source: experiments/frams/foraminifera/data/scripts/foraminifera.expdef @ 552

Last change on this file since 552 was 552, checked in by oriona, 8 years ago

Dir_changed_sec changed from global to ExpProperty?, new divisionCost and energy_nut, direction change counter added in creature lifeparams, lifespan log added.

File size: 28.0 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;
[479]29global max_chamber_volume;
[474]30global movePerStep;
[479]31global nutrientenergywaiting;
32global o;
33global reprocounter;
[481]34global changePeriod;
35global phase;
[493]36global nutrientSqrCm;
[487]37global species_genes;
[380]38
[406]39@include "foraminifera.inc"
[401]40
[380]41// -------------------------------- experiment begin --------------------------------
42
43function onExpDefLoad()
44{
45        // define genotype and creature groups
46        GenePools.clear();
47        Populations.clear();
48        GenePools[0].name = "Unused";
49
50        var pop = Populations[0];
[421]51        pop.name = "Forams";
[380]52        pop.en_assim = 0;
[404]53        pop.nnsim = 0;
[380]54        pop.enableperf = 1;
55        pop.death = 1;
56        pop.energy = 1;
[487]57        pop.selfmask = 0;
58        pop.othermask = 0;
[401]59        //pop.selfmask = 0x20002; pop.othermask = 0x10002;
[422]60        pop.perfperiod = 25;
[487]61        pop.bodysim = 0;
[380]62
[421]63        pop = Populations.addGroup("Nutrients");
[380]64        pop.nnsim = 0;
65        pop.enableperf = 0;
66        pop.death = 1;
67        pop.energy = 1;
[487]68        pop.selfmask = 0;
69        pop.othermask = 0;
[422]70        //pop.othermask = 0x10002;
[487]71        pop.bodysim = 0;
[380]72
[444]73        pop = Populations.addGroup("ReticulopodiaNutrients");
[430]74        pop.nnsim = 0;
75        pop.enableperf = 0;
76        pop.death = 0;
77        pop.energy = 0;
[487]78        pop.selfmask = 0;
79        pop.othermask = 0;
80        pop.bodysim = 0;
[444]81
[422]82        //world
83        SignalView.mode = 1;
[496]84        World.wrldwat = 200;
[493]85        World.wrldsiz = micronsToFrams(100000);
[422]86        World.wrldbnd = 1;
[486]87        ExpProperties.stress = 1;
88        ExpProperties.creath = -0.99; //just above the bottom
89        ExpProperties.autorestart = 0;
[422]90
[474]91        //time
[552]92        ExpProperties.secPerStep = 300;
[486]93        ExpProperties.foramSpeedMmPerMin = 0.05;
[474]94        movePerStep = getMovePerStep();
95
[486]96        //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
[444]97
[487]98        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files   
[493]99        ExpProperties.logPref = "";
[401]100
[422]101        //reproduction
[486]102        ExpProperties.foramPop = 20;   
103        ExpProperties.crossprob = 0;
104        ExpProperties.mutationprob = 0;
105        ExpProperties.repro_time = 720;
[493]106        ExpProperties.gametoPeriod = 21600;
[552]107        ExpProperties.divisionCost = 20;
[422]108        reprocounter = 0;
[380]109
[487]110        species_genes = [];
111
[479]112        init_chambers();
113
[493]114        curColor = retColors[0];
[422]115        //morphology
[552]116        ExpProperties.dir_change_sec = 30000;
[486]117        ExpProperties.zone1_range = micronsToFrams(1000);
118        ExpProperties.zone2_range = micronsToFrams(3000);
119        ExpProperties.chamber_growth_time = 720;
120        ExpProperties.chamberCostPerSec = 0.000001;
121        ExpProperties.chamber_proculus_haplo = micronsToFrams(50);
122        ExpProperties.chamber_difference_haplo = 0.0;
123        ExpProperties.chamber_proculus_diplo = micronsToFrams(20);
124        ExpProperties.chamber_difference_diplo = micronsToFrams(8);
[479]125
126        max_chamber_volume = [Vector.new(), Vector.new()];
[422]127        for (var j = 0; j < 2; j++)
128        {
129                for (var i = 0; i < chambers[0].size; i++)
130                {
[479]131                        max_chamber_volume[j].add(((volumeInMicrons(getProperty(j, "chamber_proculus")) + volumeInMicrons(getProperty(j, "chamber_proculus") + (i) * getProperty(j, "chamber_difference")))*(i+1))/2); 
