source: experiments/frams/foraminifera/data/scripts/foraminifera.expdef @ 567

Last change on this file since 567 was 567, checked in by oriona, 8 years ago

Chamber growth visualization added, [OFFSPRING] message added, refactoring.

File size: 30.9 KB
Line 
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 colors;
26global retColors;
27global curColor;
28global max_chamber_volume;
29global movePerStep;
30global nutrientenergywaiting;
31global reprocounter;
32global changePeriod;
33global phase;
34global nutrientSqrCm;
35global species_genes;
36global max_chambers_def;
37global foram_uid; //introduced because each replacement of a creature (while growing) would generate a new Creature.uid
38global chamber_vis_denominator;
39global curRadius;
40
41@include "foraminifera.inc"
42
43// -------------------------------- experiment begin --------------------------------
44
45function onExpDefLoad()
46{
47        // define genotype and creature groups
48        GenePools.clear();
49        Populations.clear();
50        GenePools[0].name = "Unused";
51
52        var pop = Populations[0];
53        pop.name = "Forams";
54        pop.en_assim = 0;
55        pop.nnsim = 0;
56        pop.enableperf = 1;
57        pop.death = 1;
58        pop.energy = 1;
59        pop.selfmask = 0;
60        pop.othermask = 0;
61        //pop.selfmask = 0x20002; pop.othermask = 0x10002;
62        pop.perfperiod = 25;
63        pop.bodysim = 0;
64
65        pop = Populations.addGroup("Nutrients");
66        pop.nnsim = 0;
67        pop.enableperf = 0;
68        pop.death = 1;
69        pop.energy = 1;
70        pop.selfmask = 0;
71        pop.othermask = 0;
72        //pop.othermask = 0x10002;
73        pop.bodysim = 0;
74
75        pop = Populations.addGroup("ReticulopodiaNutrients");
76        pop.nnsim = 0;
77        pop.enableperf = 0;
78        pop.death = 0;
79        pop.energy = 0;
80        pop.selfmask = 0;
81        pop.othermask = 0;
82        pop.bodysim = 0;
83
84        //world
85        SignalView.mode = 1;
86        World.wrldwat = 200;
87        World.wrldsiz = micronsToFrams(100000);
88        World.wrldbnd = 1;
89
90        movePerStep = getMovePerStep();
91
92        //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
93
94        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files   
95        ExpProperties.logPref = "";
96
97        species_genes = [];
98
99        //morphology
100        ExpProperties.zone1_range = micronsToFrams(1000);
101        ExpProperties.zone2_range = micronsToFrams(3000);
102        ExpProperties.chamber_proculus_haplo = micronsToFrams(20);
103        ExpProperties.chamber_proculus_diplo = micronsToFrams(10);
104        colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
105        retColors = ["1.0,1.0,1.0", "1.0,1.0,0.0"];
106        curColor = retColors[0];
107        curRadius = ExpProperties.zone1_range;
108
109        //nutrients
110        ExpProperties.nutrientradius = micronsToFrams(10);
111        ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
112        nutrientSqrCm = 10;
113        ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
114
115        ExpState.totaltestedcr = 0;
116        ExpState.nutrient = "";
117
118        max_chambers_def = 35;
119        chamber_vis_denominator = 6;
120        //addSpecies({"min_repro_energies" : [4,6]});
121        //addSpecies({"min_repro_energies" : [4,8]});
122       
123        //Simulator.print(create_genotype(0.2, 30, "1.0,1.0,0.0", 0.6)); //sample call
124        //Simulator.print(create_genotype(0.1, 40, "1.0,0.5,0.0", 0.1)); //sample call
125}
126
127@include "standard_placement.inc"
128
129function onExpInit()
130{
131        foram_uid = 0;
132
133        Populations[0].clear();
134        Populations[1].clear();
135        Populations[2].clear(); //reticulopodia and nutrients
136
137        if (ExpProperties.max_chamber_num_haplo == max_chambers_def && ExpProperties.max_chamber_num_diplo == max_chambers_def)
138        {
139                max_chamber_volume = [[30403.5869594578,52812.2546633948,79578.5148482541,113588.815134453,154620.677376218,205094.322220826,262572.712174265,326078.453295303,402342.518962956,498133.985678766,615066.864740109,759500.497626816,937064.025544282,1155915.25563075,1429139.14079748,1762487.92940157,2176286.62046069,2685795.63187845,3316190.12127043,4096436.04462706,5051343.25226193,6231980.1061213,7687880.79524734,9485307.02904958,11716968.9852569,14459866.4934433,17836388.9853663,22004935.7247348,27138607.2546045,33482425.1582986,41336775.1280297,50997910.7842793,62888631.7871037,77563060.9243464,95659468.591964]
