Changeset 401 for experiments/frams/foraminifera

Timestamp:

06/24/15 19:28:25 (10 years ago)

Author:

Maciej Komosinski

Message:

Extended Foraminifera simulation - physical collisions; visible haplo/diplo generations; growing; and much more

Location:

experiments/frams/foraminifera/data/scripts

Files:

• forams_benthic.expdef (moved) (moved from experiments/frams/foraminifera/data/scripts/foraminifera.expdef) (22 diffs)
• forams_benthic.show (added)
• forams_repro.inc (added)

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

@@ -1 +1 @@
 expdef:
-name:Foraminifera simulation
+name:Benthic foraminifera reproduction
 info:~
 Genes and parameter values which control reproduction are stored in user1 and user2 fields.
@@ -16 +16 @@
 code:~
 
+/*
+changes 2015-06-24:
+- xxx.get(...) changed to xxx[...]
+- xxx.set(...,...) changed to xxx[...]=...
+- function placeRandomlyNotColliding(cr) explicitly called when adding a new creature, and removed collision checking from onCreaturesBorn() which is also called when "growing" (since "growing" is implemented as creating a new creature in place of the old one, so onCreaturesBorn() is also called)
+- use creature's center (not the bbox corner) when growing
+- added "S" receptor to visualize the difference between diplo and haplo generations
+- signal.value is a MechPart (a reference) so it does not have to be updated after changing the object location
+*/
+
 global foodenergywaiting;
 global reprocounter;
+global delta_change;
+
+@include "forams_repro.inc"
 
 // -------------------------------- experiment begin --------------------------------
@@ -23 +36 @@
 function onExpDefLoad()
 {
+
         // define genotype and creature groups
         GenePools.clear();
         Populations.clear();
         GenePools[0].name = "Unused";
+
+        SignalView.mode = 1;
 
         var pop = Populations[0];
@@ -36 +52 @@
         pop.energy = 1;
         pop.selfmask = 0x10001;
-        pop.othermask = 0x30000;
+        pop.othermask = 0x20001;
+        //pop.selfmask = 0x20002; pop.othermask = 0x10002;
         pop.perfperiod = 25;
 
@@ -45 +62 @@
         pop.energy = 1;
         pop.selfmask = 0x20002;
-        pop.othermask = 0x30002;
-
-        ExpParams.genh = "/*F*/1,1.1,1.1,1.1,1,1,1";
-        ExpParams.gend = "/*F*/1,1,1,1,1,1,1";
-        ExpParams.p_mut = 50;
+        pop.othermask = 0x10000;
+
+
+        var size_h = ExpParams.haplo_rad * ExpParams.delta_rate + ExpParams.haplo_rad;
+        var size_d = ExpParams.diplo_rad * ExpParams.delta_rate + ExpParams.diplo_rad;
+        ExpParams.gend = "//0\np:sh=1,sx=" + ExpParams.diplo_rad + ",sy=" + ExpParams.diplo_rad + ",sz=" + ExpParams.diplo_rad + ", rz=3.14159265358979";
+        ExpParams.genh = "//0\np:sh=1,sx=" + size_h + ",sy=" + size_h + ",sz=" + size_h + ", rz=3.14159265358979";
         ExpParams.e_meta = 0.1;
-        ExpParams.feedrate = 0.7;
+        ExpParams.feedrate = 0.5;
         ExpParams.feede0 = 100;
         ExpParams.feedtrans = 3;
         ExpParams.creath = -0.99; //just above the bottom
-        ExpParams.foodgen = "//0\np:sh=1,sx=0.1,sy=0.1,sz=0.1";
+        ExpParams.foodgen = "//0\np:sh=2,sx=0.1,sy=0.1,sz=0.1\nn:d=T,p=0";
         ExpParams.autorestart = 0;
         ExpParams.psize = 10;
-        ExpParams.ofnumh = 14;
-        ExpParams.ofnumd = 4;
-        ExpParams.v_min_d = 200;
-        ExpParams.v_min_h = 500;
-        ExpParams.age_min_d = 150;
-        ExpParams.age_min_h = 300;
-        ExpParams.crossprob = 0.3;
+        ExpParams.logging = 0;
+
+        //number of offspring
+        ExpParams.ofnumh = 40;
+        ExpParams.ofnumd = 25;
+        //minial volume for reproduction
+        ExpParams.v_min_d = 300;
+        ExpParams.v_min_h = 300;
+        //radius of the chamber
+        ExpParams.haplo_rad = 1.2;
+        ExpParams.diplo_rad = 0.6;
+        //minimal age for reproduction
+        ExpParams.age_min_d = 100;
+        ExpParams.age_min_h = 100;
+        //crossover probability
+        ExpParams.crossprob = 0.4;
+        //mutation probability
+        ExpParams.mutationprob = 0.2;
         ExpParams.repro_time = 200;
         ExpParams.repro_thr = 1;
+
+        //size change rate
+        ExpParams.delta_rate = 0.1;
+        //grwoth speed in time steps
+        ExpParams.growth_step = 50;
 
