Changeset 847 for experiments/frams/foraminifera/data/scripts/foraminifera.expdef

Timestamp:

01/31/19 03:43:35 (6 years ago)

Author:

Maciej Komosinski

Message:

Code formatting

File:

• experiments/frams/foraminifera/data/scripts/foraminifera.expdef (modified) (53 diffs)

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

@@ -60 +60 @@
         pop.othermask = 0;
         //pop.selfmask = 0x20002; pop.othermask = 0x10002;
-        pop.perfperiod = 25; 
+        pop.perfperiod = 25;
         pop.bodysim = 0;
 
@@ -86 +86 @@
         World.wrldwat = 200;
         World.wrldsiz = micronsToFrams(100000);
-        wrldsizSquareMeters = Math.pow(framsToMicrons(World.wrldsiz)*0.000001,2);
+        wrldsizSquareMeters = Math.pow(framsToMicrons(World.wrldsiz) * 0.000001, 2);
         World.wrldbnd = 1;
 
         //ExpProperties.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
 
-        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files   
+        //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files
         ExpProperties.logPref = "";
 
@@ -99 +99 @@
         ExpProperties.chamber_proculus_haplo = micronsToFrams(20);
         ExpProperties.chamber_proculus_diplo = micronsToFrams(10);
-        colors = ["1.0,1.0,0.3","1.0,0.7,0.0"]; //yellow and orange
+        colors = ["1.0,1.0,0.3", "1.0,0.7,0.0"]; //yellow and orange
         curColor = colors[0];
         curRadius = ExpProperties.zone1_range;
@@ -105 +105 @@
         //nutrients
         ExpProperties.nutrientradius = micronsToFrams(10);
-        ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
+        ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius, 1);
         nutrientSqrCm = 10;
-        ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
+        ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz) * 0.0001, 2) / nutrientSqrCm;
 
         ExpState.totaltestedcr = 0;
@@ -116 +116 @@
         //addSpecies({"min_repro_energies" : [4,6]});
         //addSpecies({"min_repro_energies" : [4,8]});
-        
+
         //Simulator.print(create_genotype(0.2, 30, "1.0,1.0,0.0", 0.6)); //sample call
         //Simulator.print(create_genotype(0.1, 40, "1.0,0.5,0.0", 0.1)); //sample call
@@ -135 +135 @@
         if (ExpProperties.max_chamber_num_haplo == max_chambers_def && ExpProperties.max_chamber_num_diplo == max_chambers_def)
         {
-                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]
-, [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]];
+                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]
+                                      , [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]];
         }
 
@@ -143 +143 @@
                 max_chamber_volume = [Vector.new(), Vector.new()];
                 var density = 100;
-                for (var ploid = 0; ploid < 2; ploid++) 
+                for (var ploid = 0; ploid < 2; ploid++)
                 {
                         var rad = getPloidRadius(ploid);
-                        for (var cham_num = 0; cham_num < getProperty(ploid,"max_chamber_num"); cham_num++)
+                        for (var cham_num = 0; cham_num < getProperty(ploid, "max_chamber_num"); cham_num++)
                         {
-                                max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num+1, density));
-                        }                                  
+                                max_chamber_volume[ploid].add(volumeFromGeno(ploid, rad, cham_num + 1, density));
+                        }
                 }
         }
@@ -162 +162 @@
                 for (var i = 0; i < ExpProperties.foramPop; i++)
                 {
-                        addInitialForam(spec, i);       
+                        addInitialForam(spec, i);
                 }
         }
@@ -239 +239 @@
 {
         var geno = create_genotype(rad, chamber_num, colors[morphotype], 1);
-        var m=Model.newFromString(geno);
-        var mg=ModelGeometry.forModel(m);
-        mg.geom_density=density; 
+        var m = Model.newFromString(geno);
+        var mg = ModelGeometry.forModel(m);
+        mg.geom_density = density;
         var volumeInFrams = mg.volume();
 
-        return volumeInFrams/Math.pow(ExpProperties.scalingFactor,3);
-}
-
-function secToSimSteps(value_in_sec){
-        return value_in_sec/ExpProperties.secPerStep;
+        return volumeInFrams / Math.pow(ExpProperties.scalingFactor, 3);
+}
+
+function secToSimSteps(value_in_sec)
+{
+        return value_in_sec / ExpProperties.secPerStep;
 }
 
 function volumeInMicrons(radiusInFrams)
 {
-        return 4.0/3.0*Math.pi*Math.pow(framsToMicrons(radiusInFrams),3);
+        return 4.0 / 3.0 * Math.pi * Math.pow(framsToMicrons(radiusInFrams), 3);
 }
 
