03 MppLab V1.09
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;;-----------------------------------------------------------------------------| ;; SECTION A – AUTHOR IDENTIFICATION AND CODE ABSTRACT ;;-----------------------------------------------------------------------------| ;; ;; File Name: MppLab_V1.09.nlogo ;; By Orrery Software ;; Dated: 2017-03-25 ;; Author contact: ;; Garvin H Boyle ;; orrery@rogers.com ;; http://orrery-software.webs.com ;; As the author, I welcome questions, discussion of issues and suggestions ;; for improvements. ;;-----------------------------------------------------------------------------| ;; This MppLab app is a laboratory in which students can study aspects ;; of the Maximum Power Principle (MPP) of H.T. Odum. ;; Please note that there was one aspect of this model that has caused some ;; confusion when I explain it. So, I have modified the terminology within ;; the code and in the user interface, but the logic of the code has not ;; changed. The confusion arose from my "borrowing" of the mechanics of ;; Atwood's Machine (the AM) to model the chemistry of digestion. In ;; particular, I have invented a genetic factor that I am calling the ;; "genetic energy transfer factor", or getf for short. The logic ;; for doing so is as follows: ;; - Odum argued that the dynamics of the AM are a great example of the ;; trade-off between power and efficiency that is ubiquitous and a ;; fundamental characteristic of ALL energy transfers. He also argued that ;; all energy transfers take time, and that the MPP is the common time ;; regulator. ;; - I do not have empirical data for chemical digestion of one species by ;; another. In fact, to simulate a real-world trophic web, I would need data ;; for all species trying to digest all other species. And, for each such ;; potential transfer, I would need both efficiency and speed of all such ;; energy transfers. ;; - On the other hand, we have an exquisitely precise analytic description of ;; the energy transfer that happens in the AM, providing both efficiency and ;; power (rate of energy transfer), and implicit therein is the time required ;; to complete the transfer (called the drop time). ;; - So, I reasoned, I could emulate the efficiency and rate of energy transfer ;; of digestion using the analytic description of the AM. Since the mass of ;; the two components of the AM are the critical factors, I have inserted a ;; proxy for mass into all organisms, and I call that the genetic-energy- ;; transfer-factor (or getf). Whenever two organisms meet, I use their ;; respective getf values to determine (a) who is predator and who is prey; ;; (b) how long it takes for predator to digest prey; and (c) how much of the ;; consumed energy of the prey is turned to waste heat, and how much is ;; retained as "still-useful-energy" in the predator. ;; - This does not give me a simulation of any particular act of digestion, but ;; it does give me a template for emulation of all possible acts of digestion ;; (all possible efficiencies and powers) and thus allows me to investigate ;; the nature of real-world trophic webs. ;; So, to be clear, the concept of mass that we all know and understand as ;; playing a significant role in biology IS NOT EXPLICITLY USED ANYWHERE IN ;; THIS MODEL. ;; BUT, the ability of one organism to digest another organism is determined by ;; the interaction of the relative values of the getf factors. ;; AND, I use the mathematics of energy transfers that derives from the AM and ;; the masses therein to compute the effects of getf values when they ;; interact. ;; Mass in the AM is a proxy for getf in an organism, playing similar roles in ;; determining the dynamics of energetic interactions. ;;-----------------------------------------------------------------------------| ;; SECTION B – INITIAL DECLARATIONS OF GLOBALS AND BREEDS ;;-----------------------------------------------------------------------------| ;; ;;-----------------------------------------------------------------------------| ;; This