140, [3430.07716920763,6159.93090353532,9322.94192815286,13462.9896597283,18399.8550832969,24558.9218126892,31468.8148639192,39189.4977865513,48404.4292075836,60185.8639086061,74490.6048472854,92117.8178412275,113852.779747083,140714.366929552,174450.937643841,215250.242147183,266323.295274072,328858.042352538,406552.379957238,503526.321155323,621060.781025019,767240.824049468,947210.683224091,1169506.19906112,1447211.61255879,1787155.29073739,2205627.64766244,2723413.2837305,3360233.53738709,4147771.02835393,5126445.06973928,6328060.3331703,7805693.278958,9631924.72156452,11884287.1596814]];
141        }
142
143        else
144        {
145                max_chamber_volume = [Vector.new(), Vector.new()];
146                var density = 100;
147                for (var ploid = 0; ploid < 2; ploid++)
148                {
149                        var rad = getPloidRadius(ploid);
150                        for (var cham_num = 0; cham_num < getProperty(ploid,"max_chamber_num"); cham_num++)
151                        {
152                                max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num+1, density));
153                        }                                 
154                }
155        }
156
157        if (species_genes.size == 0)
158        {
159                addSpecies({}); //default
160        }
161
162        for (var spec = 0; spec < species_genes.size; spec++)
163        {
164                for (var i = 0; i < ExpProperties.foramPop; i++)
165                {
166                        addInitialForam(spec, i);       
167                }
168        }
169        ExpState.totaltestedcr = 0;
170
171        reprocounter = 0;
172        nutrientenergywaiting = 0;
173        changePeriod = 0;
174        phase = "low";
175}
176
177function onExpLoad()
178{
179        for (var pop in Populations)
180                pop.clear();
181
182        Loader.addClass(sim_params.*);
183        Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
184        Loader.run();
185
186        Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
187}
188
189function onExpLoad_Unknown()
190{
191        if (Loader.objectName == "org") // saved by the old expdef
192        {
193                var g = Genotype.newFromString("");
194                Loader.currentObject = g;
195                Interface.makeFrom(g).setAllDefault();
196                Loader.loadObject();
197                var cr = Populations[0].add(g);
198                if (cr != null)
199                {
200                        //cr.rotate(0,0,Math.rnd01*Math.twopi);
201                        if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
202                        {
203                                // [x,y,energy]
204                                cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
205                                cr.energy = g.data->genes[2];
206                        }
207                        else
208                        {
209                                cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
210                        }
211                }
212        }
213        else if (Loader.objectName == "Creature")
214        {
215                Loader.currentObject = CreatureSnapshot.new();
216                Loader.loadObject();
217                Populations[0].add(Loader.currentObject);
218        }
219}
220
221function onExpSave()
222{
223        File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
224
225        var tmpvec = [], i;
226
227        for(var cr in Populations[1])
228                tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
229
230        ExpState.nutrient = tmpvec;
231        File.writeObject(sim_params.*);
232        ExpState.nutrient = null; //vectors are only created for saving and then discarded
233
234        for (var cr in Populations[0])
235                File.writeObject(cr);
236}
237
238// -------------------------------- experiment end --------------------------------
239
240function volumeFromGeno(morphotype, rad, chamber_num, density)
241{
242        var geno = create_genotype(rad, chamber_num, colors[morphotype], 1);
243        var m=Model.newFromString(geno);
244        var mg=ModelGeometry.forModel(m);
245        mg.geom_density=density;
246        var volumeInFrams = mg.volume();
247
248        return volumeInFrams/Math.pow(ExpProperties.scalingFactor,3);
249}
250
251function secToSimSteps(value_in_sec){
252        return value_in_sec/ExpProperties.secPerStep;
253}
254
255function volumeInMicrons(radiusInFrams)
256{
257        return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
258}
259
260function energyFromVolume(base, isRadiusInFrams)
261{
262        if (isRadiusInFrams == 1) //radius in frams
263        {
