source: experiments/frams/foraminifera/data/scripts/foraminifera.expdef @ 493

Last change on this file since 493 was 493, checked in by oriona, 8 years ago

Microns to frams scaling rate changed. New world size, new log files added.

File size: 27.4 KB
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1expdef:
2name:Reproduction of benthic foraminifera
3info:~
4Basic information about this simulation:
5www.framsticks.com/foraminifera
6
7Technical information:
8Genes and parameter values which control reproduction are stored in data->genes and data->lifeparams fields.
9
10genes:
11genes which are not encoded in Ff genotype:
12min_repro_energy - Minimum energy necessary for reproduction
13hibernation - Defines foram behavior in the case of no nutrients
14
15lifeparams:
16Physiological parameters of foraminifera:
17max_energy_level - maximum energy level reached so far
18gen - generation: 0 haploid, 1 diploid
19species - species: 0 not hibernating 1 hibernating
20hibernated - 0/1 foram is/isn't hibernated
21reproduce - 0/1 foram isn't/is ready for reproduction
22~
23code:~
24
25global chambers;
26global colors;
27global retColors;
28global curColor;
29global dir_change_sec;
30global max_chamber_volume;
31global movePerStep;
32global nutrientenergywaiting;
33global o;
34global reprocounter;
35global changePeriod;
36global phase;
37global nutrientSqrCm;
38global species_genes;
39
40@include "foraminifera.inc"
41
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];
52        pop.name = "Forams";
53        pop.en_assim = 0;
54        pop.nnsim = 0;
55        pop.enableperf = 1;
56        pop.death = 1;
57        pop.energy = 1;
58        pop.selfmask = 0;
59        pop.othermask = 0;
60        //pop.selfmask = 0x20002; pop.othermask = 0x10002;
61        pop.perfperiod = 25;
62        pop.bodysim = 0;
63
64        pop = Populations.addGroup("Nutrients");
65        pop.nnsim = 0;
66        pop.enableperf = 0;
67        pop.death = 1;
68        pop.energy = 1;
69        pop.selfmask = 0;
70        pop.othermask = 0;
71        //pop.othermask = 0x10002;
72        pop.bodysim = 0;
73
74        pop = Populations.addGroup("ReticulopodiaNutrients");
75        pop.nnsim = 0;
76        pop.enableperf = 0;
77        pop.death = 0;
78        pop.energy = 0;
79        pop.selfmask = 0;
80        pop.othermask = 0;
81        pop.bodysim = 0;
82
83        //world
84        SignalView.mode = 1;
85        World.wrldwat = 500;
86        World.wrldsiz = micronsToFrams(100000);
87        World.wrldbnd = 1;
88        ExpProperties.stress = 1;
89        ExpProperties.creath = -0.99; //just above the bottom
90        ExpProperties.autorestart = 0;
91
92        //time
93        ExpProperties.secPerStep = 480;
94        ExpProperties.foramSpeedMmPerMin = 0.05;
95        movePerStep = getMovePerStep();
96
97        //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
98
99        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files   
100        ExpProperties.logPref = "";
101
102        //reproduction
103        ExpProperties.foramPop = 20;   
104        ExpProperties.crossprob = 0;
105        ExpProperties.mutationprob = 0;
106        ExpProperties.repro_time = 720;
107        ExpProperties.gametoPeriod = 21600;
108        ExpProperties.divisionCost = 15.6;
109        reprocounter = 0;
110
111        species_genes = [];
112
113        init_chambers();
114
115        curColor = retColors[0];
116        //morphology
117        dir_change_sec = 30000;
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);
126
127        max_chamber_volume = [Vector.new(), Vector.new()];
128        for (var j = 0; j < 2; j++)
129        {
130                for (var i = 0; i < chambers[0].size; i++)
131                {
132                        max_chamber_volume[j].add(((volumeInMicrons(getProperty(j, "chamber_proculus")) + volumeInMicrons(getProperty(j, "chamber_proculus") + (i) * getProperty(j, "chamber_difference")))*(i+1))/2); 
133                }                                 
134        }
135
136        //energetics
137        ExpProperties.min_repro_energ_haplo = 4;
138        ExpProperties.min_repro_energ_diplo = 6;
139
140        ExpProperties.e_meta = 0.0000005;
141        ExpProperties.energy_hib = 0.0000001;
142        ExpProperties.energy_move = 0.0000005;
143
144        ExpProperties.energies0_haplo = 20;
145        ExpProperties.energies0_diplo = 1.25;
146        ExpProperties.feedtrans = 0.001;
147        ExpProperties.e_repro_cost_haplo = 0.3;
148        ExpProperties.e_repro_cost_diplo = 0.2;
149
150        ExpProperties.e_death_level_haplo = 0.5;
151        ExpProperties.e_death_level_diplo = 0.5;
152
153        //nutrients
154        changePeriod = 0;
155        phase = "low";
156        nutrientSqrCm = 10;
