Changeset 430 for experiments/frams/foraminifera/data/scripts/foraminifera.expdef

Timestamp:

09/08/15 01:03:24 (10 years ago)

Author:

oriona

Message:

new reticulopodia range implemented, visualization of reticulopodia

File:

• experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) (28 diffs)

experiments/frams/foraminifera/data/scripts/foraminifera.expdef

@@ -13 +13 @@
 max_energy_level - maximum energy level reached so far
 gen - generation: 0 haploid, 1 diploid
-species - species: 0 not hibernating 1 hibernating
+species - species: 0 hibernating 1 not hibernating
 hibernated - 0/1 foram isn't/is hibernated
 reproduce - 0/1 foram isn't/is ready for reproduction 
@@ -35 +35 @@
 global o;
 global max_chamber_energ;
-
+global dir_change;
 
 @include "foraminifera.inc"
@@ -69 +69 @@
         //pop.othermask = 0x10002;
 
+        //ExpParams.showRet = 1; //uncomment to show reticulopodia
+
+        pop = Populations.addGroup("Reticulopodia");
+        pop.nnsim = 0;
+        pop.enableperf = 0;
+        pop.death = 0;
+        pop.energy = 0;
+        pop.selfmask = 0x20002;
+        pop.othermask = 0x10000;
+        
         //world
         SignalView.mode = 1;
-        ExpParams.world_size = 100;
-        World.wrldwat = ExpParams.world_size;
+        ExpParams.world_size = scale(40000);
+        World.wrldwat = 200;
         World.wrldsiz = ExpParams.world_size;
         World.wrldbnd = 1;
@@ -82 +92 @@
 
         //reproduction
-        ExpParams.foramPop = 3;
+        ExpParams.foramPop = 10;        
         ExpParams.crossprob = 0.4;
         ExpParams.mutationprob = 0.2;
@@ -89 +99 @@
 
         //morphology
+        dir_change = 500;
+        ExpParams.zone1_range = scale(5000);
+        ExpParams.zone2_range = scale(8000);
         init_chambers();
-        ExpParams.chamber_proculus_haplo = scale(60);
+        ExpParams.chamber_proculus_haplo = scale(50);
         ExpParams.chamber_difference_haplo = 0.0;
         ExpParams.chamber_proculus_diplo = scale(20);
@@ -100 +113 @@
                 {
                         max_chamber_energ[j].add(((Math.pow(getProperty(j, "chamber_proculus"),3) + Math.pow(getProperty(j, "chamber_proculus") + (i) * getProperty(j, "chamber_difference"),3))*(i+1))/2);
-
                 }                                  
         }
-        ExpParams.zone1_range = scale(250);
-        ExpParams.zone2_range = scale(5000);
 
         //energetics
-        ExpParams.min_repro_energ_haplo = max_chamber_energ[0][2];
-        ExpParams.min_repro_energ_diplo = max_chamber_energ[1][8];
-        ExpParams.e_meta = 0.00003 * max_chamber_energ[0][0];
-        ExpParams.energy_hib = 0.00003 * max_chamber_energ[0][0];
-        ExpParams.energy_move = 0.0003 * max_chamber_energ[0][0];
-        ExpParams.energies0_haplo = max_chamber_energ[0][0] - 0.1*max_chamber_energ[0][0];
-        ExpParams.energies0_diplo = max_chamber_energ[1][0] - 0.1*max_chamber_energ[1][0];
-        ExpParams.feedtrans = 0.05;
-        ExpParams.e_repro_cost_haplo = 0.5; 
+        ExpParams.min_repro_energ_haplo = 4;
+        ExpParams.min_repro_energ_diplo = 6;
+
+        ExpParams.e_meta = 0.0002; 
+        ExpParams.energy_hib = 0.0001;
+        ExpParams.energy_move = 0.00025;
+
+        ExpParams.energies0_haplo = max_chamber_energ[0][0] - 0.001*max_chamber_energ[0][0];
+        ExpParams.energies0_diplo = max_chamber_energ[1][0] - 0.001*max_chamber_energ[1][0];
+        ExpParams.feedtrans = 0.5;
+        ExpParams.e_repro_cost_haplo = 0.7; 
         ExpParams.e_repro_cost_diplo = 0.3;
 
