Changeset 474

Timestamp:

03/12/16 00:13:49 (9 years ago)

Author:

oriona

Message:

Parameters for time scaling added.

Location:

experiments/frams/foraminifera/data/scripts

Files:

• foraminifera.expdef (modified) (20 diffs)
• foraminifera.inc (modified) (1 diff)
• foraminifera.show (modified) (3 diffs)

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

@@ -31 +31 @@
 global max_chamber_energ;
 global dir_change;
+global movePerStep;
 
 @include "foraminifera.inc"
@@ -81 +82 @@
         ExpParams.autorestart = 0;
 
+        //time
+        ExpParams.secPerStep = 60;
+        ExpParams.foramSpeedMmPerMin = 0.1;
+        movePerStep = getMovePerStep();
+
         //ExpParams.visualize = 1; //uncomment to visualize reticulopodia and indicate nutrients positions
 
@@ -87 +93 @@
         //reproduction
         ExpParams.foramPop = 10;        
-        ExpParams.crossprob = 0.4;
-        ExpParams.mutationprob = 0.2;
+        ExpParams.crossprob = 0;
+        ExpParams.mutationprob = 0;
         ExpParams.repro_time = 20;
         reprocounter = 0;
 
         //morphology
-        dir_change = 500;
+        dir_change = 30000;
         ExpParams.zone1_range = micronsToFrams(3000);
         ExpParams.zone2_range = micronsToFrams(6000);
@@ -114 +120 @@
         ExpParams.min_repro_energ_diplo = 6;
 
-        ExpParams.e_meta = 0.0002; 
-        ExpParams.energy_hib = 0.0001;
-        ExpParams.energy_move = 0.00025;
+        ExpParams.e_meta = 0.00005; 
+        ExpParams.energy_hib = 0.000025;
+        ExpParams.energy_move = 0.00005;
 
         ExpParams.energies0_haplo = max_chamber_energ[0][0] - 0.001*max_chamber_energ[0][0];
         ExpParams.energies0_diplo = max_chamber_energ[1][0] - 0.001*max_chamber_energ[1][0];
-        ExpParams.feedtrans = 0.5;
+        ExpParams.feedtrans = 0.125;
         ExpParams.e_repro_cost_haplo = 0.7; 
         ExpParams.e_repro_cost_diplo = 0.3;
@@ -128 +134 @@
         ExpParams.energy_nut = 100 * Math.pow(ExpParams.nutrientsize, 3);
         ExpParams.nutrientPop = 1;
-        ExpParams.feedrate = 0.1;
-        nutrientenergywaiting = ExpParams.energy_nut;
+        ExpParams.feedrate = 100;
+        nutrientenergywaiting = 0;
         ExpState.totaltestedcr = 0;
         ExpState.nutrient = "";
@@ -135 +141 @@
 
 @include "standard_placement.inc"
+
+function getMovePerStep()
+{
+        return micronsToFrams((ExpParams.foramSpeedMmPerMin/60)*1000)*ExpParams.secPerStep;
+}
 
 function micronsToFrams(micrometers)
@@ -247 +258 @@
 function setForamMeta(cr, gen)
 {
-        cr.idleen = ExpParams.e_meta * max_chamber_energ[gen][Math.min(lastChamberNum(cr), max_chamber_energ[gen].size-1)];
+        cr.idleen = (ExpParams.e_meta * max_chamber_energ[gen][Math.min(lastChamberNum(cr), max_chamber_energ[gen].size-1)])*ExpParams.secPerStep;
 }
 