[422]132                }                                 
133        }
134
135        //energetics
[486]136        ExpProperties.min_repro_energ_haplo = 4;
137        ExpProperties.min_repro_energ_diplo = 6;
[430]138
[486]139        ExpProperties.e_meta = 0.0000005;
140        ExpProperties.energy_hib = 0.0000001;
141        ExpProperties.energy_move = 0.0000005;
[430]142
[493]143        ExpProperties.energies0_haplo = 20;
144        ExpProperties.energies0_diplo = 1.25;
[486]145        ExpProperties.feedtrans = 0.001;
146        ExpProperties.e_repro_cost_haplo = 0.3;
147        ExpProperties.e_repro_cost_diplo = 0.2;
[422]148
[486]149        ExpProperties.e_death_level_haplo = 0.5;
150        ExpProperties.e_death_level_diplo = 0.5;
[479]151
[422]152        //nutrients
[481]153        changePeriod = 0;
[488]154        phase = "low";
[493]155        nutrientSqrCm = 10;
[552]156        ExpProperties.foodperiod = 14400;
[502]157        ExpProperties.foodPeriodChange = 0;
[486]158        ExpProperties.nutrientradius = micronsToFrams(10);
[552]159        ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
[493]160        ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
[486]161        ExpProperties.ingestion = 0.25;
[474]162        nutrientenergywaiting = 0;
[380]163        ExpState.totaltestedcr = 0;
[421]164        ExpState.nutrient = "";
[488]165       
[493]166        //addSpecies({"min_repro_energies" : [4,6]});
167        //addSpecies({"min_repro_energies" : [4,8]});
[380]168}
169
170@include "standard_placement.inc"
171
[479]172function volumeInMicrons(radiusInFrams)
[475]173{
[479]174        return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
[475]175}
176
[479]177function energyFromVolume(base, isRadiusInFrams)
178{
179        if (isRadiusInFrams == 1) //radius in frams
180        {
[486]181                return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
[479]182        }
183        else //volume in microns
184        {
[486]185                return ExpProperties.picoCarbonPerMikro * base;
[479]186        }
187}
188
[474]189function getMovePerStep()
190{
[486]191        return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
[474]192}
193
[447]194function micronsToFrams(micrometers)
[422]195{
[493]196        return micrometers*0.01;
[422]197}
198
[447]199function framsToMicrons(framsworldunits)
[445]200{
[493]201        return framsworldunits/0.01;
[445]202}
203
[422]204function getProperty(gen, prop_id)
205{
206        var ploid = "haplo";
207        if (gen == 1) ploid = "diplo";
[486]208        return ExpProperties.[prop_id + "_" + ploid];
[422]209}
210
[487]211function getGene(cr, gen_id, gen_set)
212{
213        if (cr.data->lifeparams->gen == 0)
214                return cr.data->genes[gen_id];
215        else
216                return cr.data->genes[gen_set][gen_id];
217}
218
[479]219function addForam(species, iter, chambernum, ploid)
[422]220{
[496]221        var geno = createForamMorphology(ploid, ploid, chambernum);
[493]222        curColor = retColors[ploid];
[422]223        var cr = Populations[0].add(geno);
[479]224        cr.name = "Initial creature" + species + "_" + iter;
[422]225        placeCreatureRandomly(cr, 0, 0);
[479]226        cr.energy0 = energyFromVolume(max_chamber_volume[ploid][chambernum],0);
[422]227        cr.energy = cr.energy0;
[487]228        setGenotype({"opt" : 0, "cr" : cr, "species" : species, "energy0" : cr.energy0, "genes" : species_genes[species]});
[479]229        if (ploid == 1)
230        {
231                cr.data->lifeparams->gen = 1;
232                cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
233        }
[525]234        moveReticulopodia(cr);
[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
[552]517        else if (cr.data->lifeparams->dir_counter >= int(ExpProperties.dir_change_sec/ExpProperties.secPerStep))
[380]518        {
[476]519                cr.data->lifeparams->dir = randomDir();