@@ -121 +133 @@
         ExpParams.nutrientsize = scale(10);
         ExpParams.energy_nut = 100 * Math.pow(ExpParams.nutrientsize, 3);
-        ExpParams.nutrientPop = 10;
-        ExpParams.feedrate = 0.0025;
+        ExpParams.nutrientPop = 1;
+        ExpParams.feedrate = 0.1;
         nutrientenergywaiting = ExpParams.energy_nut;
         ExpState.totaltestedcr = 0;
@@ -157 +169 @@
         Populations[0].clear();
         Populations[1].clear();
+        Populations[2].clear();
 
         for (var i = 0; i < ExpParams.foramPop; i++)
@@ -223 +236 @@
         ExpState.nutrient = tmpvec;
         File.writeObject(sim_params.*);
-        ExpState.nutrient = null; //vectors are only created for saving and then discarded
+        ExpState.nutrient = null; //vectors are only created for saving and then discardedsetForam
 
         for (var cr in Populations[0])
@@ -233 +246 @@
 // -------------------------------- foram begin -----------------------------------
 
+function setForamMeta(cr, gen)
+{
+        cr.idleen = ExpParams.e_meta * max_chamber_energ[gen][Math.min(lastChamberNum(cr), max_chamber_energ[gen].size-1)];
+}
+
+function lastChamberNum(cr)
+{
+        return cr.numparts-1;
+}
+
 function onForamsBorn(cr)
 {
-        cr.idleen = ExpParams.e_meta;
+        setForamMeta(cr, 1);
+        if (ExpParams.showRet == 1)
+        {
+                var ret = Populations[2].add("//0\np:sh=3,sx=0.01,sy="+ExpParams.zone1_range+",sz="+ExpParams.zone1_range+",ry=1.57");
+                cr.user3 = ret;
+        }
 }
 
@@ -253 +281 @@
 function foramGrow(cr, chamber_num)
 {
-        var geno = createForamGenotype(cr.user2["gen"], cr.user2["species"], chamber_num);
+        var geno = createForamGenotype(cr.user2["gen"], cr.user2["species"], chamber_num+1);
         var cr2 = Populations[0].add(geno);
 
@@ -261 +289 @@
         setGenotype({"cr" : cr2, "parent_user1" : cr.user1, "parent_user2" : cr.user2, "opt" : 2});
         cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
-
+        setForamMeta(cr2, cr2.user2["gen"]);
+
+        if (ExpParams.showRet == 1)
+        {
+                Populations[2].delete(cr.user3);
+        }
         Populations[0].delete(cr);
 }
@@ -279 +312 @@
                 var mindist = 100000000000;
                 var mindistvec = null;
+                var eating = 0;
 
                 for (i = 0; i < n.size; i++)
                 {
-                        mp = n[i].value;
+                        mp = n[i].value.getMechPart(0);
                         distvec.set(mp.pos);
                         distvec.sub(p.pos);
                         dist = distvec.length;
-                        if (dist < mindist)
+                        if (dist < ExpParams.zone1_range)
+                        {
+                                if (n[i].value != null)
+                                {
+                                        energyTransfer(cr, n[i].value);
+                                        eating = 1;
+                                }
+                        }
+                        else if (eating == 0 && cr.user2["hibernated"] == 0 && dist < mindist)
                         {
                                 mindist = dist;
@@ -293 +335 @@
                 }
 
-                mindistvec.normalize();
-                mindistvec.scale(-0.08);
-                cr.localDrive = mindistvec;
+                if (!eating && cr.user2["hibernated"] == 0)
+                {
+                        mindistvec.normalize();
+                        mindistvec.scale(-0.08);
+                        cr.localDrive = mindistvec;
+                        moveEnergyDec(cr);
+                }
+
                 return 1;
         }
@@ -305 +352 @@
 function moveEnergyDec(cr)
 {
-        if (cr.user2["hibernated"] == 1)
-        {
-                cr.energy_m += ExpParams.energy_hib;
-        }
-        else
-        {
-                cr.energy_m += ExpParams.energy_move;
+        if (cr.user2["hibernated"] == 0)
+        {
+                cr.energy_m += ExpParams.energy_move * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)];
         }
 }
@@ -320 +363 @@
 
