Changeset 554

Timestamp:

07/31/16 23:26:43 (8 years ago)

Author:

oriona

Message:

Refactoring, change of foraminifera direction at world boundary added.

Location:

experiments/frams/foraminifera/data/scripts

Files:

• foraminifera.expdef (modified) (27 diffs)
• foraminifera.inc (modified) (6 diffs)

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

@@ -85 +85 @@
         World.wrldsiz = micronsToFrams(100000);
         World.wrldbnd = 1;
-        ExpProperties.stress = 1;
-        ExpProperties.creath = -0.99; //just above the bottom
-        ExpProperties.autorestart = 0;
-
-        //time
-        ExpProperties.secPerStep = 300;
-        ExpProperties.foramSpeedMmPerMin = 0.05;
+
         movePerStep = getMovePerStep();
 
@@ -99 +93 @@
         ExpProperties.logPref = "";
 
-        //reproduction
-        ExpProperties.foramPop = 20;    
-        ExpProperties.crossprob = 0;
-        ExpProperties.mutationprob = 0;
-        ExpProperties.repro_time = 720;
-        ExpProperties.gametoPeriod = 21600;
-        ExpProperties.divisionCost = 20;
-        reprocounter = 0;
-
         species_genes = [];
 
+        //morphology
         init_chambers();
-
         curColor = retColors[0];
-        //morphology
-        ExpProperties.dir_change_sec = 30000;
         ExpProperties.zone1_range = micronsToFrams(1000);
         ExpProperties.zone2_range = micronsToFrams(3000);
-        ExpProperties.chamber_growth_time = 720;
-        ExpProperties.chamberCostPerSec = 0.000001;
         ExpProperties.chamber_proculus_haplo = micronsToFrams(50);
         ExpProperties.chamber_difference_haplo = 0.0;
@@ -133 +114 @@
         }
 
-        //energetics
-        ExpProperties.min_repro_energ_haplo = 4;
-        ExpProperties.min_repro_energ_diplo = 6;
-
-        ExpProperties.e_meta = 0.0000005; 
-        ExpProperties.energy_hib = 0.0000001;
-        ExpProperties.energy_move = 0.0000005;
-
-        ExpProperties.energies0_haplo = 20;
-        ExpProperties.energies0_diplo = 1.25;
-        ExpProperties.feedtrans = 0.001;
-        ExpProperties.e_repro_cost_haplo = 0.3; 
-        ExpProperties.e_repro_cost_diplo = 0.2;
-
-        ExpProperties.e_death_level_haplo = 0.5;
-        ExpProperties.e_death_level_diplo = 0.5;
-
         //nutrients
-        changePeriod = 0;
-        phase = "low";
-        nutrientSqrCm = 10;
-        ExpProperties.foodperiod = 14400;
-        ExpProperties.foodPeriodChange = 0;
         ExpProperties.nutrientradius = micronsToFrams(10);
         ExpProperties.energy_nut = 200 * energyFromVolume(ExpProperties.nutrientradius,1);
+        nutrientSqrCm = 10;
         ExpProperties.nutrient_pop = Math.pow(framsToMicrons(World.wrldsiz)*0.0001,2)/nutrientSqrCm;
-        ExpProperties.ingestion = 0.25;
-        nutrientenergywaiting = 0;
+
         ExpState.totaltestedcr = 0;
         ExpState.nutrient = "";
@@ -169 +128 @@
 
 @include "standard_placement.inc"
+
+function secToSimSteps(value_in_sec){
+        return value_in_sec/ExpProperties.secPerStep;
+}
 
 function volumeInMicrons(radiusInFrams)
@@ -226 +189 @@
         cr.energy0 = energyFromVolume(max_chamber_volume[ploid][chambernum],0);
         cr.energy = cr.energy0;
-        setGenotype({"opt" : 0, "cr" : cr, "species" : species, "energy0" : cr.energy0, "genes" : species_genes[species]});
+        setGenotype({"opt" : "birth", "cr" : cr, "gen" : ploid, "species" : species, "energy0" : cr.energy0, "genes" : species_genes[species]});
         if (ploid == 1)
         {
-                cr.data->lifeparams->gen = 1;
                 cr.data->genes = [cr.data->genes, cr.data->genes]; //TODO two different genes sets
         }
@@ -277 +239 @@
         o = Populations[0][0].getMechPart(0).orient.clone();
         ExpState.totaltestedcr = 0;
+
+        reprocounter = 0;
+        nutrientenergywaiting = 0;
+        changePeriod = 0;
+        phase = "low";
 }
 