[552]520                cr.data->lifeparams->dir_counter = 0;
[476]521                cr.localDrive = cr.data->lifeparams->dir;
[422]522                moveEnergyDec(cr);
523        }
[474]524        else
525        {
[476]526                cr.localDrive = cr.data->lifeparams->dir;
[474]527        }
[502]528        moveReticulopodia(cr);
[422]529}
[401]530
[502]531function moveReticulopodia(cr)
532{
533        if (visualization(cr))
534        {
535                cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
536                cr.data->reticulopodiacreature.localDrive = cr.localDrive;
537        }
538}
539
[474]540function randomDir()
541{
[486]542        var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0); 
[474]543        dir.normalize();
544        dir.scale(-1*movePerStep);
545        return dir;
546}
547
[430]548function energyTransfer(cr1, cr2)
[422]549{
[430]550        cr1.localDrive = XYZ.new(0,0,0);
[510]551        var e =  ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
[502]552        //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
[510]553        var transferred = cr2.transferEnergyTo(cr1, e);
554        cr1.energy -= transferred*(1-ExpProperties.ingestion);
[476]555        if (cr1.data->lifeparams->hibernated == 1)
[422]556        {
[430]557                reverseHib(cr1);
[422]558        }
559}
[401]560
[430]561function reverseHib(cr)
562{
[476]563        if (cr.data->lifeparams->hibernated == 1)
[430]564        {
[479]565                setForamMeta(cr); //unhibernate
[430]566        }
567        else
568        {
[486]569                cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
[430]570        }
[476]571        cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
[430]572}
573
[493]574function createLogVector(cr, value)
575{
576        var vec = Vector.new();
577        for (var i = 0; i < species_genes.size; i++)
578        {
579                for (var j = 0; j < 2; j++)
580                {
581                        vec.add(0);
582                }
583                if (cr.data->lifeparams->species == i)
584                {
585                        vec[i*2+cr.data->lifeparams->gen] = value;             
586                }
587        }
588        return vec;
589}
[479]590
[422]591function onForamsStep(cr)
592{
[479]593        //checking for gametogenesis process
594        if (cr.data->lifeparams->division_time > 0)
[444]595        {
[479]596                cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
[444]597        }
[479]598        //checking for end of gametogenesis
599        else if (cr.data->lifeparams->division_time == 0)
[422]600        {
[479]601                //waiting for gamets fusion
[422]602        }
[479]603        //checking for chamber growth process
604        else if (cr.data->lifeparams->chamber_growth > 0)
605        {
606                cr.data->lifeparams->chamber_growth = Math.max(cr.data->lifeparams->chamber_growth-1,0);
[486]607                //Simulator.print("chamber growing, time left = " + cr.data->lifeparams->chamber_growth*ExpProperties.secPerStep);
[504]608                cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
[422]609
[479]610                //Simulator.print("energy " + cr2.energy + " subtracting " + growth_cost);
611        }
612        //checking for end of chamber growth process
613        else if (cr.data->lifeparams->chamber_growth == 0)
[430]614        {
[479]615                foramGrow(cr, lastChamberNum(cr));
616                cr.data->lifeparams->chamber_growth = -1;
617                //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
[430]618        }
[479]619        else
[422]620        {
[479]621                //update of metabolism rate
622                if (cr.data->lifeparams->hibernated == 0)
[401]623                {
[479]624                        setForamMeta(cr);
625                }
626
627                cr.getMechPart(0).orient.set(o);
628
629                if (deathConditions(cr) == 1)
630                {