@@ -295 +306 @@
 function foramGrow(cr, chamber_num)
 {
-        var geno = createForamGenotype(cr.user2["gen"], cr.user2["species"], chamber_num+1);
-        var cr2 = Populations[0].add(geno);
-
-        cr2.energy0 = cr.energy;
-        cr2.energy = cr2.energy0;
-
-        setGenotype({"cr" : cr2, "parent_user1" : cr.user1, "parent_user2" : cr.user2, "opt" : 2});
-        cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
-        setForamMeta(cr2, cr2.user2["gen"]);
-
-        if (visualization(cr))
-        {
-                Populations[2].delete(cr.user3);
-        }
-        Populations[0].delete(cr);
+        if ((chamber_num+1) < chambers[cr.user2["species"]].size)
+        {
+                var geno = createForamGenotype(cr.user2["gen"], cr.user2["species"], chamber_num+1);
+                var cr2 = Populations[0].add(geno);
+
+                cr2.energy0 = cr.energy;
+                cr2.energy = cr2.energy0;
+
+                setGenotype({"cr" : cr2, "parent_user1" : cr.user1, "parent_user2" : cr.user2, "opt" : 2});
+                cr2.moveAbs(cr.center_x - cr2.size_x / 2, cr.center_y - cr2.size_y / 2, cr.pos_z);
+                setForamMeta(cr2, cr2.user2["gen"]);
+
+                if (visualization(cr))
+                {
+                        Populations[2].delete(cr.user3);
+                }
+                Populations[0].delete(cr);
+        }
 }
 
@@ -352 +366 @@
                 {
                         mindistvec.normalize();
-                        mindistvec.scale(-0.08);
+                        mindistvec.scale(-1*movePerStep);
                         cr.localDrive = mindistvec;
                         moveEnergyDec(cr);
@@ -361 +375 @@
         
         else
+        {
                 return 0;
+        }
 }
 
@@ -368 +384 @@
         if (cr.user2["hibernated"] == 0)
         {
-                cr.energy_m += ExpParams.energy_move * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)];
+                cr.energy_m += (ExpParams.energy_move * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)])*ExpParams.secPerStep;
         }
 }
@@ -399 +415 @@
         }
         //random move
-        else if (cr.lifespan%dir_change == 0)
-        {
-                var dir = (Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), 0);  
-                dir.normalize();
-                dir.scale(-0.08);
-                cr.localDrive = dir;
+        else if (cr.lifespan%(dir_change/ExpParams.secPerStep) == 0)
+        {
+                cr.user2["dir"] = randomDir();
+                cr.localDrive = cr.user2["dir"];
                 moveEnergyDec(cr);
         }
+        else
+        {
+                cr.localDrive = cr.user2["dir"];
+        }
+}
+
+function randomDir()
+{
+        var dir = (Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), Math.rndUni(-ExpParams.zone2_range, ExpParams.zone2_range), 0);  
+        dir.normalize();
+        dir.scale(-1*movePerStep);
+        return dir;
 }
 
@@ -412 +438 @@
 {
         cr1.localDrive = XYZ.new(0,0,0);
-        var e = cr2.getPart(0).ing * ExpParams.feedtrans; //TODO efficiency dependent on age
+        var e = ExpParams.feedtrans*ExpParams.secPerStep; //TODO efficiency dependent on age
         e = Math.min(cr2.energy, e) + 0.0000001;
         //Simulator.print("transferring "+e+" to "+cr1.name+" from "+cr2.name+" ("+cr2.energy+")");
@@ -431 +457 @@
         else
         {
-                cr.idleen = ExpParams.energy_hib * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)]; //hibernate
+                cr.idleen = (ExpParams.energy_hib * max_chamber_energ[cr.user2["gen"]][Math.min(lastChamberNum(cr), (max_chamber_energ[cr.user2["gen"]].size)-1)])*ExpParams.secPerStep; //hibernate
         }
         cr.user2["hibernated"] = 1 - cr.user2["hibernated"];
@@ -536 +562 @@
 function nutrientGrowth()
 {
-        nutrientenergywaiting = nutrientenergywaiting + ExpParams.feedrate;
-        if (nutrientenergywaiting > ExpParams.energy_nut)
+        nutrientenergywaiting = nutrientenergywaiting + 1;
+        if (nutrientenergywaiting > ExpParams.feedrate/ExpParams.secPerStep)
         {
                 for (var i = 0; i < ExpParams.nutrientPop; i++)
@@ -564 +590 @@
         //reproduction --------------------------------------------
         reprocounter += 1;
-        if (reprocounter > ExpParams.repro_time)
+        if (reprocounter*ExpParams.secPerStep > ExpParams.repro_time)
         {
                 reprocounter = 0;
@@ -618 +644 @@
 
         log(log_numbers, "forams_log.txt");
-        log(log_energies,  "energies_log.txt");
+    log(log_energies,  "energies_log.txt");
 }
 