157        ExpProperties.foodperiod = 25920;
158        ExpProperties.foodPeriodChange = 6;
159        ExpProperties.nutrientradius = micronsToFrams(10);
160        ExpProperties.energy_nut = energyFromVolume(ExpProperties.nutrientradius,1);
161        ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
162        ExpProperties.ingestion = 0.25;
163        nutrientenergywaiting = 0;
164        ExpState.totaltestedcr = 0;
165        ExpState.nutrient = "";
166       
167        //addSpecies({"min_repro_energies" : [4,6]});
168        //addSpecies({"min_repro_energies" : [4,8]});
169}
170
171@include "standard_placement.inc"
172
173function volumeInMicrons(radiusInFrams)
174{
175        return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
176}
177
178function energyFromVolume(base, isRadiusInFrams)
179{
180        if (isRadiusInFrams == 1) //radius in frams
181        {
182                return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
183        }
184        else //volume in microns
185        {
186                return ExpProperties.picoCarbonPerMikro * base;
187        }
188}
189
190function getMovePerStep()
191{
192        return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
193}
194
195function micronsToFrams(micrometers)
196{
197        return micrometers*0.01;
198}
199
200function framsToMicrons(framsworldunits)
201{
202        return framsworldunits/0.01;
203}
204
205function getProperty(gen, prop_id)
206{
207        var ploid = "haplo";
208        if (gen == 1) ploid = "diplo";
209        return ExpProperties.[prop_id + "_" + ploid];
210}
211
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
220function addForam(species, iter, chambernum, ploid)
221{
222        var geno = createForamMorphology(species_genes[species]->morphotype, ploid, chambernum);
223        curColor = retColors[ploid];
224        var cr = Populations[0].add(geno);
225        cr.name = "Initial creature" + species + "_" + iter;
226        placeCreatureRandomly(cr, 0, 0);
227        cr.energy0 = energyFromVolume(max_chamber_volume[ploid][chambernum],0);
228        cr.energy = cr.energy0;
229        setGenotype({"opt" : 0, "cr" : cr, "species" : species, "energy0" : cr.energy0, "genes" : species_genes[species]});
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        }
235}
236
237function addInitialForam(species, iter)
238{
239        var ploid = 0;
240        if (Math.rnd01 > 0.5)
241        {
242                ploid = 1;
243        }       
244        //add new foram with random energy bewtween starting energy and reproduction threshold
245        addForam(species, iter, int(Math.rndUni(0,species_genes[species]->min_repro_energies[ploid])),ploid);
246}
247
248//new species can be added as a dictionary with parameter values that are different than default values
249function addSpecies(new_genes)
250{
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});
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
259function onExpInit()
260{
261        Populations[0].clear();
262        Populations[1].clear();
263        Populations[2].clear(); //reticulopodia and nutrients
264
265        if (species_genes.size == 0)
266        {
267                addSpecies({}); //default
268        }
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        }
277        o = Populations[0][0].getMechPart(0).orient.clone();
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
290        Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
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                {
304                        //cr.rotate(0,0,Math.rnd01*Math.twopi);
305                        if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
306                        {
307                                // [x,y,energy]
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];
310                        }
311                        else
312                        {
313                                cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
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
329        var tmpvec = [], i;
330
331        for(var cr in Populations[1])
332                tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
333
334        ExpState.nutrient = tmpvec;
335        File.writeObject(sim_params.*);
336        ExpState.nutrient = null; //vectors are only created for saving and then discarded
337
338        for (var cr in Populations[0])
339                File.writeObject(cr);
340}
341
342// -------------------------------- experiment end --------------------------------
343
344// -------------------------------- foram begin -----------------------------------
345
346function setForamMeta(cr)
347{
348        //percent of current energy