[493]631                        if (ExpProperties.logging == 1)
632                        {
633                                log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
[552]634                                log(createLogVector(cr, cr.lifespan),ExpProperties.logPref+"lifespan_log.txt");
[493]635                        }                       
[479]636                        Populations[0].kill(cr);
637                        return;
638                }
639
[552]640                //update direction change counter
641                cr.data->lifeparams->dir_counter += 1;
642
[479]643                foramMove(cr);
644
645                var repro = foramReproduce(cr);
646                if (repro == 1)
647                {
648                        return;
649                }
650
651                cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
652
653                //cheking conditions of chamber growth process start
654                if  (lastChamberNum(cr) != chambers[0].size-1)
655                {
656                        if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)],0)))   
657                        {
[486]658                                cr.data->lifeparams->chamber_growth = int(ExpProperties.chamber_growth_time/ExpProperties.secPerStep);
[479]659                        }       
660                }
[430]661        }       
[380]662}
663
[422]664function deathConditions(cr)
665{
[486]666        if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
[479]667        {
[422]668                return 1;
[479]669        }
[422]670        else
671                return 0;
672}
673
[421]674function onForamsDied(cr)
[380]675{
[444]676        if (visualization(cr))
[430]677        {
[476]678                Populations[2].delete(cr.data->reticulopodiacreature);
[430]679        }
[380]680        //fossilization
681        var geno = GenePools[0].add(cr.genotype);
[476]682        geno.data->genes = cr.data->genes;
683        geno.data->lifeparams = cr.data->lifeparams;
[486]684        if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
[380]685        ExpState.totaltestedcr++;
686}
687
[421]688// --------------------------------foram end -------------------------------------
[380]689
[421]690// -------------------------------- nutrient begin --------------------------------
[380]691
[479]692function createNutrientGenotype(nutrientradius)
[422]693{
[524]694        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]695}
696
[421]697function onNutrientsStep(cr)
[380]698{
[444]699        cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
[380]700}
701
[421]702function addNutrient()
[380]703{
[486]704        var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
[380]705
[421]706        cr.name = "Nutrients";
[380]707        cr.idleen = 0;
[486]708        cr.energy0 = ExpProperties.energy_nut;
[416]709        cr.energy = cr.energy0;
[421]710        cr.signals.add("nutrient");
[380]711
[430]712        cr.signals[0].value = cr;
[380]713
[422]714        placeCreatureRandomly(cr, 0, 0);
[486]715        if (ExpProperties.visualize == 1)
[444]716        {
[486]717                var nutsize = ExpProperties.nutrientradius*10;
[444]718                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]719                cr.data->reticulopodiacreature = nut;
[444]720                nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
721        }
[380]722}
723
[444]724function onNutrientsDied(cr)
725{
726        if (visualization(cr))
727        {
[476]728                Populations[2].delete(cr.data->reticulopodiacreature);
[444]729        }
730}
731
[422]732function nutrientGrowth()
[380]733{
[486]734        if (ExpProperties.foodPeriodChange > 0)
[481]735        {
736                        changePeriod += 1;
[486]737                        if (phase=="low" && (changePeriod*ExpProperties.secPerStep) >= 23328000) //9 months
[481]738                        {
[486]739                                ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