@@ -411 +378 @@
                 cr2.energy = cr2.energy0;
 
-                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : 2, "energy0" : cr.energy0});
+                setGenotype({"cr" : cr2, "parent_genes" : cr.data->genes, "parent_lifeparams" : cr.data->lifeparams, "opt" : "growth", "energy0" : cr.energy0});
                 cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
                 setForamMeta(cr2);
@@ -496 +463 @@
 
         //adjustment in z axis
-        cr.moveAbs(fence(cr.pos_x, getZoneRange(cr, 1)), fence(cr.pos_y,getZoneRange(cr, 1)), 0);
+        var change_direction = 0;
+        var new_x = fence(cr.pos_x, getZoneRange(cr, 1));
+        var new_y = fence(cr.pos_y,getZoneRange(cr, 1));
+
+        if ((new_x != cr.pos_x) || (new_y != cr.pos_y) || (cr.data->lifeparams->dir_counter >= int(secToSimSteps(ExpProperties.dir_change_sec))))
+        {
+                change_direction = 1;
+        }
+
+        cr.moveAbs(new_x, new_y, 0);
 
         //are there any nutrients in zone 1 or 2?
@@ -515 +491 @@
         }
         //random move
-        else if (cr.data->lifeparams->dir_counter >= int(ExpProperties.dir_change_sec/ExpProperties.secPerStep))
+        else if (change_direction == 1)
         {
                 cr.data->lifeparams->dir = randomDir();
@@ -656 +632 @@
                         if ((cr.data->lifeparams->max_energy_level >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][lastChamberNum(cr)],0)))    
                         {
-                                cr.data->lifeparams->chamber_growth = int(ExpProperties.chamber_growth_time/ExpProperties.secPerStep);
+                                cr.data->lifeparams->chamber_growth = int(secToSimSteps(ExpProperties.chamberGrowthSec));
                         }       
                 }
@@ -716 +692 @@
         {
                 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 nut = Populations[2].add("//0\np:sh=2,sx="+nutsize+",sy="+nutsize+",sz="+nutsize+",ry=1.5,vr=0.0,1.0,0.0");
                 cr.data->reticulopodiacreature = nut;
                 nut.moveAbs(cr.pos_x-1.5*nutsize, cr.pos_y-1.5*nutsize, 0.5);
@@ -735 +711 @@
         {
                         changePeriod += 1;
-                        if (phase=="low" && (changePeriod*ExpProperties.secPerStep) >= 23328000) //9 months
+                        if (phase=="low" && changePeriod >= secToSimSteps(23328000)) //9 months
                         {
                                 ExpProperties.foodperiod = ExpProperties.foodperiod/ExpProperties.foodPeriodChange;
@@ -742 +718 @@
                         }
                 
-                        else if (phase == "high" && (changePeriod*ExpProperties.secPerStep) >= 7776000) //3 months
+                        else if (phase == "high" && changePeriod >= secToSimSteps(7776000)) //3 months
                         {
                                 ExpProperties.foodperiod = ExpProperties.foodperiod*ExpProperties.foodPeriodChange;
@@ -750 +726 @@
         }
         nutrientenergywaiting = nutrientenergywaiting + 1;
-        if (nutrientenergywaiting*ExpProperties.secPerStep >= ExpProperties.foodperiod)
+        if (nutrientenergywaiting >= secToSimSteps(ExpProperties.foodperiod))
         {
                 for (var i = 0; i < ExpProperties.nutrient_pop; i++)
@@ -783 +759 @@
         //reproduction --------------------------------------------
         reprocounter += 1;
-        if (reprocounter*ExpProperties.secPerStep > ExpProperties.repro_time)
+        if (reprocounter > secToSimSteps(ExpProperties.reproTimeSec))
         {
                 reprocounter = 0;
@@ -881 +857 @@
 name:Show reticulopodia and nutrients
 type:d 0 1 0
-group:Foraminifera
+group:
 