349        cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
350}
351
352function lastChamberNum(cr)
353{
354        return cr.numparts-1;
355}
356
357function getZoneRange(cr, zone_num)
358{
359        return ExpProperties.["zone"+zone_num+"_range"];
360}
361
362function onForamsBorn(cr)
363{
364        setForamMeta(cr);
365        if (ExpProperties.visualize == 1)
366        {
367                var ret = Populations[2].add("//0\np:sh=3,sx=0.01,sy="+getZoneRange(cr,1)+",sz="+getZoneRange(cr,1)+",ry=1.57,vr="+curColor);
368                cr.data->reticulopodiacreature = ret;
369        }
370}
371
372function placeRandomlyNotColliding(cr)
373{
374        var retry = 100; //try 100 times
375        while (retry--)
376        {
377                placeCreatureRandomly(cr, 0, 0);
378                if (!cr.boundingBoxCollisions(0))
379                        return cr;
380        }
381
382        Populations[0].delete(cr);
383}
384
385function visualization(cr)
386{
387        var has_ret = 0;
388
389        if (cr.data->reticulopodiacreature != null)
390        {
391                if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
392                {
393                        has_ret = 1;
394                }
395        }
396
397        return has_ret;
398}
399
400function foramGrow(cr, chamber_num)
401{
402        if ((chamber_num+1) < chambers[cr.data->lifeparams->species].size)
403        {
404                curColor = retColors[cr.data->lifeparams->gen];
405                var geno = createForamMorphology(getGene(cr, "morphotype", 0), cr.data->lifeparams->gen, chamber_num+1);
406                var cr2 = Populations[0].add(geno);
407
408                cr2.energy0 = cr.energy;
409                cr2.energy = cr2.energy0;
410
411                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : 2, "energy0" : cr.energy0});
412                cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
413                setForamMeta(cr2);
414
415                if (visualization(cr))
416                {
417                        Populations[2].delete(cr.data->reticulopodiacreature);
418                }
419                Populations[0].delete(cr);
420        }
421}
422
423function stepToNearest(cr)
424{
425        var p = cr.getMechPart(0);
426        var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
427
428        //if signals are received find the source of the nearest
429        if (n.size > 0)
430        {
431                var i;
432                var mp;
433                var distvec = XYZ.new(0, 0, 0);
434                var dist;
435                var mindist = 100000000000.0;
436                var mindistvec = null;
437                var eating = 0;
438
439                for (i = 0; i < n.size; i++)
440                {
441                        mp = n[i].value.getMechPart(0);
442                        distvec.set(mp.pos);
443                        distvec.sub(p.pos);
444                        dist = distvec.length;
445                        if (dist < getZoneRange(cr,1))
446                        {
447                                if (n[i].value != null)
448                                {
449                                        energyTransfer(cr, n[i].value);
450                                        eating = 1;
451                                }
452                        }
453                        else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
454                        {
455                                mindist = dist;
456                                mindistvec = distvec.clone();
457                        }
458                }
459
460                if (!eating && cr.data->lifeparams->hibernated == 0)
461                {
462                        mindistvec.normalize();
463                        mindistvec.scale(-1*movePerStep);
464                        cr.localDrive = mindistvec;
465                        moveEnergyDec(cr);
466                }
467
468                return 1;
469        }
470       
471        else
472        {
473                return 0;
474        }
475}
476
477function moveEnergyDec(cr)
478{
479        if (cr.data->lifeparams->hibernated == 0)
480        {
481                //percent of maximal energy
482                cr.energy_m += (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
483        }
484}
485
486function fence(pos, zone)
487{
488        return Math.min(Math.max(0+zone,pos),World.wrldsiz-zone);
489}
490
491function foramMove(cr)
492{
493        //TODO moving inside sediment?
494
495        //adjustment in z axis
496        cr.moveAbs(fence(cr.pos_x, getZoneRange(cr, 1)), fence(cr.pos_y,getZoneRange(cr, 1)), 0);
497
498        //are there any nutrients in zone 1 or 2?
