source: experiments/frams/foraminifera/data/scripts/foraminifera.expdef @ 568

Last change on this file since 568 was 568, checked in by oriona, 8 years ago

Used secPerStep values added in help, setPerStep in show set to 50.

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        //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
91
92        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files   
93        ExpProperties.logPref = "";
94
95        //morphology
96        ExpProperties.zone1_range = micronsToFrams(1000);
97        ExpProperties.zone2_range = micronsToFrams(3000);
98        ExpProperties.chamber_proculus_haplo = micronsToFrams(20);
99        ExpProperties.chamber_proculus_diplo = micronsToFrams(10);
100        colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
101        retColors = ["1.0,1.0,1.0", "1.0,1.0,0.0"];
102        curColor = retColors[0];
103        curRadius = ExpProperties.zone1_range;
104
105        //nutrients
106        ExpProperties.nutrientradius = micronsToFrams(10);
107        ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
108        nutrientSqrCm = 10;
109        ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
110
111        ExpState.totaltestedcr = 0;
112        ExpState.nutrient = "";
113
114        max_chambers_def = 35;
115        chamber_vis_denominator = 6;
116        //addSpecies({"min_repro_energies" : [4,6]});
117        //addSpecies({"min_repro_energies" : [4,8]});
118       
119        //Simulator.print(create_genotype(0.2, 30, "1.0,1.0,0.0", 0.6)); //sample call
120        //Simulator.print(create_genotype(0.1, 40, "1.0,0.5,0.0", 0.1)); //sample call
121}
122
123@include "standard_placement.inc"
124
125function onExpInit()
126{
127        species_genes = [];
128        foram_uid = 0;
129        movePerStep = getMovePerStep();
130
131        Populations[0].clear();
132        Populations[1].clear();
133        Populations[2].clear(); //reticulopodia and nutrients
134
135        if (ExpProperties.max_chamber_num_haplo == max_chambers_def && ExpProperties.max_chamber_num_diplo == max_chambers_def)
136        {
137                max_chamber_volume = [[30403.5869594578,52812.2546633948,79578.5148482541,113588.815134453,154620.677376218,205094.322220826,262572.712174265,326078.453295303,402342.518962956,498133.985678766,615066.864740109,759500.497626816,937064.025544282,1155915.25563075,1429139.14079748,1762487.92940157,2176286.62046069,2685795.63187845,3316190.12127043,4096436.04462706,5051343.25226193,6231980.1061213,7687880.79524734,9485307.02904958,11716968.9852569,14459866.4934433,17836388.9853663,22004935.7247348,27138607.2546045,33482425.1582986,41336775.1280297,50997910.7842793,62888631.7871037,77563060.9243464,95659468.591964]
138, [3430.07716920763,6159.93090353532,9322.94192815286,13462.9896597283,18399.8550832969,24558.9218126892,31468.8148639192,39189.4977865513,48404.4292075836,60185.8639086061,74490.6048472854,92117.8178412275,113852.779747083,140714.366929552,174450.937643841,215250.242147183,266323.295274072,328858.042352538,406552.379957238,503526.321155323,621060.781025019,767240.824049468,947210.683224091,1169506.19906112,1447211.61255879,1787155.29073739,2205627.64766244,2723413.2837305,3360233.53738709,4147771.02835393,5126445.06973928,6328060.3331703,7805693.278958,9631924.72156452,11884287.1596814]];
139        }
140
141        else
142        {
143                max_chamber_volume = [Vector.new(), Vector.new()];
144                var density = 100;
145                for (var ploid = 0; ploid < 2; ploid++)
146                {
147                        var rad = getPloidRadius(ploid);
148                        for (var cham_num = 0; cham_num < getProperty(ploid,"max_chamber_num"); cham_num++)
149                        {
150                                max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num+1, density));
151                        }                                 
152                }
153        }
154
155        if (species_genes.size == 0)
156        {
157                addSpecies({}); //default
158        }
159
160        for (var spec = 0; spec < species_genes.size; spec++)
161        {
162                for (var i = 0; i < ExpProperties.foramPop; i++)