@@ -260 +261 @@
         if (isRadiusInFrams == 1) //radius in frams
         {
-                return ExpProperties.picoCarbonPerMikro*volumeInMicrons(base);
+                return ExpProperties.picoCarbonPerMikro * volumeInMicrons(base);
         }
         else //volume in microns
@@ -270 +271 @@
 function getMovePerStep()
 {
-        return micronsToFrams((ExpProperties.foramSpeedMmPerMin/60)*1000)*ExpProperties.secPerStep;
+        return micronsToFrams((ExpProperties.foramSpeedMmPerMin / 60) * 1000) * ExpProperties.secPerStep;
 }
 
 function micronsToFrams(micrometers)
 {
-        return micrometers*ExpProperties.scalingFactor;
+        return micrometers * ExpProperties.scalingFactor;
 }
 
 function framsToMicrons(framsworldunits)
 {
-        return framsworldunits/ExpProperties.scalingFactor;
+        return framsworldunits / ExpProperties.scalingFactor;
 }
 
@@ -292 +293 @@
 function getGene(cr, gen_id, gen_set)
 {
-        if (cr.data->lifeparams->gen == 0) 
+        if (cr.data->lifeparams->gen == 0)
                 return cr.data->genes[gen_id];
-        else 
+        else
                 return cr.data->genes[gen_set][gen_id];
 }
@@ -301 +302 @@
 {
         var radius = ExpProperties.chamber_proculus_haplo;
-                if (ploid == 1)
-                {
-                        radius = ExpProperties.chamber_proculus_diplo;
-                }
+        if (ploid == 1)
+        {
+                radius = ExpProperties.chamber_proculus_diplo;
+        }
         return radius;
 }
@@ -313 +314 @@
         for (var i = 0; i < chamber_num; i++)
         {
-                if (energy < energyFromVolume(max_chamber_volume[ploid][i],0))
-                {
-                        chamber_num = i+1;
+                if (energy < energyFromVolume(max_chamber_volume[ploid][i], 0))
+                {
+                        chamber_num = i + 1;
                         break;
-                }       
-        }                                  
-        
+                }
+        }
+
         return chamber_num;
 }
@@ -326 +327 @@
 {
         var cr = Populations[pop_num].add(geno);
-        cr.rotate(0,0,Math.rndUni(rotate_min, rotate_max));
-        return cr;      
+        cr.rotate(0, 0, Math.rndUni(rotate_min, rotate_max));
+        return cr;
 }
 
@@ -337 +338 @@
         var geno = create_genotype(radius, chambernum, colors[ploid], 1);
         curColor = colors[ploid];
-        var cr = createAndRotate(geno, 0, 2*Math.pi, 0);
+        var cr = createAndRotate(geno, 0, 2 * Math.pi, 0);
         cr.name = "Initial creature" + species + "_" + iter;
         placeRandomlyNotColliding(cr);
@@ -355 +356 @@
         {
                 ploid = 1;
-        }       
+        }
         //add new foram with random energy bewtween starting energy and reproduction threshold
         var repro_thr = species_genes[species]->min_repro_energies[ploid];
-        var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid),1),repro_thr-0.25*repro_thr);
-        addForam(species, iter, start_energy,ploid);
+        var start_energy = Math.rndUni(energyFromVolume(getPloidRadius(ploid), 1), repro_thr - 0.25 * repro_thr);
+        addForam(species, iter, start_energy, ploid);
 }
 
@@ -365 +366 @@
 function addSpecies(new_genes)
 {
-        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});
+        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});
         for (var i = 0; i < new_genes.size; i++)
         {
                 var key = new_genes.getKey(i);
-                species_genes[species_genes.size-1][key] = new_genes[key];
-        } 
+                species_genes[species_genes.size - 1][key] = new_genes[key];
+        }
 }
 
@@ -378 +379 @@
 {
         //percent of current energy
-        cr.idleen = (ExpProperties.e_meta * cr.energy)*ExpProperties.secPerStep;
+        cr.idleen = (ExpProperties.e_meta * cr.energy) * ExpProperties.secPerStep;
 }
 