         //adjustment in z axis
-        cr.moveAbs(cr.pos_x, cr.pos_y, 0.5);
-
-        //are there any nutrients in zone 1?
-        if (cr.boundingBoxCollisions() == 2)
-        {
-                if (cr.user2["hibernated"] == 1)
-                        cr.user2["hibernated"] = 0;
-                return; 
-        }
-
-        else if (cr.user2["hibernated"] == 1)
-        { 
-                moveEnergyDec(cr);
-                return;
-        }
-
-        //are there any nutrients in zone 2?
-        else
+        cr.moveAbs(cr.pos_x, cr.pos_y, 0);
+
+        //are there any nutrients in zone 1 or 2?
         {
                 var moved = stepToNearest(ExpParams.zone2_range); //TODO weighted sum of distance and energy
                 if (moved==1)
-                {
-                        moveEnergyDec(cr); 
+                { 
                         return;
                 }
@@ -348 +375 @@
 
         //no nutrients in zone 2
-
         var hibernation = 0;
         if (cr.user2["gen"] == 0) hibernation =  cr.user1["hibernation"];
@@ -355 +381 @@
         if (hibernation == 1)
         {
+                reverseHib(cr);
+                cr.localDrive = XYZ.new(0,0,0);
+        }
+        //random move
+        else if (cr.lifespan%dir_change == 0)
+        {
+                var dir = (Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), 0);//(0.1 * Math.rnd01, 0.1 * Math.rnd01, 0);        
+                dir.normalize();
+                dir.scale(-0.08);
+                cr.localDrive = dir;
                 moveEnergyDec(cr);
-                cr.user2["hibernated"] = 1;
-                cr.localDrive = XYZ.new(0,0,0);
-        }
-        //random move
+        }
+}
+
+function energyTransfer(cr1, cr2)
+{
+        cr1.localDrive = XYZ.new(0,0,0);
+        var e = cr2.getPart(0).ing * ExpParams.feedtrans; //TODO efficiency dependent on age
+        e = Math.min(cr2.energy, e) + 0.0000001;
+        //Simulator.print("transferring "+e+" to "+cr1.name+" from "+cr2.name+" ("+cr2.energy+")");
+        cr2.energy_m = cr2.energy_m + e;
+        cr1.energy_p = cr1.energy_p + e;
+        if (cr1.user2["hibernated"] == 1)
+        {
+                reverseHib(cr1);
+        }
+}
+
+function reverseHib(cr)
+{
+        if (cr.user2["hibernated"] == 1)
+        {
+                setForamMeta(cr, cr.user2["gen"]); //unhibernate
+        } 
         else
         {
-                cr.localDrive = (0.1 * Math.rnd01, 0.1 * Math.rnd01, 0);
-                moveEnergyDec(cr);
-        }
-}
-
-function onForamsCollision()
-{
-        if (Collision.Creature1.user2 != null)
-        {
-                Collision.Creature1.localDrive = XYZ.new(0,0,0);
-                var e = Collision.Part2.ing * ExpParams.feedtrans; //TODO efficiency dependent on age
-                //Simulator.print("transferring "+e+" to "+Collision.Creature1.name+" from "+Collision.Creature2.name+" ("+Collision.Creature2.energy+")");
-                Collision.Creature2.energy_m = Collision.Creature2.energy_m + e;
-                Collision.Creature1.energy_p = Collision.Creature1.energy_p + e;
-                Collision.Creature1.user2["hibernated"] = 0;
-        }
+                cr.idleen = ExpParams.energy_hib * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)]; //hibernate
+        }
+        cr.user2["hibernated"] = 1 - cr.user2["hibernated"];
 }
 
@@ -383 +425 @@
 {
         cr.getMechPart(0).orient.set(o);
+        if (ExpParams.showRet == 1)
+                cr.user3.moveAbs(cr.center_x-ExpParams.zone1_range, cr.center_y-ExpParams.zone1_range, cr.center_z-ExpParams.zone1_range-getProperty(cr.user2["gen"], "chamber_proculus"));
 
         if (deathConditions(cr) == 1)
@@ -392 +436 @@
         foramMove(cr);
 