         ExpState.totaltestedcr = 0;
@@ -73 +108 @@
         reprocounter = 0;
 
-        ExpParams.wsize = 30;
-
+        ExpParams.wsize = 50;
         World.wrldwat = 50;
         World.wrldsiz = ExpParams.wsize;
         World.wrldbnd = 1;
+
+        delta_change = 0.5;
 }
 
@@ -94 +130 @@
                 cr.energ0 = ExpParams.v_min_h - ExpParams.repro_thr;
                 cr.energy = cr.energ0;
-                cr.user1 = {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h};
-                cr.user2 = {"Va" : ExpParams.v_min_h - ExpParams.repro_thr, "gen" : 0 };
+                cr.user1 = {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h, "delta_h" : ExpParams.haplo_rad * ExpParams.delta_rate, "delta_d" : ExpParams.diplo_rad * ExpParams.delta_rate};
+                cr.user2 = {"Va" : ExpParams.v_min_h - ExpParams.repro_thr, "gen" : 0, "growth_step" : ExpParams.growth_step, "rsize" : ExpParams.haplo_rad, "vinit" : ExpParams.v_min_h - ExpParams.repro_thr};
         }
         ExpState.totaltestedcr = 0;
@@ -124 +160 @@
                 if (cr != null)
                 {
-                        cr.rotate(0, 0, Math.rnd01*Math.twopi);
+                        //cr.rotate(0,0,Math.rnd01*Math.twopi);
                         if ((typeof(g.user1) == "Vector") && (g.user1.size >= 3))
-                        { // [x,y,energy]
+                        {
+                                // [x,y,energy]
                                 cr.move(g.user1[0] - cr.center_x, g.user1[1] - cr.center_y, 0);
                                 cr.energy = g.user1[2];
@@ -132 +169 @@
                         else
                         {
-                                cr.move(Math.rnd01*World.wrldsiz - cr.center_x, Math.rnd01*World.wrldsiz - cr.center_y, 0);
+                                cr.move(Math.rnd01 * World.wrldsiz - cr.center_x, Math.rnd01 * World.wrldsiz - cr.center_y, 0);
                         }
                 }
@@ -148 +185 @@
         File.writeComment("saved by '%s.expdef'" % Simulator.expdef);
 
-        var i, tmpvec = [];
-
-        for (var cr in Populations[1])
+        var tmpvec = [], i;
+
+        for(var cr in Populations[1])
                 tmpvec.add([cr.center_x, cr.center_y, cr.energy]);
 
@@ -170 +207 @@
 }
 
+function placeRandomlyNotColliding(cr)
+{
+        var retry = 100; //try 100 times
+        while (retry--)
+        {
+                placeCreatureRandomly(cr, 0, 0);
+                if (!cr.boundingBoxCollisions(0))
+                        return cr;
+        }
+
+        Populations[0].delete(cr);
+}
+
 function readyToRepro(cr)
 {
         cr.signals.add("repro");
-        cr.signals.get(0).power = 1;
+        cr.signals[0].power = 1;
+
 }
 
 function onCreaturesStep(cr)
 {
-        cr.moveAbs(cr.pos_x, cr.pos_y, 0);
+        cr.moveAbs(cr.pos_x, cr.pos_y, 0); //adjustment in z axis
         var p = cr.getMechPart(0);
         var n = cr.signals.receiveSet("food", ExpParams.food_range);
 
+        //if signals are received find the source of the nearest
         if (n.size > 0)
         {
+
                 var i;
                 var mp;
@@ -191 +244 @@
                 var mindistvec = null;
 