[481]740                                phase = "high";
741                                changePeriod = 0;
742                        }
743               
[486]744                        else if (phase == "high" && (changePeriod*ExpProperties.secPerStep) >= 7776000) //3 months
[481]745                        {
[486]746                                ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
[481]747                                phase = "low";
748                                changePeriod = 0;
749                        }
750        }
[474]751        nutrientenergywaiting = nutrientenergywaiting + 1;
[486]752        if (nutrientenergywaiting*ExpProperties.secPerStep >= ExpProperties.foodperiod)
[380]753        {
[493]754                for (var i = 0; i < ExpProperties.nutrient_pop; i++)
[432]755                {   
[422]756                        addNutrient();
757                }
758
759                nutrientenergywaiting = 0.0;
760                Simulator.checkpoint();
[493]761
762                if (ExpProperties.logging == 1)
763                {
764                        log([ExpProperties.nutrient_pop],ExpProperties.logPref+"nutrients_log.txt");
765                }
[380]766        }
[493]767
[380]768}
769
[421]770// -------------------------------- nutrient end --------------------------------
[380]771
[422]772// -------------------------------- step begin --------------------------------
[380]773
[422]774function onStep()
775{
[432]776
777        nutrientGrowth();
[486]778        if (ExpProperties.logging == 1)
[422]779        {
780                createStatistics();
781        }
782
783        //reproduction --------------------------------------------
784        reprocounter += 1;
[486]785        if (reprocounter*ExpProperties.secPerStep > ExpProperties.repro_time)
[422]786        {
787                reprocounter = 0;
788                reproduce_parents(0);
789                reproduce_parents(1);
790        }
791
792        //check for extinction -----------------------------------------------
793        if (Populations[0].size == 0)
794        {
[486]795                if (ExpProperties.autorestart)
[422]796                {
797                        Simulator.print("no more creatures, restarting...");
798                        onExpInit();
799                }
800                else
801                {
802                        Simulator.print("no more creatures, stopped.");
803                        Simulator.stop();
804                }
805        }
[486]806        if (ExpProperties.maxSteps > 0)
[432]807        {
[486]808                if (Simulator.stepNumber >= ExpProperties.maxSteps)
[432]809                        Simulator.stop();
810        }
[422]811}
812
813function createStatistics()
814{       
[487]815        var number = [];
816        var e_inc = [];
[422]817        var e_nut = 0.0;
818
[487]819        for (var s = 0; s < species_genes.size; s++)
820        {
821                number.add([0,0]);// [haplo][diplo]
822                e_inc.add([0,0]);
823        }
824
[422]825        for (var i = 0; i < Populations[0].size; i++)
826        {
827                var cr = Populations[0].get(i);
[476]828                var gen = cr.data->lifeparams->gen;
829                var species = cr.data->lifeparams->species;
[430]830
831                number[species][gen] = number[species][gen] + 1;
832                e_inc[species][gen] = e_inc[species][gen] + cr.energy;
[422]833        }
834
835        for (var i = 0; i < Populations[1].size; i++)
836        {
837                var cr = Populations[1].get(i);
838                e_nut += cr.energy;
839        }
840
[487]841        var log_numbers = [];
842        var log_energies = [];
[422]843
[487]844        for (var s = 0; s < species_genes.size; s++)
845        {
846                for (var p = 0; p < 2; p++)
847                {
848                        log_numbers.add(number[s][p]);
849                        log_energies.add(e_inc[s][p]);
850                }
851        }
852       