@@ -388 +389 @@
 function getZoneRange(cr, zone_num)
 {
-        return ExpProperties.["zone"+zone_num+"_range"];
+        return ExpProperties.["zone" + zone_num + "_range"];
 }
 
 function addReticulopodia(cr, radius)
 {
-                if (reticulopodiaExists(cr))
-                {
-                        Populations[2].delete(cr.data->reticulopodiacreature);
-                }
-                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");
-                cr.data->reticulopodiacreature = ret;
-                ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
-                ret.locationSetBboxLow(cr.bboxCenter.x-radius, cr.bboxCenter.y-radius, cr.bboxCenter.z-radius);
+        if (reticulopodiaExists(cr))
+        {
+                Populations[2].delete(cr.data->reticulopodiacreature);
+        }
+        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");
+        cr.data->reticulopodiacreature = ret;
+        ret.getMechPart(0).orient.set(cr.getMechPart(0).orient);
+        ret.locationSetBboxLow(cr.bboxCenter.x - radius, cr.bboxCenter.y - radius, cr.bboxCenter.z - radius);
 }
 
@@ -421 +422 @@
                 if (!cr.boundingBoxCollisions(0))
                 {
-                        cr.locationSetBboxLow(cr.bboxLow.x, cr.bboxLow.y, -cr.getPart(cr.numparts-1).sx); //place slightly under the bottom surface ("z" value depends on the size of the last=largest chamber)
+                        cr.locationSetBboxLow(cr.bboxLow.x, cr.bboxLow.y, -cr.getPart(cr.numparts - 1).sx); //place slightly under the bottom surface ("z" value depends on the size of the last=largest chamber)
                         return cr;
                 }
@@ -451 +452 @@
 function foramGrow(cr, chamber_num, lastchambergrowth)
 {
-        if ((chamber_num+1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
+        if ((chamber_num + 1) <= max_chamber_volume[cr.data->lifeparams->gen].size)
         {
                 curColor = colors[cr.data->lifeparams->gen];
                 var ploid = cr.data->lifeparams->gen;
-                var geno = create_genotype(getPloidRadius(ploid), chamber_num+1, colors[ploid], lastchambergrowth);
+                var geno = create_genotype(getPloidRadius(ploid), chamber_num + 1, colors[ploid], lastchambergrowth);
                 var cr2 = createAndRotate(geno, 0, 0, 0);
 
@@ -463 +464 @@
 
                 setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
-                cr2.locationSetBboxLow(cr.bboxLow.x, cr.bboxLow.y,cr.bboxLow.z);
+                cr2.locationSetBboxLow(cr.bboxLow.x, cr.bboxLow.y, cr.bboxLow.z);
                 setForamMeta(cr2);
 
@@ -479 +480 @@
 {
         var total_time = secToSimSteps(ExpProperties.chamberGrowthSec);
-        var ret_unit = total_time/chamber_vis_denominator;
-        var chamber_unit = total_time-ret_unit;
+        var ret_unit = total_time / chamber_vis_denominator;
+        var chamber_unit = total_time - ret_unit;
 
         if (chamber_time < ret_unit || chamber_time >= chamber_unit)
         {
-                var new_rad = Math.min(Math.max((chamber_time%ret_unit)/ret_unit*getZoneRange(cr,1),0.01),getZoneRange(cr,1));
+                var new_rad = Math.min(Math.max((chamber_time % ret_unit) / ret_unit * getZoneRange(cr, 1), 0.01), getZoneRange(cr, 1));
 
                 if(chamber_time < ret_unit)
                 {
-                        new_rad = getZoneRange(cr,1)-new_rad;
+                        new_rad = getZoneRange(cr, 1) - new_rad;
                 }
 
                 curColor = colors[cr.data->lifeparams->gen];
-                addReticulopodia(cr,new_rad);
+                addReticulopodia(cr, new_rad);
 
                 if (chamber_time == 0)//checking for end of chamber growth process
                 {
-                        cr.data->lifeparams->chamber_growth = -1;       
+                        cr.data->lifeparams->chamber_growth = -1;
                 }
         }
         else
         {
-                var new_rad = 1 - Math.min(Math.max((chamber_time-ret_unit)/chamber_unit,0.01),1);
+                var new_rad = 1 - Math.min(Math.max((chamber_time - ret_unit) / chamber_unit, 0.01), 1);
                 curRadius = cr.data->reticulopodiacreature.getPart(1).sy;
-                                
+
                 if (chamber_time == ret_unit)
                 {
@@ -509 +510 @@
                 }
 