499        {
500                var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
501                if (moved==1)
502                {
503                        return;
504                }
505        }
506
507        //no nutrients in zone 2
508        if (getGene(cr, "hibernation",0) == 1)
509        {
510                reverseHib(cr);
511                cr.localDrive = XYZ.new(0,0,0);
512        }
513        //random move
514        else if (Simulator.stepNumber%int(dir_change_sec/ExpProperties.secPerStep) == 0)
515        {
516                cr.data->lifeparams->dir = randomDir();
517                cr.localDrive = cr.data->lifeparams->dir;
518                moveEnergyDec(cr);
519        }
520        else
521        {
522                cr.localDrive = cr.data->lifeparams->dir;
523        }
524}
525
526function randomDir()
527{
528        var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0); 
529        dir.normalize();
530        dir.scale(-1*movePerStep);
531        return dir;
532}
533
534function energyTransfer(cr1, cr2)
535{
536        cr1.localDrive = XYZ.new(0,0,0);
537        var e =  ExpProperties.feedtrans*cr1.energy;//ExpProperties.feedtrans*cr1.energy*ExpProperties.ingestion*ExpProperties.secPerStep; //TODO efficiency dependent on age
538        e = Math.min(cr2.energy, e);
539        e *= ExpProperties.secPerStep;
540        //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.name+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
541        cr2.energy_m = cr2.energy_m + e + 0.0000001;
542        cr1.energy_p = cr1.energy_p + e*ExpProperties.ingestion;
543        if (cr1.data->lifeparams->hibernated == 1)
544        {
545                reverseHib(cr1);
546        }
547}
548
549function reverseHib(cr)
550{
551        if (cr.data->lifeparams->hibernated == 1)
552        {
553                setForamMeta(cr); //unhibernate
554        }
555        else
556        {
557                cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
558        }
559        cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
560}
561
562function createLogVector(cr, value)
563{
564        var vec = Vector.new();
565        for (var i = 0; i < species_genes.size; i++)
566        {
567                for (var j = 0; j < 2; j++)
568                {
569                        vec.add(0);
570                }
571                if (cr.data->lifeparams->species == i)
572                {
573                        vec[i*2+cr.data->lifeparams->gen] = value;             
574                }
575        }
576        return vec;
577}
578
579function onForamsStep(cr)
580{
581        //checking for gametogenesis process
582        if (cr.data->lifeparams->division_time > 0)
583        {
584                cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
585        }
586        //checking for end of gametogenesis
587        else if (cr.data->lifeparams->division_time == 0)
588        {
589                //waiting for gamets fusion
590        }
591        //checking for chamber growth process
592        else if (cr.data->lifeparams->chamber_growth > 0)
593        {
594                cr.data->lifeparams->chamber_growth = Math.max(cr.data->lifeparams->chamber_growth-1,0);
595                //Simulator.print("chamber growing, time left = " + cr.data->lifeparams->chamber_growth*ExpProperties.secPerStep);
596                cr.energy_m += ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
597
598                //Simulator.print("energy " + cr2.energy + " subtracting " + growth_cost);
599        }
600        //checking for end of chamber growth process
601        else if (cr.data->lifeparams->chamber_growth == 0)
602        {
603                foramGrow(cr, lastChamberNum(cr));
604                cr.data->lifeparams->chamber_growth = -1;
605                //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
606        }
607        else
608        {
609                //update of metabolism rate
610                if (cr.data->lifeparams->hibernated == 0)
611                {
612                        setForamMeta(cr);
613                }
614
615                cr.getMechPart(0).orient.set(o);
616                if (visualization(cr))
617                {
618                        cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
619                }
620
621                if (deathConditions(cr) == 1)
622                {
623                        if (ExpProperties.logging == 1)
624                        {
625                                log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
626                        }                       
627                        Populations[0].kill(cr);