264                return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
265        }
266        else //volume in microns
267        {
268                return ExpProperties.picoCarbonPerMikro * base;
269        }
270}
271
272function getMovePerStep()
273{
274        return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
275}
276
277function micronsToFrams(micrometers)
278{
279        return micrometers*ExpProperties.scalingFactor;
280}
281
282function framsToMicrons(framsworldunits)
283{
284        return framsworldunits/ExpProperties.scalingFactor;
285}
286
287function getProperty(gen, prop_id)
288{
289        var ploid = "haplo";
290        if (gen == 1) ploid = "diplo";
291        return ExpProperties.[prop_id + "_" + ploid];
292}
293
294function getGene(cr, gen_id, gen_set)
295{
296        if (cr.data->lifeparams->gen == 0)
297                return cr.data->genes[gen_id];
298        else
299                return cr.data->genes[gen_set][gen_id];
300}
301
302function getPloidRadius(ploid)
303{
304        var radius = ExpProperties.chamber_proculus_haplo;
305                if (ploid == 1)
306                {
307                        radius = ExpProperties.chamber_proculus_diplo;
308                }
309        return radius;
310}
311
312function chamberNumFromEnergy(energy, ploid)
313{
314        var chamber_num = max_chamber_volume[ploid].size;
315        for (var i = 0; i < chamber_num; i++)
316        {
317                if (energy < energyFromVolume(max_chamber_volume[ploid][i],0))
318                {
319                        chamber_num = i+1;
320                        break;
321                }       
322        }                                 
323       
324        return chamber_num;
325}
326
327function addForam(species, iter, start_energy, ploid)
328{
329        var chambernum =  chamberNumFromEnergy(start_energy, ploid);
330        var radius = getPloidRadius(ploid);
331        var geno = create_genotype(radius, chambernum, colors[ploid], 1);
332        curColor = retColors[ploid];
333        var cr = Populations[0].add(geno);
334        cr.name = "Initial creature" + species + "_" + iter;
335        placeCreatureRandomly(cr, 0, 0);
336        cr.energy = start_energy;
337        setGenotype({"opt" : "birth", "cr" : cr, "gen" : ploid, "species" : species, "energy0" : cr.energy, "genes" : species_genes[species], "parentsuids" : ["c0"]});
338        if (ploid == 1)
339        {
340                cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
341        }
342        moveReticulopodia(cr);
343}
344
345function addInitialForam(species, iter)
346{
347        var ploid = 0;
348        if (Math.rnd01 > 0.5)
349        {
350                ploid = 1;
351        }       
352        //add new foram with random energy bewtween starting energy and reproduction threshold
353        var repro_thr = species_genes[species]->min_repro_energies[ploid];
354        var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid),1),repro_thr-0.25*repro_thr);
355        addForam(species, iter, start_energy,ploid);
356}
357
358//new species can be added as a dictionary with parameter values that are different than default values
359function addSpecies(new_genes)
360{
361        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});
362        for (var i = 0; i < new_genes.size; i++)
363        {
364                var key = new_genes.getKey(i);
365                species_genes[species_genes.size-1][key] = new_genes[key];
366        }
367}
368
369// -------------------------------- foram begin -----------------------------------
370
371function setForamMeta(cr)
372{
373        //percent of current energy
374        cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
375}
376
377function lastChamberNum(cr)
378{
379        return cr.numparts;
380}
381
382function getZoneRange(cr, zone_num)
383{
384        return ExpProperties.["zone"+zone_num+"_range"];
385}
386
387function addReticulopodia(cr, radius)
388{
389                if (reticulopodiaExists(cr))
390                {
391                        Populations[2].delete(cr.data->reticulopodiacreature);
392                }
393                var ret = Populations[2].add("//0\nm:Vstyle=reticulopodia\np:sh=1,sx=0.001,sy=0.001,sz=0.001\np:sh=3,sx=0.01,sy="+radius+",sz="+radius+",ry=1.57079633,vr="+curColor+"\nj:0, 1, sh=1");
394                cr.data->reticulopodiacreature = ret;
395                ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
396                ret.moveAbs(cr.center_x-radius, cr.center_y-radius, cr.center_z-radius);
397}
398
399function onForamsBorn(cr)
400{
401        setForamMeta(cr);
402        if (ExpProperties.visualize == 1)
403        {
404                addReticulopodia(cr, curRadius);
