Changeset 493 for experiments

Timestamp:

04/10/16 17:48:18 (9 years ago)

Author:

oriona

Message:

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

Location:

experiments/frams/foraminifera/data/scripts

Files:

• foraminifera.expdef (modified) (27 diffs)
• foraminifera.inc (modified) (5 diffs)
• foraminifera.show (modified) (3 diffs)

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

@@ -25 +25 @@
 global chambers;
 global colors;
-global dir_change;
+global retColors;
+global curColor;
+global dir_change_sec;
 global max_chamber_volume;
 global movePerStep;
@@ -33 +35 @@
 global changePeriod;
 global phase;
+global nutrientSqrCm;
 global species_genes; 
 
@@ -80 +83 @@
         //world
         SignalView.mode = 1;
-        World.wrldwat = 200;
-        World.wrldsiz = micronsToFrams(40000);
+        World.wrldwat = 500;
+        World.wrldsiz = micronsToFrams(100000);
         World.wrldbnd = 1;
         ExpProperties.stress = 1;
@@ -95 +98 @@
 
         //ExpProperties.logging = 1; //uncomment to enable logging simulation parameters to log files   
+        ExpProperties.logPref = "";
 
         //reproduction
@@ -101 +105 @@
         ExpProperties.mutationprob = 0;
         ExpProperties.repro_time = 720;
-        ExpProperties.gametoPeriod = 43200;
+        ExpProperties.gametoPeriod = 21600;
         ExpProperties.divisionCost = 15.6;
         reprocounter = 0;
@@ -109 +113 @@
         init_chambers();
 
+        curColor = retColors[0];
         //morphology
-        dir_change = 30000;
+        dir_change_sec = 30000;
         ExpProperties.zone1_range = micronsToFrams(1000);
         ExpProperties.zone2_range = micronsToFrams(3000);
@@ -137 +142 @@
         ExpProperties.energy_move = 0.0000005;
 
-        ExpProperties.energies0_haplo = energyFromVolume(micronsToFrams(20),1);
-        ExpProperties.energies0_diplo = energyFromVolume(micronsToFrams(1.25),1);
+        ExpProperties.energies0_haplo = 20;
+        ExpProperties.energies0_diplo = 1.25;
         ExpProperties.feedtrans = 0.001;
         ExpProperties.e_repro_cost_haplo = 0.3; 
@@ -149 +154 @@
         changePeriod = 0;
         phase = "low";
-        ExpProperties.foodperiod = 3600;
-        ExpProperties.foodPeriodChange = 0;
+        nutrientSqrCm = 10;
+        ExpProperties.foodperiod = 25920;
+        ExpProperties.foodPeriodChange = 6;
         ExpProperties.nutrientradius = micronsToFrams(10);
         ExpProperties.energy_nut = energyFromVolume(ExpProperties.nutrientradius,1);
-        ExpProperties.feedrate = 1;
+        ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
         ExpProperties.ingestion = 0.25;
         nutrientenergywaiting = 0;
@@ -159 +165 @@
         ExpState.nutrient = "";
         
-        addSpecies({"min_repro_energies" : [4,6]});
-        addSpecies({"min_repro_energies" : [4,8]});
+        //addSpecies({"min_repro_energies" : [4,6]});
+        //addSpecies({"min_repro_energies" : [4,8]});
 }
 
@@ -189 +195 @@
 function micronsToFrams(micrometers)
 {
-        return micrometers*0.025;
+        return micrometers*0.01;
 }
 
 function framsToMicrons(framsworldunits)
 {
-        return framsworldunits/0.025;
+        return framsworldunits/0.01;
 }
 
@@ -215 +221 @@
 {
         var geno = createForamMorphology(species_genes[species]->morphotype, ploid, chambernum);
+        curColor = retColors[ploid];
         var cr = Populations[0].add(geno);
         cr.name = "Initial creature" + species + "_" + iter;
@@ -235 +242 @@
                 ploid = 1;
         }       
-        //add new foram with random energy bewtween starting energy and reproduction treshold
+        //add new foram with random energy bewtween starting energy and reproduction threshold
         addForam(species, iter, int(Math.rndUni(0,species_genes[species]->min_repro_energies[ploid])),ploid);
 }
@@ -242 +249 @@
 function addSpecies(new_genes)
 {
-        species_genes.add({"min_repro_energies" : [4,6], "energies0" : [20, 1.25], "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++)
         {
@@ -358 +365 @@
         if (ExpProperties.visualize == 1)
         {
-                var ret = Populations[2].add("//0\np:sh=3,sx=0.01,sy="+getZoneRange(cr,1)+",sz="+getZoneRange(cr,1)+",ry=1.57,vr=1.0,1.0,1.0");
+                var ret = Populations[2].add("//0\np:sh=3,sx=0.01,sy="+getZoneRange(cr,1)+",sz="+getZoneRange(cr,1)+",ry=1.57,vr="+curColor);
                 cr.data->reticulopodiacreature = ret;
         }
@@ -395 +402 @@
         if ((chamber_num+1) < chambers[cr.data->lifeparams->species].size)
         {
+                curColor = retColors[cr.data->lifeparams->gen];
                 var geno = createForamMorphology(getGene(cr, "morphotype", 0), cr.data->lifeparams->gen, chamber_num+1);
                 var cr2 = Populations[0].add(geno);
@@ -476 +484 @@
 }
 
-function fence(pos)
-{
-        return Math.min(Math.max(0,pos),World.wrldsiz);
+function fence(pos, zone)
+{
+        return Math.min(Math.max(0+zone,pos),World.wrldsiz-zone);
 }
 
@@ -486 +494 @@
 
         //adjustment in z axis
-        cr.moveAbs(fence(cr.pos_x), fence(cr.pos_y), 0);
+        cr.moveAbs(fence(cr.pos_x, getZoneRange(cr, 1)), fence(cr.pos_y,getZoneRange(cr, 1)), 0);
 
         //are there any nutrients in zone 1 or 2?
@@ -504 +512 @@
         }
         //random move
-        else if (Simulator.stepNumber%int(dir_change/ExpProperties.secPerStep) == 0)
+        else if (Simulator.stepNumber%int(dir_change_sec/ExpProperties.secPerStep) == 0)
         {
                 cr.data->lifeparams->dir = randomDir();
@@ -552 +560 @@
 }
 
+function createLogVector(cr, value)
+{
+        var vec = Vector.new();
+        for (var i = 0; i < species_genes.size; i++)
+        {
+                for (var j = 0; j < 2; j++)
+                {
+                        vec.add(0);
+                }
+                if (cr.data->lifeparams->species == i)
+                {
+                        vec[i*2+cr.data->lifeparams->gen] = value;              
+                }
+        }
+        return vec;
+}
 
 function onForamsStep(cr)
@@ -592 +616 @@
                 if (visualization(cr))
                 {
-                        cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1)-getProperty(cr.data->lifeparams->gen, "chamber_proculus"));
+                        cr.data->reticulopodiacreature.moveAbs(cr.center_x-getZoneRange(cr,1), cr.center_y-getZoneRange(cr,1), cr.center_z-getZoneRange(cr,1));
                 }
 
                 if (deathConditions(cr) == 1)
                 {
+                        if (ExpProperties.logging == 1)
+                        {
+                                log(createLogVector(cr, cr.data->lifeparams->max_energy_level),ExpProperties.logPref+"fossil_log.txt");
+                        }                       
                         Populations[0].kill(cr);
                         return;
@@ -712 +740 @@
         if (nutrientenergywaiting*ExpProperties.secPerStep >= ExpProperties.foodperiod)
         {
-                for (var i = 0; i < ExpProperties.feedrate; i++)
+                for (var i = 0; i < ExpProperties.nutrient_pop; i++)
                 {    
                         addNutrient();
@@ -719 +747 @@
                 nutrientenergywaiting = 0.0;
                 Simulator.checkpoint();
-        }
+
+                if (ExpProperties.logging == 1)
+                {
+                        log([ExpProperties.nutrient_pop],ExpProperties.logPref+"nutrients_log.txt");
+                }
+        }
+
 }
 