628                        return;
629                }
630
631                foramMove(cr);
632
633                var repro = foramReproduce(cr);
634                if (repro == 1)
635                {
636                        return;
637                }
638
639                cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
640
641                //cheking conditions of chamber growth process start
642                if  (lastChamberNum(cr) != chambers[0].size-1)
643                {
644                        if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)],0)))   
645                        {
646                                cr.data->lifeparams->chamber_growth = int(ExpProperties.chamber_growth_time/ExpProperties.secPerStep);
647                        }       
648                }
649        }       
650}
651
652function deathConditions(cr)
653{
654        if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
655        {
656                return 1;
657        }
658        else
659                return 0;
660}
661
662function onForamsDied(cr)
663{
664        if (visualization(cr))
665        {
666                Populations[2].delete(cr.data->reticulopodiacreature);
667        }
668        //fossilization
669        var geno = GenePools[0].add(cr.genotype);
670        geno.data->genes = cr.data->genes;
671        geno.data->lifeparams = cr.data->lifeparams;
672        if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
673        ExpState.totaltestedcr++;
674}
675
676// --------------------------------foram end -------------------------------------
677
678// -------------------------------- nutrient begin --------------------------------
679
680function createNutrientGenotype(nutrientradius)
681{
682        return "//0\np:sh=3,sx="+nutrientradius+",sy="+nutrientradius+",sz="+nutrientradius+",ry=1.5,vr=0.0,1.0,0.0";
683}
684
685function onNutrientsStep(cr)
686{
687        cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
688}
689
690function addNutrient()
691{
692        var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
693
694        cr.name = "Nutrients";
695        cr.idleen = 0;
696        cr.energy0 = ExpProperties.energy_nut;
697        cr.energy = cr.energy0;
698        cr.signals.add("nutrient");
699
700        cr.signals[0].value = cr;
701
702        placeCreatureRandomly(cr, 0, 0);
703        if (ExpProperties.visualize == 1)
704        {
705                var nutsize = ExpProperties.nutrientradius*10;
706                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");
707                cr.data->reticulopodiacreature = nut;
708                nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
709        }
710}
711
712function onNutrientsDied(cr)
713{
714        if (visualization(cr))
715        {
716                Populations[2].delete(cr.data->reticulopodiacreature);
717        }
718}
719
720function nutrientGrowth()
721{
722        if (ExpProperties.foodPeriodChange > 0)
723        {
724                        changePeriod += 1;
725                        if (phase=="low" && (changePeriod*ExpProperties.secPerStep) >= 23328000) //9 months
726                        {
727                                ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
728                                phase = "high";
729                                changePeriod = 0;
730                        }
731               
732                        else if (phase == "high" && (changePeriod*ExpProperties.secPerStep) >= 7776000) //3 months
733                        {
734                                ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
735                                phase = "low";
736                                changePeriod = 0;
737                        }
738        }
739        nutrientenergywaiting = nutrientenergywaiting + 1;
740        if (nutrientenergywaiting*ExpProperties.secPerStep >= ExpProperties.foodperiod)
741        {
742                for (var i = 0; i < ExpProperties.nutrient_pop; i++)
743                {   
744                        addNutrient();
745                }
746
747                nutrientenergywaiting = 0.0;
748                Simulator.checkpoint();
749
750                if (ExpProperties.logging == 1)
751                {
752                        log([ExpProperties.nutrient_pop],ExpProperties.logPref+"nutrients_log.txt");
753                }
754        }
755
756}
757
758// -------------------------------- nutrient end --------------------------------
759
760// -------------------------------- step begin --------------------------------
761
762function onStep()
763{
764
765        nutrientGrowth();
766        if (ExpProperties.logging == 1)