163                {
164                        addInitialForam(spec, i);       
165                }
166        }
167        ExpState.totaltestedcr = 0;
168
169        reprocounter = 0;
170        nutrientenergywaiting = 0;
171        changePeriod = 0;
172        phase = "low";
173}
174
175function onExpLoad()
176{
177        for (var pop in Populations)
178                pop.clear();
179
180        Loader.addClass(sim_params.*);
181        Loader.setBreakLabel(Loader.BeforeUnknown, "onExpLoad_Unknown");
182        Loader.run();
183
184        Simulator.print("Loaded " + Populations[0].size + " Forams and " + Populations[1].size + " nutrient objects");
185}
186
187function onExpLoad_Unknown()
188{
189        if (Loader.objectName == "org") // saved by the old expdef
190        {
191                var g = Genotype.newFromString("");
192                Loader.currentObject = g;
193                Interface.makeFrom(g).setAllDefault();
194                Loader.loadObject();
195                var cr = Populations[0].add(g);
196                if (cr != null)
197                {
198                        //cr.rotate(0,0,Math.rnd01*Math.twopi);
199                        if ((typeof(g.data->genes) == "Vector") && (g.data->genes.size >= 3))
200                        {
201                                // [x,y,energy]
202                                cr.move(g.data->genes[0] - cr.center_x, g.data->genes[1] - cr.center_y, 0);
203                                cr.energy = g.data->genes[2];
204                        }
205                        else
206                        {
207                                cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
208                        }
209                }
210        }
211        else if (Loader.objectName == "Creature")
212        {
213                Loader.currentObject = CreatureSnapshot.new();
214                Loader.loadObject();
215                Populations[0].add(Loader.currentObject);
216        }
217}
218
219function onExpSave()
220{
221        File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
222
223        var tmpvec = [], i;
224
225        for(var cr in Populations[1])
226                tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
227
228        ExpState.nutrient = tmpvec;
229        File.writeObject(sim_params.*);
230        ExpState.nutrient = null; //vectors are only created for saving and then discarded
231
232        for (var cr in Populations[0])
233                File.writeObject(cr);
234}
235
236// -------------------------------- experiment end --------------------------------
237
238function volumeFromGeno(morphotype, rad, chamber_num, density)
239{
240        var geno = create_genotype(rad, chamber_num, colors[morphotype], 1);
241        var m=Model.newFromString(geno);
242        var mg=ModelGeometry.forModel(m);
243        mg.geom_density=density;
244        var volumeInFrams = mg.volume();
245
246        return volumeInFrams/Math.pow(ExpProperties.scalingFactor,3);
247}
248
249function secToSimSteps(value_in_sec){
250        return value_in_sec/ExpProperties.secPerStep;
251}
252
253function volumeInMicrons(radiusInFrams)
254{
255        return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
256}
257
258function energyFromVolume(base, isRadiusInFrams)
259{
260        if (isRadiusInFrams == 1) //radius in frams
261        {
262                return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
263        }
264        else //volume in microns
265        {
266                return ExpProperties.picoCarbonPerMikro * base;
267        }
268}
269
270function getMovePerStep()
271{
272        return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
273}
274
275function micronsToFrams(micrometers)
276{
277        return micrometers*ExpProperties.scalingFactor;
278}
279
280function framsToMicrons(framsworldunits)
281{
282        return framsworldunits/ExpProperties.scalingFactor;
283}
284
285function getProperty(gen, prop_id)
286{
287        var ploid = "haplo";
288        if (gen == 1) ploid = "diplo";
289        return ExpProperties.[prop_id + "_" + ploid];
290}
291
292function getGene(cr, gen_id, gen_set)
293{
294        if (cr.data->lifeparams->gen == 0)