 property:
 id:maxSteps
-name:Stop after the given number of simulation steps
+name:Maximum number of steps
 type:d 0 10000000 0
+group:
+
+property:
+id:logging
+name:Log statistics to file
+type:d 0 1 0
+group:
 
 property:
@@ -894 +877 @@
 
 property:
-id:foramSpeedMmPerMin
-name:Speed of foraminfera in mm/min
-type:f 0.1
-flags: 16
-group:Foraminifera
-
-property:
-id:gametSuccessRate
-name:Ratio of successful gamets
-type:f 0.001
-group:Foraminifera
-
-property:
-id:dir_change_sec
-name:Number of seconds before direction change
-type:d 30000
-group:Foraminifera
-
-property:
-id:gametoPeriod
-name:Time of gametogenesis
-type:f 720
-group:Foraminifera
-
-property:
-id:picoCarbonPerMikro
-name:Picograms of carbon in cubed micrometer
-type:f 0.13
-group:Foraminifera
-
-property:
 id:secPerStep
 name:Seconds per simulation step
 help:Number of seconds of foraminifera time per simulation step
-type:f 60.0
+type:f 1 480 300
+flags: 16
+group:
+
+property:
+id:foramSpeedMmPerMin
+name:Speed of foraminfera in mm/min
+type:f 0.01 0.1 0.05
 flags: 16
 group:Foraminifera
 
 property:
-id:e_repro_cost_haplo
-name:Cost of reproduction
-type:f 0.1 0.9 0.5
+id:dir_change_sec
+name:Number of seconds before direction change
+type:d 300 300000 6000
 group:Foraminifera
+
+property:
+id:foramPop
+name:Initial forams population size
+type:d 1 1000 20
+group:Foraminifera
+
+property:
+id:gametoPeriodSec
+name:Time of gametogenesis
+type:f 300 300000 21600
+group:Reproduction
+
+property:
+id:gametSuccessRate
+name:Ratio of successful gamets
+type:f 0.0001 0.01 0.001
+group:Reproduction
 
 property:
 id:divisionCost
 name:Cost of division in pG
-type:f
-group:Foraminifera
-
-property:
-id:e_repro_cost_diplo
-name:Cost of reproduction
-type:f 0.1 0.9 0.3
-group:Foraminifera
-
-property:
-id:chamber_growth_time
+type:f 15 25 20
+group:Reproduction
+
+property:
+id:min_repro_energ_haplo
+name:Min reproduction energy of haploid
+type:f 0 -1 4
+group:Energy
+
+property:
+id:min_repro_energ_diplo
+name:Min reproduction energy of diploid
+type:f 0 -1 6
+group:Energy
+
+property:
+id:repro_prob
+name:Probability of reproduction
+type:f 0 1 0.8
+group:Reproduction
+
+property:
+id:energies0_haplo
+name:Energy of offspring from diploid forams
+type:f 0 -1 20
+group:Energy
+
+property:
+id:energies0_diplo
+name:Energy of offspring from diploid forams
+type:f 0 -1 1.25
+group:Energy
+
+property:
+id:crossprob
+name:Crossover probability
+type:f 0 1 0
+group:Reproduction
+
+property:
+id:mutationprob
+name:Mutation probability
+type:f 0 1 0
+group:Reproduction
+
+property:
+id:reproTimeSec
+name:Time before reproduction
+type:d 0 10000 720
+group:Reproduction
+
+property:
+id:chamberGrowthSec
 name:Time of the chamber growth in seconds
-type:f
-group:Foraminifera
-
-property:
-id:chamberCostPerSec
-name:Cost of growning chamber per second
-type:f
+type:f 360 1440 720
 group:Foraminifera
 
@@ -977 +990 @@
 id:chamber_difference_haplo
 name:Difference in size between subsequent chambers
-type:f
+type:f 0 -1 0
 group:Foraminifera
 
@@ -983 +996 @@
 id:chamber_difference_diplo
 name:Difference in size between subsequent chambers
-type:f
+type:f 0 -1 0.08
 group:Foraminifera
 
@@ -990 +1003 @@
 name:Probability of being hunted
 type:f 0 1 0
-group:Forminifera
+group:Foraminifera
 
 property:
 id:zone1_range
 name:Zone 1 range 
-type:f 0 200
+type:f 0 200 10
 group:Foraminifera
 