@@ -808 +842 @@
         log_energies.add(e_nut);
 
-        log(log_numbers, "forams_log.txt");
-    log(log_energies,  "energies_log.txt");
+        log(log_numbers, ExpProperties.logPref+"forams_log.txt");
+    log(log_energies,  ExpProperties.logPref+"energies_log.txt");
 }
 
@@ -841 +875 @@
 name:Stop after the given number of simulation steps
 type:d 0 1000000 0
+
+property:
+id:logPref
+name:Log prefix
+type:s
 
 property:
@@ -1044 +1083 @@
 
 property:
-id:feedrate
+id:nutrient_pop
 name:Feeding rate
 type:f 0 1000000
@@ -1065 +1104 @@
 id:energy_nut
 name:Nutrient energy
-type:f 0 100000
+type:f 0 10000000
 group:Energy
 
@@ -1083 +1122 @@
 id:nutrientradius
 name:Nutrient size
-type:f 0.1 0.9 0.1
+type:f 0.001 0.9 0.1
 group:Energy
 

experiments/frams/foraminifera/data/scripts/foraminifera.inc

@@ -5 +5 @@
 {
         colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
+        retColors = ["1.0,1.0,1.0", "1.0,0.0,0.0"];
         chambers = [ ["0.0,0.0,0.0,",  //coiled
         "1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
@@ -108 +109 @@
                 new_genes = [parent.data->genes, parent2.data->genes];
                 gen = 1 - parent.data->lifeparams->gen;
+
+                if (ExpProperties.logging == 1)
+                {
+                                log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
+                                log(createLogVector(parent2, parent2.energy),ExpProperties.logPref+"repro_energies_log.txt");
+                                log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
+                }       
         }
 
@@ -122 +130 @@
         var energy0 =getEnergy0( getGene(parent,"energies0", 0)[0]); 
         var number = ((1 - (getProperty(parent.data->lifeparams->gen, "e_repro_cost"))) * parent.energy) / energy0;
+
+                if (ExpProperties.logging == 1)
+                {
+                        log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
+                        log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
+                }       
 
         Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
@@ -189 +203 @@
                                                 print_repro_info(parent1);
                                                 print_repro_info(parent2);
-                                                //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " reproduced: "+Simulator.stepNumber);
                                                 pop.kill(parent1);
                                                 pop.kill(parent2);
                                                 parent1 = null;
                                                 parent2 = null;
-                                                
                                         }
                                 }       
@@ -280 +292 @@
 function createOffspring(geno, energy, parent_genes, parent_lifeparams)
 {
+        curColor = retColors[1-parent_lifeparams->gen];
         var cr = Populations[0].add(geno);
         cr.energy0 = energy;

experiments/frams/foraminifera/data/scripts/foraminifera.show

@@ -23 +23 @@
         GLDisplay.minfps = 10;
         TrackingCam.cam_h = 15; //more side view
-        Params = { "feedrate" : [200,100,50], "feedtrans" : [0.05,0.125,0.25],"energy_nut" :[0.5,1.5,3.0], "stress" : [0,1], "visualize" : [0,1]};
+        Params = { "foodperiod" : [43200,25920,10800], "feedtrans" : [0.001,0.001,0.001],"energy_nut" :[144.54,544.54,944.54], "stress" : [0,1], "visualize" : [0,1]};
         ShowProperties.visualize=1;
 }
@@ -57 +57 @@
 }
 
-function ShowProperties_feedrate_set()
+function ShowProperties_foodperiod_set()
 {
-        setShowParam("feedrate");
+        setShowParam("foodperiod");
 }
 
@@ -85 +85 @@
 
 property:
-id:feedrate
-name:Feeding rate
+id:foodperiod
+name:Feeding period
 type:d 0 2 1 ~Low~Medium~High