767        {
768                createStatistics();
769        }
770
771        //reproduction --------------------------------------------
772        reprocounter += 1;
773        if (reprocounter*ExpProperties.secPerStep > ExpProperties.repro_time)
774        {
775                reprocounter = 0;
776                reproduce_parents(0);
777                reproduce_parents(1);
778        }
779
780        //check for extinction -----------------------------------------------
781        if (Populations[0].size == 0)
782        {
783                if (ExpProperties.autorestart)
784                {
785                        Simulator.print("no more creatures, restarting...");
786                        onExpInit();
787                }
788                else
789                {
790                        Simulator.print("no more creatures, stopped.");
791                        Simulator.stop();
792                }
793        }
794        if (ExpProperties.maxSteps > 0)
795        {
796                if (Simulator.stepNumber >= ExpProperties.maxSteps)
797                        Simulator.stop();
798        }
799}
800
801function createStatistics()
802{       
803        var number = [];
804        var e_inc = [];
805        var e_nut = 0.0;
806
807        for (var s = 0; s < species_genes.size; s++)
808        {
809                number.add([0,0]);// [haplo][diplo]
810                e_inc.add([0,0]);
811        }
812
813        for (var i = 0; i < Populations[0].size; i++)
814        {
815                var cr = Populations[0].get(i);
816                var gen = cr.data->lifeparams->gen;
817                var species = cr.data->lifeparams->species;
818
819                number[species][gen] = number[species][gen] + 1;
820                e_inc[species][gen] = e_inc[species][gen] + cr.energy;
821        }
822
823        for (var i = 0; i < Populations[1].size; i++)
824        {
825                var cr = Populations[1].get(i);
826                e_nut += cr.energy;
827        }
828
829        var log_numbers = [];
830        var log_energies = [];
831
832        for (var s = 0; s < species_genes.size; s++)
833        {
834                for (var p = 0; p < 2; p++)
835                {
836                        log_numbers.add(number[s][p]);
837                        log_energies.add(e_inc[s][p]);
838                }
839        }
840       
841        log_numbers.add(Populations[1].size);
842        log_energies.add(e_nut);
843
844        log(log_numbers, ExpProperties.logPref+"forams_log.txt");
845    log(log_energies,  ExpProperties.logPref+"energies_log.txt");
846}
847
848function log(tolog, fname)
849{
850        var f = File.appendDirect(fname, "forams data");
851        f.writeString("" + Simulator.stepNumber);
852        for (var  i = 0; i < tolog.size; i++)
853        {
854                f.writeString(";" + tolog[i]);
855        }
856        f.writeString("\n");
857        f.close();
858}
859
860// -------------------------------- step end --------------------------------
861//TODO default params values in frams instead of microns/seconds
862
863@include "standard_events.inc"
864
865~
866
867property:
868id:visualize
869name:Show reticulopodia and nutrients
870type:d 0 1 0
871group:Foraminifera
872
873property:
874id:maxSteps
875name:Stop after the given number of simulation steps
876type:d 0 1000000 0
877
878property:
879id:logPref
880name:Log prefix
881type:s
882
883property:
884id:foramSpeedMmPerMin
885name:Speed of foraminfera in mm/min
886type:f 0.1
887flags: 16
888group:Foraminifera
889
890property:
891id:gametSuccessRate
892name:Ratio of successful gamets
893type:f 0.001
894group:Foraminifera
895
896property:
897id:gametoPeriod
898name:Time of gametogenesis
899type:f 720
900group:Foraminifera
901
902property:
903id:picoCarbonPerMikro
904name:Picograms of carbon in cubed micrometer
905type:f 0.13
906group:Foraminifera
907
908property:
909id:secPerStep
910name:Seconds per simulation step
911type:f 60.0
912flags: 16
913group:Foraminifera
914
915property:
916id:e_repro_cost_haplo
917name:Cost of reproduction
918type:f 0.1 0.9 0.5
919group:Foraminifera
920
921property:
922id:divisionCost
923name:Cost of division in pG
924type:f
925group:Foraminifera
926
927property:
928id:e_repro_cost_diplo
929name:Cost of reproduction
930type:f 0.1 0.9 0.3
931group:Foraminifera
932
933property:
934id:chamber_growth_time
935name:Time of the chamber growth in seconds
936type:f
937group:Foraminifera
938
939property:
940id:chamberCostPerSec
941name:Cost of growning chamber per second
942type:f
943group:Foraminifera
944
945property:
946id:chamber_proculus_haplo
947name:Size of proculus
948type:f
949group:Foraminifera
950
951property:
952id:chamber_proculus_diplo
953name:Size of proculus
954type:f
955group:Foraminifera
956
957property:
958id:chamber_difference_haplo
959name:Difference in size between subsequent chambers
960type:f
961group:Foraminifera
962
963property:
964id:chamber_difference_diplo
965name:Difference in size between subsequent chambers
966type:f
967group:Foraminifera
968
969property:
970id:hunted_prob
971name:Probability of being hunted
972type:f 0 1 0
973group:Forminifera
974
975property:
976id:zone1_range
977name:Zone 1 range
978type:f 0 200
979group:Foraminifera
980
981property:
982id:zone2_range
983name:Zone 2 range
984type:f 0 3000
985group:Foraminifera
986
987property:
988id:colors
989name:Haploid and diploid colors
990type:x
991group:Foraminifera
992
993property:
994id:min_repro_energ_haplo
995name:Min reproduction energy of forams
996type:f
997group:Foraminifera
998
999property:
1000id:min_repro_energ_diplo
1001name:Min reproduction energy of forams
1002type:f
1003group:Foraminifera
1004
1005property:
1006id:repro_prob
1007name:Probability of reproduction
1008type:f 0 1 0.8
1009group:Foraminifera
1010
1011property:
1012id:energies0_haplo
1013name:Energy of offspring from diploid forams
1014type:f
1015group:Foraminifera
1016
1017property:
1018id:energies0_diplo
1019name:Energy of offspring from diploid forams
1020type:f
1021group:Foraminifera
1022
1023property:
1024id:e_death_level_haplo
1025name:Minimal level of energy to sustain life of haploid
1026type:f 0 20 0.2
1027group:Foraminifera
1028
1029property:
1030id:e_death_level_diplo
1031name:Minimal level of energy to sustain life of diploid
1032type:f 0 20 0.2
1033group:Foraminifera
1034
1035property:
1036id:energy_hib
1037name:Energy used for hibernation during one step
1038type:f 0 1 0.001
1039group:Foraminifera
1040
1041property:
1042id:energy_move
1043name:Energy used for movement during one step
1044type:f 0 20 0.001
1045group:Foraminifera
1046
1047property:
1048id:min_vol
1049name:Minimal volume for reproduction
1050type:f 100 900 100
1051group:Foraminifera
1052
1053property:
1054id:max_size
1055name:Maximal size
1056type:d 1 10 5
1057group:Foraminifera
1058
1059property:
1060id:foramPop
1061name:Initial forams population size
1062type:d 1 1000 100
1063group:Foraminifera
1064
1065property:
1066id:crossprob
1067name:Crossover probability
1068type:f 0 1 0
1069group:Foraminifera
1070
1071property:
1072id:mutationprob
1073name:Mutation probability
1074type:f 0 1 0
1075group:Foraminifera
1076
1077property:
1078id:e_meta
1079name:Idle metabolism
1080type:f 0 1
1081group:Energy
1082help:Each stick consumes this amount of energy in one time step
1083
1084property:
1085id:nutrient_pop
1086name:Feeding rate
1087type:f 0 1000000
1088group:Energy
1089help:How fast energy is created in the world
1090
1091property:
1092id:foodPeriodChange
1093name:Set variable feed rate
1094type:f 0
1095group:Energy
1096
1097property:
1098id:ingestion
1099name:Ingestion rate
1100type:f
1101group:Energy
1102
1103property:
1104id:energy_nut
1105name:Nutrient energy
1106type:f 0 10000000
1107group:Energy
1108
1109property:
1110id:feedtrans
1111name:Energy transfer per second
1112type:f 0 100000
1113group:Energy
1114
1115property:
1116id:foodperiod
1117name:Time between food occurrences
1118type:f 0 1000000
1119group:Energy
1120
1121property:
1122id:nutrientradius
1123name:Nutrient size
1124type:f 0.001 0.9 0.1
1125group:Energy
1126
1127property:
1128id:stress
1129name:Environmental stress
1130type:d 0 1 1
1131group:World
1132
1133property:
1134id:repro_trigger
1135name:Reproduction trigger
1136type:d 0 1 1
1137group:World
1138
1139property:
1140id:repro_time
1141name:Time before reproduction
1142type:d 0 10000
1143
1144property:
1145id:creath
1146name:Creation height
1147type:f -1 50
1148help:~
1149Vertical position (above the surface) where new Forams are revived.
1150Negative values are only used in the water area:
1151  0   = at the surface
1152-0.5 = half depth
1153-1   = just above the bottom~
1154
1155state:
1156id:nutrient
1157name:Nutrient locations
1158help:vector of vectors [x,y,energy]
1159type:x
1160flags:32
1161
1162property:
1163id:autorestart
1164name:Restart after extinction
1165help:Restart automatically this experiment after the last creature has died?
1166type:d 0 1
1167
1168state:
1169id:notes
1170name:Notes
1171type:s 1
1172help:~
1173You can write anything here
1174(it will be saved to the experiment file)~
1175
1176state:
1177id:totaltestedcr
1178name:Evaluated Forams
1179help:Total number of the Forams evaluated in the experiment
1180type:d
1181flags:16
1182
1183property:
1184id:logging
1185name:Log statistics to file
1186type:d 0 1 0
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