+        var repro = foramReproduce(cr);
+        if (repro == 1)
+        {
+                return;
+        }
+
         cr.user2["max_energy_level"] = Math.max(cr.energy, cr.user2["max_energy_level"]);
-        if  (cr.numparts <= chambers[0].size)
-        {
-                if ((cr.user2["max_energy_level"] >= max_chamber_energ[cr.user2["gen"]][cr.numparts-1]))        
+        if  (lastChamberNum(cr) <= chambers[0].size-1)
+        {
+                if ((cr.user2["max_energy_level"] >= max_chamber_energ[cr.user2["gen"]][lastChamberNum(cr)]))   
                 {
-                        foramGrow(cr, cr.numparts); 
-                        return;
+                        foramGrow(cr, lastChamberNum(cr)); 
                 }       
-        }
-
-        foramReproduce(cr);     
+        }       
 }
 
@@ -415 +462 @@
 function onForamsDied(cr)
 {
+        if (ExpParams.showRet == 1)
+        {
+                Populations[2].delete(cr.user3);
+        }
         //fossilization
         var geno = GenePools[0].add(cr.genotype);
@@ -429 +480 @@
 function createNutrientGenotype(nutrientsize, zone1_range)
 {
-        return "//0\np:sh=3,sx="+nutrientsize+",sy="+(zone1_range + nutrientsize)+",sz="+(zone1_range+nutrientsize)+",ry=1.5,vr=0.0,1.0,0.0"; 
+        return "//0\np:sh=3,sx="+(nutrientsize+25)+",sy="+nutrientsize+",sz="+nutrientsize+",ry=1.5,vr=0.0,1.0,0.0"; 
 }
 
@@ -447 +498 @@
         cr.signals.add("nutrient");
 
-        cr.signals[0].value = cr.getMechPart(0);
+        cr.signals[0].value = cr;
 
         placeCreatureRandomly(cr, 0, 0);
@@ -503 +554 @@
                 }
         }
+        if (Simulator.stepNumber == 150000)
+                Simulator.stop();
 }
 
 function createStatistics()
 {       
-        var number_ploidy = [0, 0];
-        var number_species = [0, 0];
-        var e_inc = [0.0, 0.0];
+        var number = [[0, 0],[0,0]]; // [species][gen]
+        var e_inc = [[0, 0],[0,0]];
         var e_nut = 0.0;
 
@@ -516 +568 @@
                 var cr = Populations[0].get(i);
                 var gen = cr.user2["gen"];
-                number_ploidy[gen] = number_ploidy[gen] + 1;
                 var species = cr.user2["species"];
-                number_species[species] = number_species[species] + 1; 
-                e_inc[gen] = e_inc[gen] + cr.energy;
+
+                number[species][gen] = number[species][gen] + 1; 
+                e_inc[species][gen] = e_inc[species][gen] + cr.energy;
         }
 
@@ -528 +580 @@
         }
 
-        var log_numbers = [number_ploidy[0], number_ploidy[1], Populations[1].size];
-        var log_species = [number_species[0], number_species[1]];
-        var log_energy = [e_inc[0], e_inc[1], e_nut];
-
-        log(log_numbers, "log_sizes.txt");
-        log(log_species, "log_species.txt");
-        log(log_energy, "log_energy.txt");
+        var log_numbers = [number[0][0], number[0][1], number[1][0], number[1][1], Populations[1].size];
+        var log_energies = [e_inc[0][0], e_inc[0][1], e_inc[1][0], e_inc[1][1], e_nut];
+
+        log(log_numbers, "forams_log.txt");
+        log(log_energies, "energies_log.txt");
 }
 
 function log(tolog, fname)
 {
-        var f = File.appendDirect(fname, "forams data");
+        var f = File.appendDirect(fname, "forams data"); 
         f.writeString("" + Simulator.stepNumber);
         for (var  i = 0; i < tolog.size; i++)
@@ -554 +604 @@
 
 ~
+
+prop:
+id:showRet
+name:Show reticulopodia
+type:d 0 1 0
+group:Foraminifera
 
 prop:
@@ -734 +790 @@
 id:world_size
 name:World size
-type:d 10 1000 20
+type:d 10 10000 20
 group:World