405        }
406        moveReticulopodia(cr);
407}
408
409function placeRandomlyNotColliding(cr)
410{
411        var retry = 100; //try 100 times
412        while (retry--)
413        {
414                placeCreatureRandomly(cr, 0, 0);
415                if (!cr.boundingBoxCollisions(0))
416                        return cr;
417        }
418
419        Populations[0].delete(cr);
420}
421
422function reticulopodiaExists(cr)
423{
424        var has_ret = 0;
425
426        if (cr.data->reticulopodiacreature != null)
427        {
428                if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
429                {
430                        has_ret = 1;
431                }
432        }
433
434        return has_ret;
435}
436
437function visualization(cr)
438{
439        return reticulopodiaExists(cr);
440}
441
442function foramGrow(cr, chamber_num, lastchambergrowth)
443{
444        if ((chamber_num+1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
445        {
446                curColor = retColors[cr.data->lifeparams->gen];
447                var ploid = cr.data->lifeparams->gen;
448                var geno = create_genotype(getPloidRadius(ploid), chamber_num+1, colors[ploid], lastchambergrowth);
449                var cr2 = Populations[0].add(geno);
450
451                cr2.energy0 = cr.energy;
452                cr2.energy = cr2.energy0;
453
454                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
455                cr2.moveAbs(cr.pos_x, cr.pos_y,cr.pos_z);
456                setForamMeta(cr2);
457
458                if (reticulopodiaExists(cr))
459                {
460                        Populations[2].delete(cr.data->reticulopodiacreature);
461                }
462                Populations[0].delete(cr);
463                return cr2;
464        }
465        return cr;
466}
467
468function stepToNearest(cr)
469{
470        var p = cr.getMechPart(0);
471        var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
472
473        //if signals are received find the source of the nearest
474        if (n.size > 0)
475        {
476                var i;
477                var mp;
478                var distvec = XYZ.new(0, 0, 0);
479                var dist;
480                var mindist = 100000000000.0;
481                var mindistvec = null;
482                var eating = 0;
483
484                for (i = 0; i < n.size; i++)
485                {
486                        mp = n[i].value.getMechPart(0);
487                        distvec.set(mp.pos);
488                        distvec.sub(p.pos);
489                        dist = distvec.length;
490                        if (dist < getZoneRange(cr,1))
491                        {
492                                if (n[i].value != null)
493                                {
494                                        energyTransfer(cr, n[i].value);
495                                        eating = 1;
496                                }
497                        }
498                        else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
499                        {
500                                mindist = dist;
501                                mindistvec = distvec.clone();
502                        }
503                }
504
505                if (!eating && cr.data->lifeparams->hibernated == 0)
506                {
507                        mindistvec.normalize();
508                        mindistvec.scale(-1*movePerStep);
509                        cr.localDrive = mindistvec;
510                        moveEnergyDec(cr);
511                }
512
513                return 1;
514        }
515       
516        else
517        {
518                return 0;
519        }
520}
521
522function moveEnergyDec(cr)
523{
524        if (cr.data->lifeparams->hibernated == 0)
525        {
526                //percent of maximal energy
527                cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
528        }
529}
530
531function fence(pos, zone)
532{
533        return Math.min(Math.max(0,pos),World.wrldsiz);
534}
535
536function foramMove(cr)
537{
538        //TODO moving inside sediment?
539
540        //adjustment in z axis
541        var change_direction = 0;
542        var new_x = fence(cr.pos_x, getZoneRange(cr, 1));
543        var new_y = fence(cr.pos_y,getZoneRange(cr, 1));
544
545        if ((new_x != cr.pos_x) || (new_y != cr.pos_y) || (cr.data->lifeparams->dir_counter >= int(secToSimSteps(ExpProperties.dir_change_sec))))
546        {
547                change_direction = 1;
548        }
549
550        cr.moveAbs(new_x, new_y, 0);
551
552        //are there any nutrients in zone 1 or 2?