295                return cr.data->genes[gen_id];
296        else
297                return cr.data->genes[gen_set][gen_id];
298}
299
300function getPloidRadius(ploid)
301{
302        var radius = ExpProperties.chamber_proculus_haplo;
303                if (ploid == 1)
304                {
305                        radius = ExpProperties.chamber_proculus_diplo;
306                }
307        return radius;
308}
309
310function chamberNumFromEnergy(energy, ploid)
311{
312        var chamber_num = max_chamber_volume[ploid].size;
313        for (var i = 0; i < chamber_num; i++)
314        {
315                if (energy < energyFromVolume(max_chamber_volume[ploid][i],0))
316                {
317                        chamber_num = i+1;
318                        break;
319                }       
320        }                                 
321       
322        return chamber_num;
323}
324
325function addForam(species, iter, start_energy, ploid)
326{
327        var chambernum =  chamberNumFromEnergy(start_energy, ploid);
328        var radius = getPloidRadius(ploid);
329        var geno = create_genotype(radius, chambernum, colors[ploid], 1);
330        curColor = retColors[ploid];
331        var cr = Populations[0].add(geno);
332        cr.name = "Initial creature" + species + "_" + iter;
333        placeCreatureRandomly(cr, 0, 0);
334        cr.energy = start_energy;
335        setGenotype({"opt" : "birth", "cr" : cr, "gen" : ploid, "species" : species, "energy0" : cr.energy, "genes" : species_genes[species], "parentsuids" : ["c0"]});
336        if (ploid == 1)
337        {
338                cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
339        }
340        moveReticulopodia(cr);
341}
342
343function addInitialForam(species, iter)
344{
345        var ploid = 0;
346        if (Math.rnd01 > 0.5)
347        {
348                ploid = 1;
349        }       
350        //add new foram with random energy bewtween starting energy and reproduction threshold
351        var repro_thr = species_genes[species]->min_repro_energies[ploid];
352        var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid),1),repro_thr-0.25*repro_thr);
353        addForam(species, iter, start_energy,ploid);
354}
355
356//new species can be added as a dictionary with parameter values that are different than default values
357function addSpecies(new_genes)
358{
359        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});
360        for (var i = 0; i < new_genes.size; i++)
361        {
362                var key = new_genes.getKey(i);
363                species_genes[species_genes.size-1][key] = new_genes[key];
364        }
365}
366
367// -------------------------------- foram begin -----------------------------------
368
369function setForamMeta(cr)
370{
371        //percent of current energy
372        cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
373}
374
375function lastChamberNum(cr)
376{
377        return cr.numparts;
378}
379
380function getZoneRange(cr, zone_num)
381{
382        return ExpProperties.["zone"+zone_num+"_range"];
383}
384
385function addReticulopodia(cr, radius)
386{
387                if (reticulopodiaExists(cr))
388                {
389                        Populations[2].delete(cr.data->reticulopodiacreature);
390                }
391                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");
392                cr.data->reticulopodiacreature = ret;
393                ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
394                ret.moveAbs(cr.center_x-radius, cr.center_y-radius, cr.center_z-radius);
395}
396
397function onForamsBorn(cr)
398{
399        setForamMeta(cr);
400        if (ExpProperties.visualize == 1)
401        {
402                addReticulopodia(cr, curRadius);
403        }
404        moveReticulopodia(cr);
405}
406
407function placeRandomlyNotColliding(cr)
408{
409        var retry = 100; //try 100 times
410        while (retry--)
411        {
412                placeCreatureRandomly(cr, 0, 0);
413                if (!cr.boundingBoxCollisions(0))
414                        return cr;
415        }
416
417        Populations[0].delete(cr);
418}
419
420function reticulopodiaExists(cr)
421{
422        var has_ret = 0;
423