-                if (Math.rnd01 < 0.8)
-                {
-                        for (i = 0;i < n.size;i++)
-                        {
-                                mp = n[i].value;
-                                distvec.set(mp.pos);
-                                distvec.sub(p.pos);
-                                dist = distvec.length;
-                                if (dist < mindist)
-                                {
-                                        mindist = dist;
-                                        mindistvec = distvec.clone();
-                                }
-                        }
-                }
-                else
-                {
-                        mp = n[Math.random(n.size)].value;
+                for (i = 0; i < n.size; i++)
+                {
+                        mp = n[i].value;
                         distvec.set(mp.pos);
                         distvec.sub(p.pos);
-                        mindistvec = distvec.clone();
+                        dist = distvec.length;
+                        if (dist < mindist)
+                        {
+                                mindist = dist;
+                                mindistvec = distvec.clone();
+                        }
                 }
 
                 mindistvec.normalize();
-                mindistvec.scale( -0.1);
+                mindistvec.scale(-0.08);
                 cr.localDrive = mindistvec;
         }
+
         else
         {
-                cr.localDrive = (0.1, 0, 0);
-        }
-
-        var properAge = cr.user2["Va"] >= cr.user1["vamin"];
-        var properSize = cr.user1["amin"] <= cr.lifespan;
-
-        //if creature has proper age and cytoplasm amount
-        if ( properAge && properSize )
-        {
-                //reproduce with probability repro_prob
-                if (Math.rnd01 <= ExpParams.repro_prob)
+                cr.localDrive = (0.1 * Math.rnd01, 0.1 * Math.rnd01, 0);
+        }
+
+        //energy costs depend on size
+        if (cr.energy > 100)
+        {
+                // cr.energy_m = cr.user2["Va"]/cr.user2["vinit"];
+        }
+
+        if (cr.lifespan >= ExpParams.max_age)
+        {
+                Populations[0].kill(cr);
+        }
+
+        //foram growth
+        else if (cr.lifespan == cr.user2["growth_step"])
+        {
+                var pos = [cr.center_x, cr.center_y, cr.center_z];
+                var energy = cr.energy;
+                var cr2 = null;
+                if (cr.user2["gen"] == 0)
+                {
+                        var new_r = ExpParams.haplo_rad * Math.min(Math.max(cr.user2["Va"] / cr.user2["vinit"] * 0.5, 1), 2.5);
+                        cr.user2["rsize"] = new_r;
+                        cr2 = Populations[0].add("//0\np:sh=1,sx=" + cr.user2["rsize"] + ",sy=" + cr.user2["rsize"] + ",sz=" + cr.user2["rsize"] + ", rz=3.14159265358979");
+                        cr2.user1 = {"vamin" : cr.user1["vamin"], "amin": cr.user1["amin"], "delta_h" : cr.user1["delta_h"], "delta_d" : cr.user1["delta_d"]};
+                }
+                else if (cr.user2["gen"] == 1)
+                {
+                        var new_r = ExpParams.diplo_rad * Math.min(Math.max(cr.user2["Va"] / cr.user2["vinit"] * 0.5, 1), 2.5);
+                        cr.user2["rsize"] = new_r;
+
+                        var geno = "//0\np:sh=1,sx=" + cr.user2["rsize"] + ",sy=" + cr.user2["rsize"] + ",sz=" + cr.user2["rsize"] + ", rz=3.14159265358979";
+                        geno += "\nn:p=0,d=\"S\""; //TODO is this the only difference with haploid code? TODO why initial genotypes are not used as defined in ExpParams?
+                        //TODO maybe it would be nice if they rotated so the "S" would show where they are going (direction/intention)
+                        cr2 = Populations[0].add(geno);
+
+
+                        cr2.user1 = [ {"vamin" : cr.user1[0]["vamin"], "amin": cr.user1[0]["amin"], "delta_h" : cr.user1[0].get("delta_h"), "delta_d" : cr.user1[0]["delta_d"]  }, {"vamin" : cr.user1[1]["vamin"], "amin": cr.user1[1]["amin"], "delta_h" : cr.user1[1]["delta_h"], "delta_d" : cr.user1[1]["delta_d"]  }];
+                }
+                cr2.energy = energy;
+                cr2.user2 = {"Va" : cr.user2["Va"], "gen" : cr.user2["gen"], "growth_step" : cr.user2["growth_step"], "rsize" : cr.user2["rsize"], "vinit": cr.user2["vinit"]};
+                cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
+
+                Populations[0].delete(cr);
+        }
+        else
+        {
+                var properSize = 0;
+
+                if (cr.user2["gen"] == 0)
+                {
+                        properSize = cr.user2["Va"] >= cr.user1["vamin"];
+                }
+                else
+                {
+                        properSize = cr.user2["Va"] >= cr.user1[0]["vamin"];
+                }
+
+                //if creature has proper age and cytoplasm amount
+                if ( properSize )
+                {
+                        //reproduce with probability repro_prob
+                        if (Math.rnd01 <= ExpParams.repro_prob)
+                        {
+                                readyToRepro(cr);
+                        }
+                }
+                if ( properSize && (cr.signals.receive("repro") > 0))
                 {
                         readyToRepro(cr);
                 }
-        }
-        if ( properAge && properSize && (cr.signals.receive("repro") > 0))
-        {
-                readyToRepro(cr);
         }
 }
@@ -270 +368 @@
         cr.signals.add("food");
 
-        cr.signals.get(0).value = cr.getMechPart(0);
-
-        var retry = 50; //try 50 times
+        cr.signals[0].value = cr.getMechPart(0);
+
+        var retry = 100; //try 100 times
         while (retry--)
         {
                 placeCreatureRandomly(cr, 0, 0);
-                cr.signals.get(0).value = cr.getMechPart(0);
                 if (!cr.boundingBoxCollisions(0))
                         return cr;
@@ -292 +389 @@
                 Collision.Creature1.energy_m = Collision.Creature1.energy_m + e;
                 Collision.Creature2.energy_p = Collision.Creature2.energy_p + e;
-                var ener = float(Collision.Creature2.user2.get("Va"));
+                var ener = float(Collision.Creature2.user2["Va"]);
                 var sum = float(float(ener) + float(e));
-                Collision.Creature2.user2.set("Va", float(sum));
+                Collision.Creature2.user2["Va"] = float(sum);
         }
 }
@@ -300 +397 @@
 // -------------------------------- food end --------------------------------
 
-// -------------------------------- step begin --------------------------------
-
-function reproduce(repro_list, number)
-{
-        for (var i = 0; i < repro_list.size; i++)
-        {
-                var parent = Populations[0].get(repro_list[i]);
-
-                var energ = parent.user2["Va"] / number;
-                for (var j = 0; j < number; j++)
-                {
-                        var cr = Populations[0].add(ExpParams.gend);
-                        cr.energ0 = energ;
-                        cr.energy = cr.energ0;
-                        if (parent.user2["gen"] == 0)
-                        {
-                                cr.user1 = {"vamin" : ExpParams.v_min_d, "amin": ExpParams.age_min_d};
-                        }
-                        else
-                        {
-                                cr.user1 = {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h};
-                        }
-                        cr.user2 = { "Va" : cr.energ0, "gen" : 1 - parent.user2["gen"] };
-                        placeCreatureRandomly(cr, 0, 0);
-                }
-        }
-        for (var j = 0; j < repro_list.size; j++)
-        {
-                Populations[0].kill(repro_list[j]);
-        }
-}
 
 function log(tolog, fname)
 {
-        var f = File.appendDirect(fname, "description");
+        var f = File.appendDirect(fname, "forams data");
         f.writeString("" + Simulator.stepNumber);
-        for (var i = 0; i < tolog.size; i++)
+        for (var  i = 0; i < tolog.size; i++)
         {
                 f.writeString(";" + tolog[i]);
@@ -346 +412 @@
 