553        {
554                var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
555                if (moved==1)
556                {
557                        moveReticulopodia(cr);
558                        return;
559                }
560        }
561
562        //no nutrients in zone 2
563        if (getGene(cr, "hibernation",0) == 1)
564        {
565                reverseHib(cr);
566                cr.localDrive = XYZ.new(0,0,0);
567        }
568        //random move
569        else if (change_direction == 1)
570        {
571                cr.data->lifeparams->dir = randomDir();
572                cr.data->lifeparams->dir_counter = 0;
573                cr.localDrive = cr.data->lifeparams->dir;
574                moveEnergyDec(cr);
575        }
576        else
577        {
578                cr.localDrive = cr.data->lifeparams->dir;
579        }
580        moveReticulopodia(cr);
581}
582
583function moveReticulopodia(cr)
584{
585        if (visualization(cr))
586        {
587                cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
588                cr.data->reticulopodiacreature.localDrive = cr.localDrive;
589        }
590}
591
592function randomDir()
593{
594        var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0); 
595        dir.normalize();
596        dir.scale(-1*movePerStep);
597        return dir;
598}
599
600function energyTransfer(cr1, cr2)
601{
602        cr1.localDrive = XYZ.new(0,0,0);
603        var e =  ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
604        //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
605        var transferred = cr2.transferEnergyTo(cr1, e);
606        cr1.energy -= transferred*(1-ExpProperties.ingestion);
607        if (cr1.data->lifeparams->hibernated == 1)
608        {
609                reverseHib(cr1);
610        }
611}
612
613function reverseHib(cr)
614{
615        if (cr.data->lifeparams->hibernated == 1)
616        {
617                setForamMeta(cr); //unhibernate
618        }
619        else
620        {
621                cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
622        }
623        cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
624}
625
626function onForamsStep(cr)
627{
628        //checking for gametogenesis process
629        if (cr.data->lifeparams->division_time > 0)
630        {
631                cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
632        }
633        //checking for end of gametogenesis
634        else if (cr.data->lifeparams->division_time == 0)
635        {
636                //waiting for gamets fusion
637        }
638        //checking for chamber growth process
639        else if (cr.data->lifeparams->chamber_growth > 0)
640        {
641                var chamber_time = Math.max(cr.data->lifeparams->chamber_growth-1,0);
642                cr.data->lifeparams->chamber_growth = chamber_time;
643                cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
644
645                if (visualization(cr))
646                {
647                        var total_time = secToSimSteps(ExpProperties.chamberGrowthSec);
648                        var ret_unit = total_time/chamber_vis_denominator;
649                        var chamber_unit = total_time-ret_unit;
650
651                        if (chamber_time < ret_unit || chamber_time >= chamber_unit)
652                        {
653                                var new_rad = Math.min(Math.max((chamber_time%ret_unit)/ret_unit*getZoneRange(cr,1),0.01),getZoneRange(cr,1));
654
655                                if(chamber_time < ret_unit)
656                                        new_rad = getZoneRange(cr,1)-new_rad;
657
658                                addReticulopodia(cr,new_rad);
659                        }
660                        else
661                        {
662                                var new_rad = 1 - Math.min(Math.max((chamber_time-ret_unit)/chamber_unit,0.01),1);
663                                curRadius = cr.data->reticulopodiacreature.getPart(1).sy;
664                               
665                                if (chamber_time == ret_unit){
666                                        new_rad == 1;
667                                }
668       
669                                var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen)-1, new_rad);
670                                curRadius = getZoneRange(new_cr,1);
671
672                                if (chamber_time == 0)//checking for end of chamber growth process
673                                {
674                                        new_cr.data->lifeparams->chamber_growth = -1;   
675                                }
676                        }
677                }
678        }
679        //checking for end of chamber growth process
680        else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr)==0)
681        {       
682                foramGrow(cr, lastChamberNum(cr), 1);
683                cr.data->lifeparams->chamber_growth = -1;
684                //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
685        }
686        else
687        {