424        if (cr.data->reticulopodiacreature != null)
425        {
426                if (Populations[2].findUID(cr.data->reticulopodiacreature.uid) != null)
427                {
428                        has_ret = 1;
429                }
430        }
431
432        return has_ret;
433}
434
435function visualization(cr)
436{
437        return reticulopodiaExists(cr);
438}
439
440function foramGrow(cr, chamber_num, lastchambergrowth)
441{
442        if ((chamber_num+1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
443        {
444                curColor = retColors[cr.data->lifeparams->gen];
445                var ploid = cr.data->lifeparams->gen;
446                var geno = create_genotype(getPloidRadius(ploid), chamber_num+1, colors[ploid], lastchambergrowth);
447                var cr2 = Populations[0].add(geno);
448
449                cr2.energy0 = cr.energy;
450                cr2.energy = cr2.energy0;
451
452                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
453                cr2.moveAbs(cr.pos_x, cr.pos_y,cr.pos_z);
454                setForamMeta(cr2);
455
456                if (reticulopodiaExists(cr))
457                {
458                        Populations[2].delete(cr.data->reticulopodiacreature);
459                }
460                Populations[0].delete(cr);
461                return cr2;
462        }
463        return cr;
464}
465
466function stepToNearest(cr)
467{
468        var p = cr.getMechPart(0);
469        var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
470
471        //if signals are received find the source of the nearest
472        if (n.size > 0)
473        {
474                var i;
475                var mp;
476                var distvec = XYZ.new(0, 0, 0);
477                var dist;
478                var mindist = 100000000000.0;
479                var mindistvec = null;
480                var eating = 0;
481
482                for (i = 0; i < n.size; i++)
483                {
484                        mp = n[i].value.getMechPart(0);
485                        distvec.set(mp.pos);
486                        distvec.sub(p.pos);
487                        dist = distvec.length;
488                        if (dist < getZoneRange(cr,1))
489                        {
490                                if (n[i].value != null)
491                                {
492                                        energyTransfer(cr, n[i].value);
493                                        eating = 1;
494                                }
495                        }
496                        else if (eating == 0 && cr.data->lifeparams->hibernated == 0 && dist < mindist)
497                        {
498                                mindist = dist;
499                                mindistvec = distvec.clone();
500                        }
501                }
502
503                if (!eating && cr.data->lifeparams->hibernated == 0)
504                {
505                        mindistvec.normalize();
506                        mindistvec.scale(-1*movePerStep);
507                        cr.localDrive = mindistvec;
508                        moveEnergyDec(cr);
509                }
510
511                return 1;
512        }
513       
514        else
515        {
516                return 0;
517        }
518}
519
520function moveEnergyDec(cr)
521{
522        if (cr.data->lifeparams->hibernated == 0)
523        {
524                //percent of maximal energy
525                cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
526        }
527}
528
529function fence(pos, zone)
530{
531        return Math.min(Math.max(0,pos),World.wrldsiz);
532}
533
534function foramMove(cr)
535{
536        //TODO moving inside sediment?
537
538        //adjustment in z axis
539        var change_direction = 0;
540        var new_x = fence(cr.pos_x, getZoneRange(cr, 1));
541        var new_y = fence(cr.pos_y,getZoneRange(cr, 1));
542
543        if ((new_x != cr.pos_x) || (new_y != cr.pos_y) || (cr.data->lifeparams->dir_counter >= int(secToSimSteps(ExpProperties.dir_change_sec))))
544        {
545                change_direction = 1;
546        }
547
548        cr.moveAbs(new_x, new_y, 0);
549
550        //are there any nutrients in zone 1 or 2?