-                var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen)-1, new_rad);
-                curRadius = getZoneRange(new_cr,1);
+                var new_cr = foramGrow(cr, chamberNumFromEnergy(cr.data->lifeparams->max_energy_level, cr.data->lifeparams->gen) - 1, new_rad);
+                curRadius = getZoneRange(new_cr, 1);
         }
 }
@@ -517 +518 @@
 {
         var p = XYZ.new(cr.bboxCenter.x, cr.bboxCenter.y, cr.bboxCenter.z);
-        var n = cr.signals.receiveSet("nutrient", getZoneRange(cr,2));
+        var n = cr.signals.receiveSet("nutrient", getZoneRange(cr, 2));
 
         //if signals are received find the source of the nearest
@@ -536 +537 @@
                         distvec.sub(p);
                         dist = distvec.length;
-                        if (dist < getZoneRange(cr,1))
+                        if (dist < getZoneRange(cr, 1))
                         {
                                 if (n[i].value != null)
@@ -562 +563 @@
                 return 1;
         }
-        
+
         else
         {
@@ -574 +575 @@
         {
                 //percent of maximal energy
-                cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level)*ExpProperties.secPerStep;
+                cr.energy -= (ExpProperties.energy_move * cr.data->lifeparams->max_energy_level) * ExpProperties.secPerStep;
         }
 }
@@ -580 +581 @@
 function fence(center, zone)
 {
-        return Math.min(Math.max(0+zone,center),World.wrldsiz-zone); //add and subtract zone from the world size to prevent reticulopodia from crossing the fence
+        return Math.min(Math.max(0 + zone, center), World.wrldsiz - zone); //add and subtract zone from the world size to prevent reticulopodia from crossing the fence
 }
 
@@ -588 +589 @@
         {
                 var moved = stepToNearest(cr); //TODO weighted sum of distance and energy
-                if (moved==1)
-                { 
+                if (moved == 1)
+                {
                         moveReticulopodia(cr);
                         return;
@@ -595 +596 @@
         }
 
-        //Prevents forams from crossing the world border. In the case of touching the border with the reticulopodia direction of the movement should be changed. 
+        //Prevents forams from crossing the world border. In the case of touching the border with the reticulopodia direction of the movement should be changed.
         var change_direction = 0;
         var new_x = fence(cr.bboxCenter.x, getZoneRange(cr, 1));
@@ -603 +604 @@
         {
                 change_direction = 1;
-                cr.locationSetBboxLow(new_x-cr.bboxSize.x/2, new_y-cr.bboxSize.y/2, -cr.getPart(cr.numparts-1).sx);//place slightly under the bottom surface ("z" value depends on the size of the last=largest chamber)
+                cr.locationSetBboxLow(new_x - cr.bboxSize.x / 2, new_y - cr.bboxSize.y / 2, -cr.getPart(cr.numparts - 1).sx); //place slightly under the bottom surface ("z" value depends on the size of the last=largest chamber)
         }
 