688                //update of metabolism rate
689                if (cr.data->lifeparams->hibernated == 0)
690                {
691                        setForamMeta(cr);
692                }
693
694                if (deathConditions(cr) == 1)
695                {
696                        if (ExpProperties.logging == 1)
697                        {
698                                log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
699                                log(createLogVector(cr, cr.lifespan),ExpProperties.logPref+"lifespan_log.txt");
700                        }                       
701                        Populations[0].kill(cr);
702                        return;
703                }
704
705                //update direction change counter
706                cr.data->lifeparams->dir_counter += 1;
707
708                foramMove(cr);
709
710                var repro = foramReproduce(cr);
711                if (repro == 1)
712                {
713                        return;
714                }
715
716                cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
717
718                //cheking conditions of chamber growth process start
719                if  (lastChamberNum(cr) < max_chamber_volume[cr.data->lifeparams->gen].size)
720                {
721                        if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)-1],0))) 
722                        {
723                                cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
724                        }       
725                }
726        }       
727}
728
729function deathConditions(cr)
730{
731        if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
732        {
733                return 1;
734        }
735        else
736                return 0;
737}
738
739function onForamsDied(cr)
740{
741        if (visualization(cr))
742        {
743                Populations[2].delete(cr.data->reticulopodiacreature);
744        }
745        //fossilization
746        var geno = GenePools[0].add(cr.genotype);
747        geno.data->genes = cr.data->genes;
748        geno.data->lifeparams = cr.data->lifeparams;
749        if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
750        ExpState.totaltestedcr++;
751}
752
753// --------------------------------foram end -------------------------------------
754
755// -------------------------------- nutrient begin --------------------------------
756
757function createNutrientGenotype(nutrientradius)
758{
759        return "//0\nm:Vstyle=nutrient\np:sh=3,sx="+nutrientradius+",sy="+nutrientradius+",sz="+nutrientradius+",ry=1.57,vr=0.0,1.0,0.0";
760}
761
762function onNutrientsStep(cr)
763{
764        cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
765}
766
767function addNutrient()
768{
769        var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
770
771        cr.name = "Nutrients";
772        cr.idleen = 0;
773        cr.energy0 = ExpProperties.energy_nut;
774        cr.energy = cr.energy0;
775        cr.signals.add("nutrient");
776
777        cr.signals[0].value = cr;
778
779        placeCreatureRandomly(cr, 0, 0);
780        if (ExpProperties.visualize == 1)
781        {
782                var nutsize = ExpProperties.nutrientradius*10;
783                var nut = Populations[2].add("//0\nm:Vstyle=nutrient_visual\np:sh=2,sx="+nutsize+",sy="+nutsize+",sz="+nutsize+",ry=1.5,vr=0.0,1.0,0.0");
784                cr.data->reticulopodiacreature = nut;
785                nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
786        }
787}
788
789function onNutrientsDied(cr)
790{
791        if (visualization(cr))
792        {
793                Populations[2].delete(cr.data->reticulopodiacreature);
794        }
795}
796
797function nutrientGrowth()
798{
799        if (ExpProperties.foodPeriodChange > 0)
800        {
801                        changePeriod += 1;
802                        if (phase=="low" && changePeriod >= secToSimSteps(23328000)) //9 months
803                        {
804                                ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
805                                phase = "high";
806                                changePeriod = 0;
807                        }
808               
809                        else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
810                        {
811                                ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
812                                phase = "low";
813                                changePeriod = 0;
814                        }
815        }
816        nutrientenergywaiting = nutrientenergywaiting + 1;
817        if (nutrientenergywaiting >= secToSimSteps(ExpProperties.foodperiod))
818        {
819                for (var i = 0; i < ExpProperties.nutrient_pop; i++)
820                {   
821                        addNutrient();
822                }
823
824                nutrientenergywaiting = 0.0;
825                Simulator.checkpoint();
826
827                if (ExpProperties.logging == 1)
828                {
829                        log([ExpProperties.nutrient_pop],ExpProperties.logPref+"nutrients_log.txt");