551        {
552                var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
553                if (moved==1)
554                {
555                        moveReticulopodia(cr);
556                        return;
557                }
558        }
559
560        //no nutrients in zone 2
561        if (getGene(cr, "hibernation",0) == 1)
562        {
563                reverseHib(cr);
564                cr.localDrive = XYZ.new(0,0,0);
565        }
566        //random move
567        else if (change_direction == 1)
568        {
569                cr.data->lifeparams->dir = randomDir();
570                cr.data->lifeparams->dir_counter = 0;
571                cr.localDrive = cr.data->lifeparams->dir;
572                moveEnergyDec(cr);
573        }
574        else
575        {
576                cr.localDrive = cr.data->lifeparams->dir;
577        }
578        moveReticulopodia(cr);
579}
580
581function moveReticulopodia(cr)
582{
583        if (visualization(cr))
584        {
585                cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
586                cr.data->reticulopodiacreature.localDrive = cr.localDrive;
587        }
588}
589
590function randomDir()
591{
592        var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0); 
593        dir.normalize();
594        dir.scale(-1*movePerStep);
595        return dir;
596}
597
598function energyTransfer(cr1, cr2)
599{
600        cr1.localDrive = XYZ.new(0,0,0);
601        var e =  ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
602        //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
603        var transferred = cr2.transferEnergyTo(cr1, e);
604        cr1.energy -= transferred*(1-ExpProperties.ingestion);
605        if (cr1.data->lifeparams->hibernated == 1)
606        {
607                reverseHib(cr1);
608        }
609}
610
611function reverseHib(cr)
612{
613        if (cr.data->lifeparams->hibernated == 1)
614        {
615                setForamMeta(cr); //unhibernate
616        }
617        else
618        {
619                cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
620        }
621        cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
622}
623
624function onForamsStep(cr)
625{
626        //checking for gametogenesis process
627        if (cr.data->lifeparams->division_time > 0)
628        {
629                cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
630        }
631        //checking for end of gametogenesis
632        else if (cr.data->lifeparams->division_time == 0)
633        {
634                //waiting for gamets fusion
635        }
636        //checking for chamber growth process
637        else if (cr.data->lifeparams->chamber_growth > 0)
638        {
639                var chamber_time = Math.max(cr.data->lifeparams->chamber_growth-1,0);
640                cr.data->lifeparams->chamber_growth = chamber_time;
641                cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
642
643                if (visualization(cr))
644                {
645                        var total_time = secToSimSteps(ExpProperties.chamberGrowthSec);
646                        var ret_unit = total_time/chamber_vis_denominator;
647                        var chamber_unit = total_time-ret_unit;
648
649                        if (chamber_time < ret_unit || chamber_time >= chamber_unit)
650                        {
651                                var new_rad = Math.min(Math.max((chamber_time%ret_unit)/ret_unit*getZoneRange(cr,1),0.01),getZoneRange(cr,1));
652
653                                if(chamber_time < ret_unit)
654                                        new_rad = getZoneRange(cr,1)-new_rad;
655
656                                addReticulopodia(cr,new_rad);
657                        }
658                        else
659                        {
660                                var new_rad = 1 - Math.min(Math.max((chamber_time-ret_unit)/chamber_unit,0.01),1);
661                                curRadius = cr.data->reticulopodiacreature.getPart(1).sy;
662                               
663                                if (chamber_time == ret_unit){
664                                        new_rad == 1;
665                                }
666       
667                                var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen)-1, new_rad);
668                                curRadius = getZoneRange(new_cr,1);
669
670                                if (chamber_time == 0)//checking for end of chamber growth process
671                                {
672                                        new_cr.data->lifeparams->chamber_growth = -1;   
673                                }
674                        }
675                }
676        }
677        //checking for end of chamber growth process
678        else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr)==0)
679        {       
680                foramGrow(cr, lastChamberNum(cr), 1);
681                cr.data->lifeparams->chamber_growth = -1;