         //no nutrients in zone 2
-        if (getGene(cr, "hibernation",0) == 1)
+        if (getGene(cr, "hibernation", 0) == 1)
         {
                 reverseHib(cr);
-                cr.drive = XYZ.new(0,0,0);
+                cr.drive = XYZ.new(0, 0, 0);
         }
         //random move
@@ -631 +632 @@
         if (visualization(cr))
         {
-                cr.data->reticulopodiacreature.locationSetBboxLow(cr.bboxCenter.x-getZoneRange(cr,1), cr.bboxCenter.y-getZoneRange(cr,1), cr.bboxCenter.z-getZoneRange(cr,1));
+                cr.data->reticulopodiacreature.locationSetBboxLow(cr.bboxCenter.x - getZoneRange(cr, 1), cr.bboxCenter.y - getZoneRange(cr, 1), cr.bboxCenter.z - getZoneRange(cr, 1));
                 cr.data->reticulopodiacreature.drive = cr.drive;
         }
@@ -638 +639 @@
 function randomDir()
 {
-        var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0);  
+        var dir = (Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), Math.rndUni(-ExpProperties.zone2_range, ExpProperties.zone2_range), 0);
         dir.normalize();
-        dir.scale(-1*movePerStep);
+        dir.scale(-1 * movePerStep);
         return dir;
 }
@@ -646 +647 @@
 function energyTransfer(cr1, cr2)
 {
-        cr1.drive = XYZ.new(0,0,0);
-        var e =  ExpProperties.feedtrans*cr1.energy*ExpProperties.secPerStep; //TODO efficiency dependent on age
+        cr1.drive = XYZ.new(0, 0, 0);
+        var e =  ExpProperties.feedtrans * cr1.energy * ExpProperties.secPerStep; //TODO efficiency dependent on age
         //Simulator.print("transferring "+e +"("+e*ExpProperties.ingestion+")"+" to "+cr1.name +" ("+ cr1.energy+") " +" from "+cr2.uid+" ("+cr2.energy+") "+ e/ExpProperties.secPerStep+ " per sec");
         var transferred = cr2.transferEnergyTo(cr1, e);
-        cr1.energy -= transferred*(1-ExpProperties.ingestion);
+        cr1.energy -= transferred * (1 - ExpProperties.ingestion);
         if (cr1.data->lifeparams->hibernated == 1)
         {
@@ -662 +663 @@
         {
                 setForamMeta(cr); //unhibernate
-        } 
+        }
         else
         {
-                cr.idleen = (ExpProperties.energy_hib * cr.energy)*ExpProperties.secPerStep; //hibernate
+                cr.idleen = (ExpProperties.energy_hib * cr.energy) * ExpProperties.secPerStep; //hibernate
         }
         cr.data->lifeparams->hibernated = 1 - cr.data->lifeparams->hibernated;
@@ -675 +676 @@
         if (cr.data->lifeparams->division_time > 0)
         {
-                cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time-1,0);
+                cr.data->lifeparams->division_time = Math.max(cr.data->lifeparams->division_time - 1, 0);
         }
         //checking for end of gametogenesis
@@ -685 +686 @@
         else if (cr.data->lifeparams->chamber_growth > 0)
         {
-                var chamber_time = Math.max(cr.data->lifeparams->chamber_growth-1,0);
+                var chamber_time = Math.max(cr.data->lifeparams->chamber_growth - 1, 0);
                 cr.data->lifeparams->chamber_growth = chamber_time;
                 cr.energy -= ExpProperties.chamberCostPerSec * cr.energy * ExpProperties.secPerStep;
@@ -695 +696 @@
         }
         //checking for end of the chamber growth process
-        else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr)==0)
-        {       
-                foramGrow(cr, lastChamberNum(cr), 1); 
+        else if (cr.data->lifeparams->chamber_growth == 0 && visualization(cr) == 0)
+        {
+                foramGrow(cr, lastChamberNum(cr), 1);
                 cr.data->lifeparams->chamber_growth = -1;
                 //Simulator.print("chamber "+ (lastChamberNum(cr) + 1) +" complete");
@@ -713 +714 @@
                         if (ExpProperties.logging == 1)
                         {
-                                log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
-                                log(createLogVector(cr, cr.lifespan),ExpProperties.logPref+"lifespan_log.txt");
-                        }                       
+                                log(createLogVector(cr, cr.data->lifeparams->max_energy_level), ExpProperties.logPref + "fossil_log.txt");
+                                log(createLogVector(cr, cr.lifespan), ExpProperties.logPref + "lifespan_log.txt");
+                        }
                         Populations[0].kill(cr);
                         return;
@@ -736 +737 @@
                 if  (lastChamberNum(cr) < max_chamber_volume[cr.data->lifeparams->gen].size)
                 {
-                        if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)-1],0)))  
+                        if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr) - 1], 0)))
                         {
                                 cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
-                        }       
-                }
-        }       
+                        }
+                }
+        }
 }
 
 function deathConditions(cr)
 {
-        if ((cr.energy <= getProperty(cr.data->lifeparams->gen,"e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
+        if ((cr.energy <= getProperty(cr.data->lifeparams->gen, "e_death_level")*cr.data->lifeparams->max_energy_level) || (Math.rnd01 < ExpProperties.hunted_prob))
         {
                 return 1;
@@ -774 +775 @@
 function createNutrientGenotype(nutrientradius)
 {
-        return "//0\nm:Vstyle=nutrient\np:sh=3,sx="+nutrientradius+",sy="+nutrientradius+",sz="+nutrientradius+",ry=1.57,vr=0.0,1.0,0.0";
+        return "//0\nm:Vstyle=nutrient\np:sh=3,sx=" + nutrientradius + ",sy=" + nutrientradius + ",sz=" + nutrientradius + ",ry=1.57,vr=0.0,1.0,0.0";
 }
 