@@ -1001 +1014 @@
 id:zone2_range
 name:Zone 2 range
-type:f 0 3000
+type:f 0 3000 30
 group:Foraminifera
 
 property:
-id:colors
-name:Haploid and diploid colors
-type:x
-group:Foraminifera
-
-property:
-id:min_repro_energ_haplo
-name:Min reproduction energy of forams
-type:f
-group:Foraminifera
-
-property:
-id:min_repro_energ_diplo
-name:Min reproduction energy of forams
-type:f
-group:Foraminifera
-
-property:
-id:repro_prob
-name:Probability of reproduction
-type:f 0 1 0.8
-group:Foraminifera
-
-property:
-id:energies0_haplo
-name:Energy of offspring from diploid forams
-type:f
-group:Foraminifera
-
-property:
-id:energies0_diplo
-name:Energy of offspring from diploid forams
-type:f
-group:Foraminifera
+id:chamberCostPerSec
+name:Cost of growning chamber per second
+type:f 0 1 0.000001
+group:Energy
 
 property:
 id:e_death_level_haplo
 name:Minimal level of energy to sustain life of haploid
-type:f 0 20 0.2
-group:Foraminifera
+type:f 0 1 0.5
+group:Energy
 
 property:
 id:e_death_level_diplo
 name:Minimal level of energy to sustain life of diploid
-type:f 0 20 0.2
-group:Foraminifera
+type:f 0 1 0.5
+group:Energy
 
 property:
 id:energy_hib
 name:Energy used for hibernation during one step
-type:f 0 1 0.001
-group:Foraminifera
+type:f 0 1 0.0000001
+group:Energy
 
 property:
 id:energy_move
 name:Energy used for movement during one step
-type:f 0 20 0.001
-group:Foraminifera
-
-property:
-id:min_vol
-name:Minimal volume for reproduction
-type:f 100 900 100
-group:Foraminifera
-
-property:
-id:max_size
-name:Maximal size
-type:d 1 10 5 
-group:Foraminifera
-
-property:
-id:foramPop
-name:Initial forams population size
-type:d 1 1000 100
-group:Foraminifera
-
-property:
-id:crossprob
-name:Crossover probability
-type:f 0 1 0
-group:Foraminifera
-
-property:
-id:mutationprob
-name:Mutation probability
-type:f 0 1 0
-group:Foraminifera
+type:f 0 1 0.0000005
+group:Energy
 
 property:
 id:e_meta
 name:Idle metabolism
-type:f 0 1
+type:f 0 1 0.0000005
 group:Energy
 help:Each stick consumes this amount of energy in one time step
-
-property:
-id:nutrient_pop
-name:Feeding rate
-type:f 0 1000000
-group:Energy
-help:How fast energy is created in the world
-
-property:
-id:foodPeriodChange
-name:Set variable feed rate
-type:f 0
-group:Energy
 
 property:
 id:ingestion
 name:Ingestion rate
-type:f
-group:Energy
+type:f 0 -1 0.25
+group:Energy
+
+property:
+id:nutrient_pop
+name:Nutrient population
+type:f 0 1000000
+group:Energy
+help:How fast energy is created in the world
 
 property:
@@ -1127 +1074 @@
 
 property:
-id:feedtrans
-name:Energy transfer per second
-type:f 0 100000
-group:Energy
-
-property:
-id:foodperiod
-name:Time between food occurrences
-type:f 0 1000000
-group:Energy
-
-property:
 id:nutrientradius
 name:Nutrient size
@@ -1145 +1080 @@
 
 property:
+id:picoCarbonPerMikro
+name:Picograms of carbon in cubed micrometer
+type:f 0 -1 0.13
+group:Energy
+
+property:
+id:feedtrans
+name:Energy transfer per second
+type:f 0 1 0.001
+group:Energy
+
+property:
+id:foodperiod
+name:Time between food occurrences
+type:f 0 1000000 14400
+group:Energy
+
+property:
+id:foodPeriodChange
+name:Set variable feed rate
+type:f 0 -1 0
+group:Energy
+
+property:
 id:stress
 name:Environmental stress
 type:d 0 1 1
-group:World
+group:
 
 property:
@@ -1154 +1113 @@
 name:Reproduction trigger
 type:d 0 1 1
-group:World
-
-property:
-id:repro_time
-name:Time before reproduction
-type:d 0 10000
+group:Reproduction
 
 property:
 id:creath
 name:Creation height
-type:f -1 50
+type:f -1 50 -0.99
 help:~
 Vertical position (above the surface) where new Forams are revived.
@@ -1172 +1126 @@
 -1   = just above the bottom~
 