682                //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
683        }
684        else
685        {
686                //update of metabolism rate
687                if (cr.data->lifeparams->hibernated == 0)
688                {
689                        setForamMeta(cr);
690                }
691
692                if (deathConditions(cr) == 1)
693                {
694                        if (ExpProperties.logging == 1)
695                        {
696                                log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
697                                log(createLogVector(cr, cr.lifespan),ExpProperties.logPref+"lifespan_log.txt");
698                        }                       
699                        Populations[0].kill(cr);
700                        return;
701                }
702
703                //update direction change counter
704                cr.data->lifeparams->dir_counter += 1;
705
706                foramMove(cr);
707
708                var repro = foramReproduce(cr);
709                if (repro == 1)
710                {
711                        return;
712                }
713
714                cr.data->lifeparams->max_energy_level = Math.max(cr.energy, cr.data->lifeparams->max_energy_level);
715
716                //cheking conditions of chamber growth process start
717                if  (lastChamberNum(cr) < max_chamber_volume[cr.data->lifeparams->gen].size)
718                {
719                        if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)-1],0))) 
720                        {
721                                cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
722                        }       
723                }
724        }       
725}
726
727function deathConditions(cr)
728{
729        if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
730        {
731                return 1;
732        }
733        else
734                return 0;
735}
736
737function onForamsDied(cr)
738{
739        if (visualization(cr))
740        {
741                Populations[2].delete(cr.data->reticulopodiacreature);
742        }
743        //fossilization
744        var geno = GenePools[0].add(cr.genotype);
745        geno.data->genes = cr.data->genes;
746        geno.data->lifeparams = cr.data->lifeparams;
747        if (ExpProperties.logging == 1) Simulator.print("\"" + cr.name + "\" died...");
748        ExpState.totaltestedcr++;
749}
750
751// --------------------------------foram end -------------------------------------
752
753// -------------------------------- nutrient begin --------------------------------
754
755function createNutrientGenotype(nutrientradius)
756{
757        return "//0\nm:Vstyle=nutrient\np:sh=3,sx="+nutrientradius+",sy="+nutrientradius+",sz="+nutrientradius+",ry=1.57,vr=0.0,1.0,0.0";
758}
759
760function onNutrientsStep(cr)
761{
762        cr.moveAbs(cr.pos_x % World.wrldsiz, cr.pos_y % World.wrldsiz, 0.5);
763}
764
765function addNutrient()
766{
767        var cr = Populations[1].add(createNutrientGenotype(ExpProperties.nutrientradius));
768
769        cr.name = "Nutrients";
770        cr.idleen = 0;
771        cr.energy0 = ExpProperties.energy_nut;
772        cr.energy = cr.energy0;
773        cr.signals.add("nutrient");
774
775        cr.signals[0].value = cr;
776
777        placeCreatureRandomly(cr, 0, 0);
778        if (ExpProperties.visualize == 1)
779        {
780                var nutsize = ExpProperties.nutrientradius*10;
781                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");
782                cr.data->reticulopodiacreature = nut;
783                nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
784        }
785}
786
787function onNutrientsDied(cr)
788{
789        if (visualization(cr))
790        {
791                Populations[2].delete(cr.data->reticulopodiacreature);
792        }
793}
794
795function nutrientGrowth()
796{
797        if (ExpProperties.foodPeriodChange > 0)
798        {
799                        changePeriod += 1;
800                        if (phase=="low" && changePeriod >= secToSimSteps(23328000)) //9 months
801                        {
802                                ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
803                                phase = "high";
804                                changePeriod = 0;
805                        }
806               
807                        else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
808                        {
809                                ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
810                                phase = "low";
811                                changePeriod = 0;
812                        }
813        }
814        nutrientenergywaiting = nutrientenergywaiting + 1;
815        if (nutrientenergywaiting >= secToSimSteps(ExpProperties.foodperiod))
816        {
817                for (var i = 0; i < ExpProperties.nutrient_pop; i++)
818                {   
819                        addNutrient();
820                }
821
822                nutrientenergywaiting = 0.0;