@@ -797 +798 @@
         if (ExpProperties.visualize == 1)
         {
-                var nutsize = ExpProperties.nutrientradius*10;
-                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");
+                var nutsize = ExpProperties.nutrientradius * 10;
+                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");
                 cr.data->reticulopodiacreature = nut;
-                nut.locationSetBboxLow( cr.bboxLow.x+cr.bboxSize.x/2-nut.bboxSize.x/2,  cr.bboxLow.y+cr.bboxSize.y/2-nut.bboxSize.y/2, -nutsize); 
+                nut.locationSetBboxLow( cr.bboxLow.x + cr.bboxSize.x / 2 - nut.bboxSize.x / 2,  cr.bboxLow.y + cr.bboxSize.y / 2 - nut.bboxSize.y / 2, -nutsize);
         }
 }
@@ -815 +816 @@
 {
         counter += increase;
-        var unitcount = int(counter/unitsize);
-        counter -= unitcount*unitsize;
+        var unitcount = int(counter / unitsize);
+        counter -= unitcount * unitsize;
         return {"counter" : counter, "number" : unitcount};
 }
@@ -824 +825 @@
         if (ExpProperties.foodfluxChange > 0)
         {
-                        changePeriod += 1;
-                        if (phase=="low" && changePeriod >= secToSimSteps(23328000)) //9 months
-                        {
-                                ExpProperties.foodflux = ExpProperties.foodflux/ExpProperties.foodfluxChange;
-                                phase = "high";
-                                changePeriod = 0;
-                        }
-                
-                        else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
-                        {
-                                ExpProperties.foodflux = ExpProperties.foodflux*ExpProperties.foodfluxChange;
-                                phase = "low";
-                                changePeriod = 0;
-                        }
-        }
-
-        var nutrientNum = getNumberCounter(nutrient_num_counter, ExpProperties.foodflux*wrldsizSquareMeters*ExpProperties.secPerStep,ExpProperties.energy_nut*0.000000000001); 
+                changePeriod += 1;
+                if (phase == "low" && changePeriod >= secToSimSteps(23328000)) //9 months
+                {
+                        ExpProperties.foodflux = ExpProperties.foodflux / ExpProperties.foodfluxChange;
+                        phase = "high";
+                        changePeriod = 0;
+                }
+
+                else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
+                {
+                        ExpProperties.foodflux = ExpProperties.foodflux * ExpProperties.foodfluxChange;
+                        phase = "low";
+                        changePeriod = 0;
+                }
+        }
+
+        var nutrientNum = getNumberCounter(nutrient_num_counter, ExpProperties.foodflux * wrldsizSquareMeters * ExpProperties.secPerStep, ExpProperties.energy_nut * 0.000000000001);
 
         nutrient_num_counter = nutrientNum["counter"];
 
         for (var i = 0; i < nutrientNum["number"]; i++)
-        {    
+        {
                 addNutrient();
         }
@@ -851 +852 @@
         if (ExpProperties.logging == 1 && nutrientNum["number"] > 0)
         {
-                log([nutrientNum["number"]],ExpProperties.logPref+"nutrients_log.txt");
+                log([nutrientNum["number"]], ExpProperties.logPref + "nutrients_log.txt");
         }
 
@@ -878 +879 @@
                         reproduce_parents(s);
                 }
-                
+
         }
 
@@ -903 +904 @@
 
 function createStatistics()
-{       
+{
         var number = [];
         var e_inc = [];
@@ -910 +911 @@
         for (var s = 0; s < species_genes.size; s++)
         {
-                number.add([0,0]);// [haplo][diplo]
-                e_inc.add([0,0]);
+                number.add([0, 0]); // [haplo][diplo]
+                e_inc.add([0, 0]);
         }
 
@@ -920 +921 @@
                 var species = cr.data->lifeparams->species;
 
-                number[species][gen] = number[species][gen] + 1; 
+                number[species][gen] = number[species][gen] + 1;
                 e_inc[species][gen] = e_inc[species][gen] + cr.energy;
         }
@@ -941 +942 @@
                 }
         }
-        
+
         log_numbers.add(Populations[1].size);
         log_energies.add(e_nut);
 
-        log(log_numbers, ExpProperties.logPref+"forams_log.txt");
-    log(log_energies,  ExpProperties.logPref+"energies_log.txt");
+        log(log_numbers, ExpProperties.logPref + "forams_log.txt");
+        log(log_energies,  ExpProperties.logPref + "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++)
@@ -972 +973 @@
                 if (cr.data->lifeparams->species == i)
                 {
-                        vec[i*2+cr.data->lifeparams->gen] = value;              
+                        vec[i * 2 + cr.data->lifeparams->gen] = value;
                 }
         }