Changeset 404 for experiments/frams/foraminifera/data/scripts/forams_benthic.expdef

Timestamp:

06/30/15 23:02:42 (9 years ago)

Author:

oriona

Message:

removed unused part of code, refactorization

File:

• experiments/frams/foraminifera/data/scripts/forams_benthic.expdef (modified) (16 diffs)

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

@@ -34 +34 @@
 global foodenergywaiting;
 global reprocounter;
-global delta_change;
 
 @include "forams_repro.inc"
@@ -53 +52 @@
         pop.name = "Creatures";
         pop.en_assim = 0;
-        pop.nnsim = 1;
+        pop.nnsim = 0;
         pop.enableperf = 1;
         pop.death = 1;
@@ -70 +69 @@
         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";
+        //radius of the chamber
+        ExpParams.rads = [1.2, 0.6];
+        //inital genotypes 
+        ExpParams.genh = "//0\np:sh=1,sx=" + ExpParams.rads[0] + ",sy=" + ExpParams.rads[0] + ",sz=" + ExpParams.rads[0] + ", rz=3.14159265358979"; 
+        ExpParams.gend = "//0\np:sh=1,sx=" + ExpParams.rads[1] + ",sy=" + ExpParams.rads[1] + ",sz=" + ExpParams.rads[1] + ", rz=3.14159265358979";
+        ExpParams.gend += "\nn:p=0,d=\"S\"";
         ExpParams.e_meta = 0.1;
         ExpParams.feedrate = 0.5;
@@ -91 +91 @@
         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;
@@ -104 +101 @@
         ExpParams.repro_thr = 1;
 
-        //size change rate
-        ExpParams.delta_rate = 0.1;
         //grwoth speed in time steps
         ExpParams.growth_step = 50;
@@ -118 +113 @@
         World.wrldsiz = ExpParams.wsize;
         World.wrldbnd = 1;
-
-        delta_change = 0.5;
 }
 
@@ -136 +129 @@
                 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, "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};
+                cr.user1 = {"vamin" : ExpParams.v_min_h, "amin": ExpParams.age_min_h};
+                cr.user2 = {"Va" : ExpParams.v_min_h - ExpParams.repro_thr, "gen" : 0, "growth_step" : ExpParams.growth_step, "rsize" : ExpParams.rads[0], "vinit" : ExpParams.v_min_h - ExpParams.repro_thr};
         }
         ExpState.totaltestedcr = 0;
@@ -230 +223 @@
         cr.signals.add("repro");
         cr.signals[0].power = 1;
-
 }
 
 function onCreaturesStep(cr)
 {
-        cr.moveAbs(cr.pos_x, cr.pos_y, 0); //adjustment in z axis
+        //TODO moving inside sediment?
+        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);
@@ -276 +269 @@
         if (cr.energy > 100)
         {
+                //TODO energy costs dependant on size
                 // cr.energy_m = cr.user2["Va"]/cr.user2["vinit"];
         }
@@ -281 +275 @@
         if (cr.lifespan >= ExpParams.max_age)
         {
+                //TODO what is max age value? should there be one?
                 Populations[0].kill(cr);
+                return;
         }
 
         //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?
+        if (cr.lifespan == cr.user2["growth_step"])
+        {
+                //TODO how size is related to the energy?
+                cr.user2["rsize"] = ExpParams.rads[cr.user2["gen"]] * Math.min(Math.max(float(cr.user2["Va"] / cr.user2["vinit"]) * 0.5, 1.0), 2.5);
+                var geno = "//0\np:sh=1,sx=" + cr.user2["rsize"] + ",sy=" + cr.user2["rsize"] + ",sz=" + cr.user2["rsize"] + ", rz=3.14159265358979";
+                if (cr.user2["gen"] == 1)
+                {
+                        geno += "\nn:p=0,d=\"S\""; //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"]};
+                }
+                var cr2 = Populations[0].add(geno);
+                cr2.energy = cr.energy;
+                setGenotype(cr2, cr.user1, cr.user2);
                 cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
 
@@ -355 +337 @@
 }
 
+function setGenotype(cr, new_user1, new_user2)
+{
+        cr.user2 = {"Va" : new_user2["Va"], "gen" : new_user2["gen"], "growth_step" : new_user2["growth_step"], "rsize" : new_user2["rsize"], "vinit": new_user2["vinit"]};
+        if (cr.user2["gen"] == 0)
+        {
+                cr.user1 = {"vamin" : new_user1["vamin"], "amin": new_user1["amin"] };
+        }
+        else if (cr.user2["gen"] == 1)
+        {
+                cr.user1 = [ {"vamin" : new_user1[0]["vamin"], "amin": new_user1[0]["amin"] }, {"vamin" : new_user1[1]["vamin"], "amin": new_user1[1]["amin"] }];
+        }       
+
+}
+
 // -------------------------------- creature end --------------------------------
 
@@ -376 +372 @@
         cr.signals[0].value = cr.getMechPart(0);
 
-        var retry = 100; //try 100 times
-        while (retry--)
-        {
-                placeCreatureRandomly(cr, 0, 0);
-                if (!cr.boundingBoxCollisions(0))
-                        return cr;
-        }
-
-        return cr;
+        placeRandomlyNotColliding(cr);
 }
 
@@ -395 +383 @@
                 Collision.Creature1.energy_m = Collision.Creature1.energy_m + e;
                 Collision.Creature2.energy_p = Collision.Creature2.energy_p + e;
-                var ener = float(Collision.Creature2.user2["Va"]);
-                var sum = float(float(ener) + float(e));
-                Collision.Creature2.user2["Va"] = float(sum);
+                Collision.Creature2.user2["Va"] = float(Collision.Creature2.user2["Va"]) + float(e);
         }
 }
@@ -434 +420 @@
 
 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
-type:d 1 1000 10
-
-prop:
-id:age_min
-name:Minimal age for reproduction
-type:d 100 10000 200
+type:d 10 10000 1000
+
+prop:
+id:rads
+name: haploid and diploid radius
+type:x
 
 prop:
@@ -489 +455 @@
 prop:
 id:repro_thr
-name:Threshold for reproduction
+name:amount of energy initial creatures need to gather to reproduce
 type:d 1 1000 1
 
@@ -615 +581 @@
 flags:16
 
+prop:
+id:foodPop
+name:food size
+type:d 1 1000 10
+
 state:
 id:food