830                }
831        }
832
833}
834
835// -------------------------------- nutrient end --------------------------------
836
837// -------------------------------- step begin --------------------------------
838
839function onStep()
840{
841
842        nutrientGrowth();
843        if (ExpProperties.logging == 1)
844        {
845                createStatistics();
846        }
847
848        //reproduction --------------------------------------------
849        reprocounter += 1;
850        if (reprocounter > secToSimSteps(ExpProperties.reproTimeSec))
851        {
852                reprocounter = 0;
853                for (var s = 0; s < species_genes.size; s++)
854                {
855                        reproduce_parents(s);
856                }
857               
858        }
859
860        //check for extinction -----------------------------------------------
861        if (Populations[0].size == 0)
862        {
863                if (ExpProperties.autorestart)
864                {
865                        Simulator.print("no more creatures, restarting...");
866                        onExpInit();
867                }
868                else
869                {
870                        Simulator.print("no more creatures, stopped.");
871                        Simulator.stop();
872                }
873        }
874        if (ExpProperties.maxSteps > 0)
875        {
876                if (Simulator.stepNumber >= ExpProperties.maxSteps)
877                        Simulator.stop();
878        }
879}
880
881function createStatistics()
882{       
883        var number = [];
884        var e_inc = [];
885        var e_nut = 0.0;
886
887        for (var s = 0; s < species_genes.size; s++)
888        {
889                number.add([0,0]);// [haplo][diplo]
890                e_inc.add([0,0]);
891        }
892
893        for (var i = 0; i < Populations[0].size; i++)
894        {
895                var cr = Populations[0].get(i);
896                var gen = cr.data->lifeparams->gen;
897                var species = cr.data->lifeparams->species;
898
899                number[species][gen] = number[species][gen] + 1;
900                e_inc[species][gen] = e_inc[species][gen] + cr.energy;
901        }
902
903        for (var i = 0; i < Populations[1].size; i++)
904        {
905                var cr = Populations[1].get(i);
906                e_nut += cr.energy;
907        }
908
909        var log_numbers = [];
910        var log_energies = [];
911
912        for (var s = 0; s < species_genes.size; s++)
913        {
914                for (var p = 0; p < 2; p++)
915                {
916                        log_numbers.add(number[s][p]);
917                        log_energies.add(e_inc[s][p]);
918                }
919        }
920       
921        log_numbers.add(Populations[1].size);
922        log_energies.add(e_nut);
923
924        log(log_numbers, ExpProperties.logPref+"forams_log.txt");
925    log(log_energies,  ExpProperties.logPref+"energies_log.txt");
926}
927
928function log(tolog, fname)
929{
930        var f = File.appendDirect(fname, "forams data");
931        f.writeString("" + Simulator.stepNumber);
932        for (var  i = 0; i < tolog.size; i++)
933        {
934                f.writeString(";" + tolog[i]);
935        }
936        f.writeString("\n");
937        f.close();
938}
939
940function createLogVector(cr, value)
941{
942        var vec = Vector.new();
943        for (var i = 0; i < species_genes.size; i++)
944        {
945                for (var j = 0; j < 2; j++)
946                {
947                        vec.add(0);
948                }
949                if (cr.data->lifeparams->species == i)
950                {
951                        vec[i*2+cr.data->lifeparams->gen] = value;             
952                }
953        }
954        return vec;
955}
956
957
958// -------------------------------- step end --------------------------------
959//TODO default params values in frams instead of microns/seconds
960
961@include "standard_events.inc"
962
963~
964
965property:
966id:visualize
967name:Show reticulopodia and nutrients
968type:d 0 1 0
969group:
970
971property:
972id:maxSteps
973name:Maximum number of steps
974type:d 0 10000000 0
975group:
976
977property:
978id:scalingFactor
979name:Scaling factor for micrometers
980type:f 0 -1 0.01
981group:
982
983property:
984id:logging
985name:Log statistics to file
986type:d 0 1 0
987group:
988
989property:
990id:logPref
991name:Log prefix
992type:s
993
994property:
995id:secPerStep
996name:Seconds per simulation step
997help:Number of seconds of foraminifera time per simulation step
998type:f 1 480 300
999flags: 16
1000group:
1001
1002property:
1003id:foramSpeedMmPerMin
1004name:Speed of foraminfera in mm/min
1005type:f 0.01 0.1 0.05
1006flags: 16
1007group:Foraminifera
1008
1009property:
1010id:dir_change_sec
1011name:Number of seconds before direction change
1012type:d 300 300000 6000
1013group:Foraminifera
1014
1015property:
1016id:foramPop
1017name:Initial forams population size
1018type:d 1 1000 20
1019group:Foraminifera
1020
1021property:
1022id:gametoPeriodSec
1023name:Time of gametogenesis