 
-function onStep()
-{
-        var haploids = 0;
-        var diploids = 0;
-        var e_inc_h = 0.0;
-        var e_inc_d = 0.0;
-        var e_nut = 0.0;
-
-        for (var i = 0; i < Populations[0].size; i++)
-        {
-                var cr = Populations[0].get(i);
-                if (cr.user2["gen"] == 0)
-                {
-                        haploids += 1;
-                        e_inc_h += cr.energy;
-                }
-                else
-                {
-                        diploids += 1;
-                        e_inc_d += cr.energy;
-                }
-        }
-
-        for (var i = 0; i < Populations[1].size; i++)
-        {
-                var cr = Populations[1].get(i);
-                e_nut += cr.energy;
-        }
-
-        if (haploids < 2 && diploids == 0)
-        {
-                Simulator.print("no more creatures, stopped.");
-                Simulator.stop();
-        }
-
-        var l1 = Vector.new();
-        l1 = [haploids, diploids, Populations[1].size];
-        var l2 = Vector.new();
-        l2 = [e_inc_h, e_inc_d, e_nut];
-
-        log(l1, "log.txt");
-        log(l2, "log2.txt");
-        //food growth ---------------------------------------------
-        foodenergywaiting = foodenergywaiting + ExpParams.feedrate;
-        if (foodenergywaiting > ExpParams.feede0)
-        {
-                for (var i = 0; i < ExpParams.foodPop; i++)
-                {
-                        addfood();
-                }
-
-                foodenergywaiting = 0.0;
-                Simulator.checkpoint();
-        }
-
-        //reproduction --------------------------------------------
-        reprocounter += 1;
-        if (reprocounter > ExpParams.repro_time)
-        {
-                reprocounter = 0;
-                var to_repro_h = Vector.new();
-                var to_repro_d = Vector.new();
-                for (var i = 0; i < Populations[0].size; i++)
-                {
-                        var cr = Populations[0].get(i);
-                        if (cr.signals.size > 0)
-                        {
-                                if (cr.user2["gen"] == 0)
-                                {
-                                        to_repro_h.add(i);
-                                }
-                                else
-                                {
-                                        to_repro_d.add(i);
-                                }
-                        }
-                }
-                if (to_repro_h.size > 0)
-                {
-                        reproduce(to_repro_h, ExpParams.ofnumh);
-                }
-                if (to_repro_d.size > 1)
-                {
-                        reproduce(to_repro_d, ExpParams.ofnumd);
-                }
-        }
-
-        //check for death -----------------------------------------------
-        if (Populations[0].size == 0)
-        {
-                if (ExpParams.autorestart)
-                {
-                        Simulator.print("no more creatures, restarting...");
-                        onExpInit();
-                }
-                else
-                {
-                        Simulator.print("no more creatures, stopped.");
-                        Simulator.stop();
-                }
-        }
-}
-
-// -------------------------------- step end --------------------------------
-
 
 @include "standard_events.inc"
@@ -457 +418 @@
 
 prop:
+id:max_age
+name:Maximal age
+type:d 100 1000 500
+
+prop:
 id:wsize
-name:world size
+name:World size
 type:d 10 1000 20
 
 prop:
+id:haplo_rad
+name:Haploid radius
+type:f 0.1 3 1.2
+
+prop:
+id:growth_step
+name:Growth step
+type:d 50 10000 1000
+
+prop:
+id:delta_rate
+name:Delta rate
+type:f 0.0001 0.1 0.001
+
+prop:
+id:diplo_rad
+name:Diploid radius
+type:f 0.1 3 0.6
+
+prop:
 id:foodPop
-name:food size
+name:Food size
 type:d 1 1000 10
 
 prop:
 id:age_min
-name:minimal age for reproduction
+name:Minimal age for reproduction
 type:d 100 10000 200
 
@@ -486 +472 @@
 id:v_min_h
 name:Min reproduction energy of haploid forams
-type:d 100 10000 300
+type:f 10 10000 300
 group:Foraminifera
 
@@ -492 +478 @@
 id:v_min_d
 name:Min reproduction energy of diploid forams
-type:d 100 10000 150
+type:f 10 10000 150
 group:Foraminifera
 
 prop:
 id:repro_thr
-name:treshold for reproduction
+name:Threshold for reproduction
 type:d 1 1000 1
 
 prop:
 id:food_range
-name:range of food smell
+name:Range of food smell
 type:d 0 10000 10000
 
 prop:
 id:repro_time
-name:time before reproduction
+name:Time before reproduction
 type:d 0 1000
 
 prop:
 id:psize
-name:initial population size
+name:Initial population size
 type:d 1 1000 100
+
+prop:
+id:logging
+name:Log statistics to file
+type:d 0 1 0
 
 prop:
@@ -529 +520 @@
 prop:
 id:repro_prob
-name:probability of reproduction
+name:Probability of reproduction
 type:f 0 1 0.9
 
 prop:
 id:crossprob
-name:crossover probability
-type:f 0 1
+name:Crossover probability
+type:f 0 1 0
+
+prop:
+id:mutationprob
+name:Mutation probability
+type:f 0 1 0
 
 prop:
@@ -561 +557 @@
 
 prop:
-id:p_mut
-name:Mutations
-type:f 0 100
-
-prop:
 id:e_meta
 name:Idle metabolism
@@ -600 +591 @@
 id:autorestart
 name:Restart after extinction
-group:
 help:Restart automatically this experiment after the last creature has died?
 type:d 0 1