+property:
+id:autorestart
+name:Restart after extinction
+help:Restart automatically this experiment after the last creature has died?
+type:d 0 1 0
+
 state:
 id:nutrient
@@ -1178 +1138 @@
 type:x
 flags:32
-
-property:
-id:autorestart
-name:Restart after extinction
-help:Restart automatically this experiment after the last creature has died?
-type:d 0 1
 
 state:
@@ -1199 +1153 @@
 type:d
 flags:16
-
-property:
-id:logging
-name:Log statistics to file
-type:d 0 1 0

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

@@ -30 +30 @@
 function createForamMorphology(morphotype, gen, chamber_num)
 {
-        var rad = getProperty(gen, "chamber_proculus"); 
         var geno = "//0\nm:Vstyle=foram\n" + chambers[morphotype][0] + "vr=" + colors[gen];
 
@@ -37 +36 @@
         for (var i = 0; i < chamber_num; i++)
         {
-                //rad = getProperty(gen, "chamber_proculus") + getProperty(gen, "chamber_difference") * (i + 1);
                 geno += "\n" + chambers[morphotype][i+1]  + "vr=" +  colors[gen];
         }
@@ -46 +44 @@
         }
 
-        //if (morphotype == 0) geno += "\nn:p=0,d=\"S\"";
         return geno;
 }
@@ -52 +49 @@
 function setGenotype(mode)
 {
-        if (mode->opt == 0) //initial
-        {
-                mode->cr.data->genes = String.deserialize(String.serialize(mode->genes)); 
-                mode->cr.data->lifeparams = {"max_energy_level" : mode->energy0, "gen" : 0,  "hibernated" : 0, "species" : mode->species, "reproduce" : 0, "dir" : randomDir(), "dir_counter" : Math.random(ExpProperties.dir_change_sec), "chamber_growth" : -1, "division_time" : -1};
-        }
-        else if (mode->opt  == 1) //child
-        {
-                mode->cr.data->lifeparams = {"max_energy_level" : mode->energy0, "gen" : 1 - mode->parent_lifeparams->gen,  "hibernated" : 0, "species" : mode->parent_lifeparams->species, "reproduce" : 0, "dir" : randomDir(), "dir_counter" : Math.random(ExpProperties.dir_change_sec), "chamber_growth" : -1, "division_time" : -1};
-                mode->cr.data->genes = String.deserialize(String.serialize(mode->parent_genes));
-        }
-        else //grow
+        if (mode->opt == "growth")
         {
                 mode->cr.data->genes = mode->parent_genes;
                 mode->cr.data->lifeparams = mode->parent_lifeparams;
+        }
+
+        else if (mode->opt == "birth")
+        {
+                mode->cr.data->genes = String.deserialize(String.serialize(mode->genes));
+                mode->cr.data->lifeparams = {"max_energy_level" : mode->energy0, "gen" : mode->gen,  "hibernated" : 0, "species" : mode->species, "reproduce" : 0, "dir" : randomDir(), "dir_counter" : Math.random(int(secToSimSteps(ExpProperties.dir_change_sec))), "chamber_growth" : -1, "division_time" : -1};                    
+
         }
 }
@@ -192 +186 @@
                                         if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
                                         {
-                                                var time = int(ExpProperties.gametoPeriod/ExpProperties.secPerStep);
+                                                var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
                                                 parent1.data->lifeparams->division_time = time;
                                                 parent2.data->lifeparams->division_time = time;
@@ -298 +292 @@
         cr.energy0 = energy;
         cr.energy = cr.energy0;
-        setGenotype({"cr" : cr, "parent_genes" : parent_genes, "parent_lifeparams" : parent_lifeparams, "opt" : 1, "energy0" : cr.energy0});
+        setGenotype({"opt" : "birth", "cr" : cr, "gen" : 1 - parent_lifeparams->gen, "species" : parent_lifeparams->species, "energy0" : cr.energy0, "genes" : parent_genes});
         placeRandomlyNotColliding(cr);
 }