823                Simulator.checkpoint();
824
825                if (ExpProperties.logging == 1)
826                {
827                        log([ExpProperties.nutrient_pop],ExpProperties.logPref+"nutrients_log.txt");
828                }
829        }
830
831}
832
833// -------------------------------- nutrient end --------------------------------
834
835// -------------------------------- step begin --------------------------------
836
837function onStep()
838{
839
840        nutrientGrowth();
841        if (ExpProperties.logging == 1)
842        {
843                createStatistics();
844        }
845
846        //reproduction --------------------------------------------
847        reprocounter += 1;
848        if (reprocounter > secToSimSteps(ExpProperties.reproTimeSec))
849        {
850                reprocounter = 0;
851                for (var s = 0; s < species_genes.size; s++)
852                {
853                        reproduce_parents(s);
854                }
855               
856        }
857
858        //check for extinction -----------------------------------------------
859        if (Populations[0].size == 0)
860        {
861                if (ExpProperties.autorestart)
862                {
863                        Simulator.print("no more creatures, restarting...");
864                        onExpInit();
865                }
866                else
867                {
868                        Simulator.print("no more creatures, stopped.");
869                        Simulator.stop();
870                }
871        }
872        if (ExpProperties.maxSteps > 0)
873        {
874                if (Simulator.stepNumber >= ExpProperties.maxSteps)
875                        Simulator.stop();
876        }
877}
878
879function createStatistics()
880{       
881        var number = [];
882        var e_inc = [];
883        var e_nut = 0.0;
884
885        for (var s = 0; s < species_genes.size; s++)
886        {
887                number.add([0,0]);// [haplo][diplo]
888                e_inc.add([0,0]);
889        }
890
891        for (var i = 0; i < Populations[0].size; i++)
892        {
893                var cr = Populations[0].get(i);
894                var gen = cr.data->lifeparams->gen;
895                var species = cr.data->lifeparams->species;
896
897                number[species][gen] = number[species][gen] + 1;
898                e_inc[species][gen] = e_inc[species][gen] + cr.energy;
899        }
900
901        for (var i = 0; i < Populations[1].size; i++)
902        {
903                var cr = Populations[1].get(i);
904                e_nut += cr.energy;
905        }
906
907        var log_numbers = [];
908        var log_energies = [];
909
910        for (var s = 0; s < species_genes.size; s++)
911        {
912                for (var p = 0; p < 2; p++)
913                {
914                        log_numbers.add(number[s][p]);
915                        log_energies.add(e_inc[s][p]);
916                }
917        }
918       
919        log_numbers.add(Populations[1].size);
920        log_energies.add(e_nut);
921
922        log(log_numbers, ExpProperties.logPref+"forams_log.txt");
923    log(log_energies,  ExpProperties.logPref+"energies_log.txt");
924}
925
926function log(tolog, fname)
927{
928        var f = File.appendDirect(fname, "forams data");
929        f.writeString("" + Simulator.stepNumber);
930        for (var  i = 0; i < tolog.size; i++)
931        {
932                f.writeString(";" + tolog[i]);
933        }
934        f.writeString("\n");
935        f.close();
936}
937
938function createLogVector(cr, value)
939{
940        var vec = Vector.new();
941        for (var i = 0; i < species_genes.size; i++)
942        {
943                for (var j = 0; j < 2; j++)
944                {
945                        vec.add(0);
946                }
947                if (cr.data->lifeparams->species == i)
948                {
949                        vec[i*2+cr.data->lifeparams->gen] = value;             
950                }
951        }
952        return vec;
953}
954
955
956// -------------------------------- step end --------------------------------
957//TODO default params values in frams instead of microns/seconds
958
959@include "standard_events.inc"
960
961~
962
963property:
964id:visualize
965name:Show reticulopodia and nutrients
966type:d 0 1 0
967group:
968
969property:
970id:maxSteps
971name:Maximum number of steps
972type:d 0 10000000 0
973group:
974
975property:
976id:scalingFactor
977name:Scaling factor for micrometers
978type:f 0 -1 0.01
979group:
980
981property:
982id:logging
983name:Log statistics to file
984type:d 0 1 0
985group:
986
987property:
988id:logPref
989name:Log prefix
990type:s
991
992property:
993id:secPerStep
994name:Seconds per simulation step
995help:~
996Number of seconds of foraminifera time per simulation step
997For experiments is equal to 300, for visualization is equal to 50~
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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