853        log_numbers.add(Populations[1].size);
854        log_energies.add(e_nut);
855
[493]856        log(log_numbers, ExpProperties.logPref+"forams_log.txt");
857    log(log_energies,  ExpProperties.logPref+"energies_log.txt");
[422]858}
859
[380]860function log(tolog, fname)
861{
[430]862        var f = File.appendDirect(fname, "forams data");
[380]863        f.writeString("" + Simulator.stepNumber);
[401]864        for (var  i = 0; i < tolog.size; i++)
[380]865        {
866                f.writeString(";" + tolog[i]);
867        }
868        f.writeString("\n");
869        f.close();
870}
871
[422]872// -------------------------------- step end --------------------------------
[479]873//TODO default params values in frams instead of microns/seconds
[380]874
[401]875@include "standard_events.inc"
[380]876
[401]877~
[380]878
[486]879property:
[444]880id:visualize
881name:Show reticulopodia and nutrients
[430]882type:d 0 1 0
883group:Foraminifera
884
[486]885property:
[434]886id:maxSteps
[432]887name:Stop after the given number of simulation steps
[552]888type:d 0 10000000 0
[432]889
[486]890property:
[493]891id:logPref
892name:Log prefix
893type:s
894
895property:
[474]896id:foramSpeedMmPerMin
897name:Speed of foraminfera in mm/min
898type:f 0.1
899flags: 16
900group:Foraminifera
901
[486]902property:
[479]903id:gametSuccessRate
904name:Ratio of successful gamets
905type:f 0.001
906group:Foraminifera
907
[486]908property:
[552]909id:dir_change_sec
910name:Number of seconds before direction change
911type:d 30000
912group:Foraminifera
913
914property:
[479]915id:gametoPeriod
916name:Time of gametogenesis
917type:f 720
918group:Foraminifera
919
[486]920property:
[479]921id:picoCarbonPerMikro
922name:Picograms of carbon in cubed micrometer
923type:f 0.13
924group:Foraminifera
925
[486]926property:
[474]927id:secPerStep
928name:Seconds per simulation step
[524]929help:Number of seconds of foraminifera time per simulation step
[474]930type:f 60.0
931flags: 16
932group:Foraminifera
933
[486]934property:
[422]935id:e_repro_cost_haplo
[423]936name:Cost of reproduction
[422]937type:f 0.1 0.9 0.5
[421]938group:Foraminifera
[380]939
[486]940property:
[479]941id:divisionCost
942name:Cost of division in pG
943type:f
944group:Foraminifera
945
[486]946property:
[422]947id:e_repro_cost_diplo
[423]948name:Cost of reproduction
[422]949type:f 0.1 0.9 0.3
950group:Foraminifera
[380]951
[486]952property:
[479]953id:chamber_growth_time
954name:Time of the chamber growth in seconds
955type:f
956group:Foraminifera
957
[486]958property:
[479]959id:chamberCostPerSec
960name:Cost of growning chamber per second
961type:f
962group:Foraminifera
963
[486]964property:
[422]965id:chamber_proculus_haplo
[423]966name:Size of proculus
[422]967type:f
[421]968group:Foraminifera
[380]969
[486]970property:
[422]971id:chamber_proculus_diplo
[423]972name:Size of proculus
[422]973type:f
[380]974group:Foraminifera
975
[486]976property:
[422]977id:chamber_difference_haplo
[423]978name:Difference in size between subsequent chambers
[422]979type:f
[380]980group:Foraminifera
981
[486]982property:
[422]983id:chamber_difference_diplo
[423]984name:Difference in size between subsequent chambers
[422]985type:f
[380]986group:Foraminifera
987
[486]988property:
[422]989id:hunted_prob
990name:Probability of being hunted
991type:f 0 1 0
992group:Forminifera
[380]993
[486]994property:
[422]995id:zone1_range
996name:Zone 1 range
997type:f 0 200
998group:Foraminifera
[380]999
[486]1000property:
[422]1001id:zone2_range
1002name:Zone 2 range
1003type:f 0 3000
[421]1004group:Foraminifera
[380]1005
[486]1006property:
[422]1007id:colors
1008name:Haploid and diploid colors
1009type:x
[380]1010group:Foraminifera
1011
[486]1012property:
[422]1013id:min_repro_energ_haplo
1014name:Min reproduction energy of forams
1015type:f
[380]1016group:Foraminifera
1017
[486]1018property:
[422]1019id:min_repro_energ_diplo
1020name:Min reproduction energy of forams
1021type:f
1022group:Foraminifera
1023
[486]1024property:
[380]1025id:repro_prob
[401]1026name:Probability of reproduction