@@ -649 +675 @@
 name:Stop after the given number of simulation steps
 type:d 0 1000000 0
+
+prop:
+id:foramSpeedMmPerMin
+name:Speed of foraminfera in mm/min
+type:f 0.1
+flags: 16
+group:Foraminifera
+
+prop:
+id:secPerStep
+name:Seconds per simulation step
+type:f 60.0
+flags: 16
+group:Foraminifera
 
 prop:
@@ -798 +838 @@
 id:feedrate
 name:Feeding rate
-type:f 0 100
+type:f 0 1000000
 group:Energy
 help:How fast energy is created in the world
@@ -841 +881 @@
 id:repro_time
 name:Time before reproduction
-type:d 0 1000
+type:d 0 10000
 
 prop:

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

@@ -56 +56 @@
         {
                 mode["cr"].user1 = {"min_repro_energies" : [max_chamber_energ[0][getProperty(0, "min_repro_energ")], max_chamber_energ[1][getProperty(1, "min_repro_energ")]], "hibernation" : mode["species"]};
-                mode["cr"].user2 = {"max_energy_level" : getProperty(0,"energies0"), "gen" : 0,  "hibernated" : 0, "species" : mode["species"], "reproduce" : 0};
+                mode["cr"].user2 = {"max_energy_level" : getProperty(0,"energies0"), "gen" : 0,  "hibernated" : 0, "species" : mode["species"], "reproduce" : 0, "dir" : randomDir()};
         }
         else if (mode["opt"]  == 1) //child
         {
-                mode["cr"].user2 = {"max_energy_level" : getProperty(1 - mode["parent_user2"]["gen"],"energies0"), "gen" : 1 - mode["parent_user2"]["gen"],  "hibernated" : 0, "species" : mode["parent_user2"]["species"], "reproduce" : 0};
+                mode["cr"].user2 = {"max_energy_level" : getProperty(1 - mode["parent_user2"]["gen"],"energies0"), "gen" : 1 - mode["parent_user2"]["gen"],  "hibernated" : 0, "species" : mode["parent_user2"]["species"], "reproduce" : 0, "dir" : randomDir()};
                 mode["cr"].user1 = mode["parent_user1"];
         }

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

@@ -23 +23 @@
         GLDisplay.minfps = 10;
         TrackingCam.cam_h = 15; //more side view
-        Params = { "feedrate" : [0.05,0.1,0.2], "feedtrans" : [0.01,0.05,0.1],"energy_nut" :[0.5,1.5,3.0], "stress" : [0,1], "visualize" : [0,1]};
+        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]};
         ShowParams.visualize=1;
 }
@@ -30 +30 @@
 {
         //just a draft, this function and all constants in expdef need serious review
-        var foramSpeedMmPerMin=0.1; //0.1 mm/minute based on http://drs.nio.org/drs/bitstream/handle/2264/418/ONGC_Bull_37%281%29_53.pdf
-        var localDriveMicronsPerStep=framsToMicrons(0.08); //0.08 is used in expdef as distance (in frams units) per simulation step. TODO Use a variable/constant/function from expdef instead of copying this value here
-        var foramSpeedMmPerSec=foramSpeedMmPerMin/60;
+        var localDriveMicronsPerStep=framsToMicrons(getMovePerStep());
+        var foramSpeedMmPerSec=ExpParams.foramSpeedMmPerMin/60;
         var localDriveMmPerStep=localDriveMicronsPerStep/1000;
         var localDriveMmPerSec=localDriveMmPerStep*Simulator.simspeed;
@@ -93 +92 @@
 id:feedtrans
 name:Energy transfer
-type:d 0 2 1 ~0.01~0.05~0.1
+type:d 0 2 1 ~0.05~0.125~0.25
 
 prop: