[421]697function addNutrient()
[380]698{
[486]699        var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
[380]700
[421]701        cr.name = "Nutrients";
[380]702        cr.idleen = 0;
[486]703        cr.energy0 = ExpProperties.energy_nut;
[416]704        cr.energy = cr.energy0;
[421]705        cr.signals.add("nutrient");
[380]706
[430]707        cr.signals[0].value = cr;
[380]708
[422]709        placeCreatureRandomly(cr, 0, 0);
[486]710        if (ExpProperties.visualize == 1)
[444]711        {
[486]712                var nutsize = ExpProperties.nutrientradius*10;
[444]713                var nut = Populations[2].add("//0\np:sh=2,sx="+nutsize+",sy="+nutsize+",sz="+nutsize+",ry=1.5,vr=0.0,1.0,0.0");
[476]714                cr.data->reticulopodiacreature = nut;
[444]715                nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
716        }
[380]717}
718
[444]719function onNutrientsDied(cr)
720{
721        if (visualization(cr))
722        {
[476]723                Populations[2].delete(cr.data->reticulopodiacreature);
[444]724        }
725}
726
[422]727function nutrientGrowth()
[380]728{
[486]729        if (ExpProperties.foodPeriodChange > 0)
[481]730        {
731                        changePeriod += 1;
[486]732                        if (phase=="low" && (changePeriod*ExpProperties.secPerStep) >= 23328000) //9 months
[481]733                        {
[486]734                                ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
[481]735                                phase = "high";
736                                changePeriod = 0;
737                        }
738               
[486]739                        else if (phase == "high" && (changePeriod*ExpProperties.secPerStep) >= 7776000) //3 months
[481]740                        {
[486]741                                ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
[481]742                                phase = "low";
743                                changePeriod = 0;
744                        }
745        }
[474]746        nutrientenergywaiting = nutrientenergywaiting + 1;
[486]747        if (nutrientenergywaiting*ExpProperties.secPerStep >= ExpProperties.foodperiod)
[380]748        {
[493]749                for (var i = 0; i < ExpProperties.nutrient_pop; i++)
[432]750                {   
[422]751                        addNutrient();
752                }
753
754                nutrientenergywaiting = 0.0;
755                Simulator.checkpoint();
[493]756
757                if (ExpProperties.logging == 1)
758                {
759                        log([ExpProperties.nutrient_pop],ExpProperties.logPref+"nutrients_log.txt");
760                }
[380]761        }
[493]762
[380]763}
764
[421]765// -------------------------------- nutrient end --------------------------------
[380]766
[422]767// -------------------------------- step begin --------------------------------
[380]768
[422]769function onStep()
770{
[432]771
772        nutrientGrowth();
[486]773        if (ExpProperties.logging == 1)
[422]774        {
775                createStatistics();
776        }
777
778        //reproduction --------------------------------------------
779        reprocounter += 1;
[486]780        if (reprocounter*ExpProperties.secPerStep > ExpProperties.repro_time)
[422]781        {
782                reprocounter = 0;
783                reproduce_parents(0);
784                reproduce_parents(1);
785        }
786
787        //check for extinction -----------------------------------------------
788        if (Populations[0].size == 0)
789        {
[486]790                if (ExpProperties.autorestart)
[422]791                {
792                        Simulator.print("no more creatures, restarting...");
793                        onExpInit();
794                }
795                else
796                {
797                        Simulator.print("no more creatures, stopped.");
798                        Simulator.stop();
799                }
800        }
[486]801        if (ExpProperties.maxSteps > 0)
[432]802        {
[486]803                if (Simulator.stepNumber >= ExpProperties.maxSteps)
[432]804                        Simulator.stop();
805        }
[422]806}
807
808function createStatistics()
809{       
[487]810        var number = [];
811        var e_inc = [];
[422]812        var e_nut = 0.0;
813
[487]814        for (var s = 0; s < species_genes.size; s++)
815        {
816                number.add([0,0]);// [haplo][diplo]
817                e_inc.add([0,0]);
818        }
819
[422]820        for (var i = 0; i < Populations[0].size; i++)
821        {
822                var cr = Populations[0].get(i);
[476]823                var gen = cr.data->lifeparams->gen;
824                var species = cr.data->lifeparams->species;
[430]825
826                number[species][gen] = number[species][gen] + 1;
827                e_inc[species][gen] = e_inc[species][gen] + cr.energy;
[422]828        }
829
830        for (var i = 0; i < Populations[1].size; i++)
831        {
832                var cr = Populations[1].get(i);
833                e_nut += cr.energy;
834        }
835
[487]836        var log_numbers = [];
837        var log_energies = [];
[422]838
[487]839        for (var s = 0; s < species_genes.size; s++)
840        {
841                for (var p = 0; p < 2; p++)
842                {
843                        log_numbers.add(number[s][p]);
844                        log_energies.add(e_inc[s][p]);
845                }
846        }
847       
848        log_numbers.add(Populations[1].size);
849        log_energies.add(e_nut);
850
[493]851        log(log_numbers, ExpProperties.logPref+"forams_log.txt");
852    log(log_energies,  ExpProperties.logPref+"energies_log.txt");
[422]853}
854
[380]855function log(tolog, fname)
856{
[430]857        var f = File.appendDirect(fname, "forams data");
[380]858        f.writeString("" + Simulator.stepNumber);
[401]859        for (var  i = 0; i < tolog.size; i++)
[380]860        {
861                f.writeString(";" + tolog[i]);
862        }
863        f.writeString("\n");
864        f.close();
865}
866
[422]867// -------------------------------- step end --------------------------------
[479]868//TODO default params values in frams instead of microns/seconds
[380]869
[401]870@include "standard_events.inc"
[380]871
[401]872~
[380]873
[486]874property:
[444]875id:visualize
876name:Show reticulopodia and nutrients
[430]877type:d 0 1 0
878group:Foraminifera
879
[486]880property:
[434]881id:maxSteps
[432]882name:Stop after the given number of simulation steps
[434]883type:d 0 1000000 0
[432]884
[486]885property:
[493]886id:logPref
887name:Log prefix
888type:s
889
890property:
[474]891id:foramSpeedMmPerMin
892name:Speed of foraminfera in mm/min
893type:f 0.1
894flags: 16
895group:Foraminifera
896
[486]897property:
[479]898id:gametSuccessRate
899name:Ratio of successful gamets
900type:f 0.001
901group:Foraminifera
902
[486]903property:
[479]904id:gametoPeriod
905name:Time of gametogenesis
906type:f 720
907group:Foraminifera
908
[486]909property:
[479]910id:picoCarbonPerMikro
911name:Picograms of carbon in cubed micrometer
912type:f 0.13
913group:Foraminifera
914
[486]915property:
[474]916id:secPerStep
917name:Seconds per simulation step
918type:f 60.0
919flags: 16
920group:Foraminifera
921
[486]922property:
[422]923id:e_repro_cost_haplo
[423]924name:Cost of reproduction
[422]925type:f 0.1 0.9 0.5
[421]926group:Foraminifera
[380]927
[486]928property:
[479]929id:divisionCost
930name:Cost of division in pG
931type:f
932group:Foraminifera
933
[486]934property:
[422]935id:e_repro_cost_diplo
[423]936name:Cost of reproduction
[422]937type:f 0.1 0.9 0.3
938group:Foraminifera
[380]939
[486]940property:
[479]941id:chamber_growth_time
942name:Time of the chamber growth in seconds
943type:f
944group:Foraminifera
945
[486]946property:
[479]947id:chamberCostPerSec
948name:Cost of growning chamber per second
949type:f
950group:Foraminifera
951
[486]952property:
[422]953id:chamber_proculus_haplo
[423]954name:Size of proculus
[422]955type:f
[421]956group:Foraminifera
[380]957
[486]958property:
[422]959id:chamber_proculus_diplo
[423]960name:Size of proculus
[422]961type:f
[380]962group:Foraminifera
963
[486]964property:
[422]965id:chamber_difference_haplo
[423]966name:Difference in size between subsequent chambers
[422]967type:f
[380]968group:Foraminifera
969
[486]970property:
[422]971id:chamber_difference_diplo
[423]972name:Difference in size between subsequent chambers
[422]973type:f
[380]974group:Foraminifera
975
[486]976property:
[422]977id:hunted_prob
978name:Probability of being hunted
979type:f 0 1 0
980group:Forminifera
[380]981
[486]982property:
[422]983id:zone1_range
984name:Zone 1 range
985type:f 0 200
986group:Foraminifera
[380]987
[486]988property:
[422]989id:zone2_range
990name:Zone 2 range
991type:f 0 3000
[421]992group:Foraminifera
[380]993
[486]994property:
[422]995id:colors
996name:Haploid and diploid colors
997type:x
[380]998group:Foraminifera
999
[486]1000property:
[422]1001id:min_repro_energ_haplo
1002name:Min reproduction energy of forams
1003type:f
[380]1004group:Foraminifera
1005
[486]1006property:
[422]1007id:min_repro_energ_diplo
1008name:Min reproduction energy of forams
1009type:f
1010group:Foraminifera
1011
[486]1012property:
[380]1013id:repro_prob
[401]1014name:Probability of reproduction
[422]1015type:f 0 1 0.8
[421]1016group:Foraminifera
[380]1017
[486]1018property:
[422]1019id:energies0_haplo
1020name:Energy of offspring from diploid forams
1021type:f
1022group:Foraminifera
1023
[486]1024property:
[422]1025id:energies0_diplo
1026name:Energy of offspring from diploid forams
1027type:f
1028group:Foraminifera
1029
[486]1030property:
[475]1031id:e_death_level_haplo
1032name:Minimal level of energy to sustain life of haploid
[479]1033type:f 0 20 0.2
[475]1034group:Foraminifera
1035
[486]1036property:
[475]1037id:e_death_level_diplo
1038name:Minimal level of energy to sustain life of diploid
[479]1039type:f 0 20 0.2
[475]1040group:Foraminifera
1041
[486]1042property:
[422]1043id:energy_hib
1044name:Energy used for hibernation during one step
1045type:f 0 1 0.001
1046group:Foraminifera
1047
[486]1048property:
[422]1049id:energy_move
1050name:Energy used for movement during one step
1051type:f 0 20 0.001
1052group:Foraminifera
1053
[486]1054property:
[422]1055id:min_vol
1056name:Minimal volume for reproduction
1057type:f 100 900 100
1058group:Foraminifera
1059
[486]1060property:
[422]1061id:max_size
1062name:Maximal size
1063type:d 1 10 5
1064group:Foraminifera
1065
[486]1066property:
[422]1067id:foramPop
1068name:Initial forams population size
1069type:d 1 1000 100
1070group:Foraminifera
1071
[486]1072property:
[380]1073id:crossprob
[401]1074name:Crossover probability
1075type:f 0 1 0
[421]1076group:Foraminifera
[380]1077
[486]1078property:
[401]1079id:mutationprob
1080name:Mutation probability
1081type:f 0 1 0
[421]1082group:Foraminifera
[401]1083
[486]1084property:
[380]1085id:e_meta
1086name:Idle metabolism
1087type:f 0 1
1088group:Energy
1089help:Each stick consumes this amount of energy in one time step
1090
[486]1091property:
[493]1092id:nutrient_pop
[380]1093name:Feeding rate
[474]1094type:f 0 1000000
[380]1095group:Energy
1096help:How fast energy is created in the world
1097
[486]1098property:
[481]1099id:foodPeriodChange
1100name:Set variable feed rate
1101type:f 0
1102group:Energy
1103
[486]1104property:
[479]1105id:ingestion
1106name:Ingestion rate
1107type:f
1108group:Energy
1109
[486]1110property:
[422]1111id:energy_nut
[428]1112name:Nutrient energy
[493]1113type:f 0 10000000
[380]1114group:Energy
1115
[486]1116property:
[380]1117id:feedtrans
[479]1118name:Energy transfer per second
1119type:f 0 100000
[380]1120group:Energy
[422]1121
[486]1122property:
[479]1123id:foodperiod
1124name:Time between food occurrences
[481]1125type:f 0 1000000
[422]1126group:Energy
1127
[486]1128property:
[479]1129id:nutrientradius
1130name:Nutrient size
[493]1131type:f 0.001 0.9 0.1
[421]1132group:Energy
1133
[486]1134property:
[422]1135id:stress
1136name:Environmental stress
1137type:d 0 1 1
1138group:World
1139
[486]1140property:
[422]1141id:repro_trigger
1142name:Reproduction trigger
1143type:d 0 1 1
1144group:World
1145
[486]1146property:
[422]1147id:repro_time
1148name:Time before reproduction
[474]1149type:d 0 10000
[422]1150
[486]1151property:
[422]1152id:creath
1153name:Creation height
1154type:f -1 50
1155help:~
1156Vertical position (above the surface) where new Forams are revived.
1157Negative values are only used in the water area:
1158  0   = at the surface
1159-0.5 = half depth
1160-1   = just above the bottom~
1161
[421]1162state:
1163id:nutrient
[428]1164name:Nutrient locations
[421]1165help:vector of vectors [x,y,energy]
1166type:x
1167flags:32
1168
[486]1169property:
[380]1170id:autorestart
1171name:Restart after extinction
1172help:Restart automatically this experiment after the last creature has died?
1173type:d 0 1
1174
1175state:
1176id:notes
1177name:Notes
1178type:s 1
1179help:~
1180You can write anything here
1181(it will be saved to the experiment file)~
1182
1183state:
1184id:totaltestedcr
[421]1185name:Evaluated Forams
1186help:Total number of the Forams evaluated in the experiment
[380]1187type:d
1188flags:16
1189
[486]1190property:
[421]1191id:logging
1192name:Log statistics to file
1193type:d 0 1 0
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