[422]1027type:f 0 1 0.8
[421]1028group:Foraminifera
[380]1029
[486]1030property:
[422]1031id:energies0_haplo
1032name:Energy of offspring from diploid forams
1033type:f
1034group:Foraminifera
1035
[486]1036property:
[422]1037id:energies0_diplo
1038name:Energy of offspring from diploid forams
1039type:f
1040group:Foraminifera
1041
[486]1042property:
[475]1043id:e_death_level_haplo
1044name:Minimal level of energy to sustain life of haploid
[479]1045type:f 0 20 0.2
[475]1046group:Foraminifera
1047
[486]1048property:
[475]1049id:e_death_level_diplo
1050name:Minimal level of energy to sustain life of diploid
[479]1051type:f 0 20 0.2
[475]1052group:Foraminifera
1053
[486]1054property:
[422]1055id:energy_hib
1056name:Energy used for hibernation during one step
1057type:f 0 1 0.001
1058group:Foraminifera
1059
[486]1060property:
[422]1061id:energy_move
1062name:Energy used for movement during one step
1063type:f 0 20 0.001
1064group:Foraminifera
1065
[486]1066property:
[422]1067id:min_vol
1068name:Minimal volume for reproduction
1069type:f 100 900 100
1070group:Foraminifera
1071
[486]1072property:
[422]1073id:max_size
1074name:Maximal size
1075type:d 1 10 5
1076group:Foraminifera
1077
[486]1078property:
[422]1079id:foramPop
1080name:Initial forams population size
1081type:d 1 1000 100
1082group:Foraminifera
1083
[486]1084property:
[380]1085id:crossprob
[401]1086name:Crossover probability
1087type:f 0 1 0
[421]1088group:Foraminifera
[380]1089
[486]1090property:
[401]1091id:mutationprob
1092name:Mutation probability
1093type:f 0 1 0
[421]1094group:Foraminifera
[401]1095
[486]1096property:
[380]1097id:e_meta
1098name:Idle metabolism
1099type:f 0 1
1100group:Energy
1101help:Each stick consumes this amount of energy in one time step
1102
[486]1103property:
[493]1104id:nutrient_pop
[380]1105name:Feeding rate
[474]1106type:f 0 1000000
[380]1107group:Energy
1108help:How fast energy is created in the world
1109
[486]1110property:
[481]1111id:foodPeriodChange
1112name:Set variable feed rate
1113type:f 0
1114group:Energy
1115
[486]1116property:
[479]1117id:ingestion
1118name:Ingestion rate
1119type:f
1120group:Energy
1121
[486]1122property:
[422]1123id:energy_nut
[428]1124name:Nutrient energy
[493]1125type:f 0 10000000
[380]1126group:Energy
1127
[486]1128property:
[380]1129id:feedtrans
[479]1130name:Energy transfer per second
1131type:f 0 100000
[380]1132group:Energy
[422]1133
[486]1134property:
[479]1135id:foodperiod
1136name:Time between food occurrences
[481]1137type:f 0 1000000
[422]1138group:Energy
1139
[486]1140property:
[479]1141id:nutrientradius
1142name:Nutrient size
[493]1143type:f 0.001 0.9 0.1
[421]1144group:Energy
1145
[486]1146property:
[422]1147id:stress
1148name:Environmental stress
1149type:d 0 1 1
1150group:World
1151
[486]1152property:
[422]1153id:repro_trigger
1154name:Reproduction trigger
1155type:d 0 1 1
1156group:World
1157
[486]1158property:
[422]1159id:repro_time
1160name:Time before reproduction
[474]1161type:d 0 10000
[422]1162
[486]1163property:
[422]1164id:creath
1165name:Creation height
1166type:f -1 50
1167help:~
1168Vertical position (above the surface) where new Forams are revived.
1169Negative values are only used in the water area:
1170  0   = at the surface
1171-0.5 = half depth
1172-1   = just above the bottom~
1173
[421]1174state:
1175id:nutrient
[428]1176name:Nutrient locations
[421]1177help:vector of vectors [x,y,energy]
1178type:x
1179flags:32
1180
[486]1181property:
[380]1182id:autorestart
1183name:Restart after extinction
1184help:Restart automatically this experiment after the last creature has died?
1185type:d 0 1
1186
1187state:
1188id:notes
1189name:Notes
1190type:s 1
1191help:~
1192You can write anything here
1193(it will be saved to the experiment file)~
1194
1195state:
1196id:totaltestedcr
[421]1197name:Evaluated Forams
1198help:Total number of the Forams evaluated in the experiment
[380]1199type:d
1200flags:16
1201
[486]1202property:
[421]1203id:logging
1204name:Log statistics to file
1205type:d 0 1 0
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