1024type:f 300 300000 21600
1025group:Reproduction
1026
1027property:
1028id:gametSuccessRate
1029name:Ratio of successful gamets
1030type:f 0.0001 0.01 0.001
1031group:Reproduction
1032
1033property:
1034id:divisionCost
1035name:Cost of division in pG
1036type:f 15 25 20
1037group:Reproduction
1038
1039property:
1040id:min_repro_energ_haplo
1041name:Min reproduction energy of haploid in pg
1042type:f 0 -1 350000
1043group:Energy
1044
1045property:
1046id:min_repro_energ_diplo
1047name:Min reproduction energy of diploid in pg
1048type:f 0 -1 600000
1049group:Energy
1050
1051property:
1052id:repro_prob
1053name:Probability of reproduction
1054type:f 0 1 0.8
1055group:Reproduction
1056
1057property:
1058id:energies0_haplo
1059name:Energy of offspring from diploid forams
1060type:f 0 -1 20
1061group:Energy
1062
1063property:
1064id:energies0_diplo
1065name:Energy of offspring from diploid forams
1066type:f 0 -1 1.25
1067group:Energy
1068
1069property:
1070id:max_chamber_num_haplo
1071name:Maximum number of haploid chambers
1072type:f 1 50 35
1073group:Energy
1074
1075property:
1076id:max_chamber_num_diplo
1077name:Maximum number of diploid chambers
1078type:f 1 50 35
1079group:Energy
1080
1081
1082property:
1083id:crossprob
1084name:Crossover probability
1085type:f 0 1 0
1086group:Reproduction
1087
1088property:
1089id:mutationprob
1090name:Mutation probability
1091type:f 0 1 0
1092group:Reproduction
1093
1094property:
1095id:reproTimeSec
1096name:Time before reproduction
1097type:d 0 10000 720
1098group:Reproduction
1099
1100property:
1101id:chamberGrowthSec
1102name:Time of the chamber growth in seconds
1103type:f 720 43200 43200
1104group:Foraminifera
1105
1106property:
1107id:chamber_proculus_haplo
1108name:Size of proculus
1109type:f
1110group:Foraminifera
1111
1112property:
1113id:chamber_proculus_diplo
1114name:Size of proculus
1115type:f
1116group:Foraminifera
1117
1118property:
1119id:hunted_prob
1120name:Probability of being hunted
1121type:f 0 1 0
1122group:Foraminifera
1123
1124property:
1125id:zone1_range
1126name:Zone 1 range in frams units
1127type:f 0 200 10
1128group:Foraminifera
1129
1130property:
1131id:zone2_range
1132name:Zone 2 range in frams units
1133type:f 0 3000 30
1134group:Foraminifera
1135
1136property:
1137id:chamberCostPerSec
1138name:Cost of growning chamber per second
1139type:f 0 1 0.000001
1140group:Energy
1141
1142property:
1143id:e_death_level_haplo
1144name:Minimal level of energy to sustain life of haploid
1145type:f 0 1 0.5
1146group:Energy
1147
1148property:
1149id:e_death_level_diplo
1150name:Minimal level of energy to sustain life of diploid
1151type:f 0 1 0.5
1152group:Energy
1153
1154property:
1155id:energy_hib
1156name:Energy used for hibernation during one step
1157type:f 0 1 0.0000001
1158group:Energy
1159
1160property:
1161id:energy_move
1162name:Energy used for movement during one step
1163type:f 0 1 0.0000005
1164group:Energy
1165
1166property:
1167id:e_meta
1168name:Idle metabolism
1169type:f 0 1 0.0000005
1170group:Energy
1171help:Foraminifera consumes this proportion of its energy in one time step
1172
1173property:
1174id:ingestion
1175name:Ingestion rate
1176type:f 0 -1 0.25
1177group:Energy
1178
1179property:
1180id:nutrient_pop
1181name:Nutrient population
1182type:f 0 1000000
1183group:Energy
1184help:How fast energy is created in the world
1185
1186property:
1187id:energy_nut
1188name:Nutrient energy
1189type:f 0 10000000
1190group:Energy
1191
1192property:
1193id:nutrientradius
1194name:Nutrient size
1195type:f 0.001 0.9 0.1
1196group:Energy
1197
1198property:
1199id:picoCarbonPerMikro
1200name:Picograms of carbon in cubic micrometer
1201type:f 0 -1 0.13
1202group:Energy
1203
1204property:
1205id:feedtrans
1206name:Energy transfer per second
1207type:f 0 1 0.001
1208group:Energy
1209
1210property:
1211id:foodperiod
1212name:Time between food occurrences
1213type:f 0 1000000 14400
1214group:Energy
1215
1216property:
1217id:foodPeriodChange
1218name:Set variable feed rate
1219type:f 0 -1 0
1220group:Energy
1221
1222property:
1223id:stress
1224name:Environmental stress
1225type:d 0 1 1
1226group:
1227
1228property:
1229id:repro_trigger
1230name:Reproduction trigger
1231type:d 0 1 1
1232group:Reproduction
1233
1234property:
1235id:creath
1236name:Creation height
1237type:f -1 50 -0.99
1238help:~
1239Vertical position (above the surface) where new Forams are revived.
1240Negative values are only used in the water area:
1241  0   = at the surface
1242-0.5 = half depth
1243-1   = just above the bottom~
1244
1245property:
1246id:autorestart
1247name:Restart after extinction
1248help:Restart automatically this experiment after the last creature has died?
1249type:d 0 1 0
1250
1251state:
1252id:nutrient
1253name:Nutrient locations
1254help:vector of vectors [x,y,energy]
1255type:x
1256flags:32
1257
1258state:
1259id:notes
1260name:Notes
1261type:s 1
1262help:~
1263You can write anything here
1264(it will be saved to the experiment file)~
1265
1266state:
1267id:totaltestedcr
1268name:Evaluated Forams
1269help:Total number of the Forams evaluated in the experiment
1270type:d
1271flags:16
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