program was developed on NetLogo Version 5.0.5 ;; ;;-----------------------------------------------------------------------------| ;; code-determined global variables globals [ ;; The version should be coded in this global variable to be included in ;; output files. gs-Version ;; Note: Some global variables are declared inside of switches, sliders and ;; choosers when the interface is constructed and are not declared here. ;; For the sake of clarity and completeness, they are noted here. ;; There are several uses of global variables: ;; - Toggles (switches), and choosers which enable or disable features; ;; - Numbers (in variables or sliders) which act as parameters; ;; - Numbers (in variables) which collect data. ;; ;; Those marked as 'native Boolean' have values of true or false. ;; Those marked as 'numeric Boolean' have values of 1 or 0. ;;--------------------- ;; MODELING ENVIRONMENT ;;--------------------- ;; Assumed “Model Settings” on startup ;; horizontal wrap: on ;; vertical wrap: on ;; location of origin: centre ;; patch size: 9.63 pixels ;;-----------------------------------------------------------------------------| ;; Implicit global variables due to model settings – patch locations ;; min-pxcor -15 ;; max-pxcor 15 ;; min-pycor -15 ;; max-pycor 15 ;;---------------------------- ;; SCENARIO SELECTION CONTROLS ;;---------------------------- ;; gs-scenario ;; Chooser, string converts to a scenario number g-scenario-number ;; scenario no., 0 or 1; interpretation of gs-scenario ;; The possible scenarios. ge-scenario-herbivores ;; scenario 0 ge-scenario-omnivores ;; scenario 1 ;; To halt a scenario at a pre-determined tick. ;; g-halt-at-tick ;; Has it's own input box ;; Initialize the Pseudo Random Number Generator (PRNG). ;; g-use-this-seed ;; Slider, ( 1 <= g-use-this-seed <= 100 ) ;;----------------------------------------------- ;; BIOPHYSICAL SUB-SYSTEM CONTROLS AND PARAMETERS ;;----------------------------------------------- ;; Atwood's Machine parameters (Sliders) ;; g-drop-distance ;; The distance a mass falls (D) in the AM. ;; g-acceleration ;; Acceleration due to gravity (g). ;; Biophyscial life function parameters, autotrophs. ;; g-a-target-population ;; The target carrying capacity [50, 10, 10000]. g-a-initial-getf ;; Initial getf (mass) of autotrophs on startup. ;; Biophyscial life function parameters, heterotrophs. gb-h-heterotrophs-on ;; Creates heterotrophs g-h-initial-getf ;; Initial getf (mass) of heterotrophs on startup. g-h-DAT ;; Death Age Threshold ;; g-h-RET-factor ;; Repreductive Energy Threshold Slider [0.1,0.01,1.0] ;; g-h-EPM-factor ;; Energy Per Move (expended) Slider [0,.0001,.1] ;; g-h-ub-upper-bound ;; Upper bound on the ub gene Slider [2,.1,20] ;; g-h-lb-lower-bound ;; lower bound on the lb gene Slider [1,.1,4] ;; g-h-initial-population ;; The number of heterotrophs deployed by button. ;; g-h-mutation-factor ;; delta-getf (delta-mass) Slider [0,.01,1] ;; g-h-satiation-factor ;; feeding trigger Slider [0,.01,1] ;; gb-h-ub-gene-active ;; Switch activates ub gene for prey selection. ;; gb-h-lb-gene-active ;; Switch activates lb gene for prey selection. ;; List to hold counts of cause of death. gl-causes-of-death-a-per-tick gl-causes-of-death-a-cumulative gl-causes-of-death-h-per-tick gl-causes-of-death-h-cumulative ;; Global enumeration (ge-) codes codes for cause of death. ge-cod-none ge-cod-hunger ge-cod-fission ge-cod-old-age ge-cod-as-prey ge-cod-toggled ;; List to hold counts of cause of birth. gl-causes-of-birth-a-per-tick gl-causes-of-birth-a-cumulative gl-causes-of-birth-h-per-tick gl-causes-of-birth-h-cumulative ;; Global enumeration (ge-) codes for cause of birth. ge-cob-generated ge-cob-fission ;; Control on type of participation in OAM (b-is-in-oam). ;; Global enumeration (ge-) codes for status in oam. ge-not-in-oam ;; Should be assigned a zero. ge-rh-hoam ;; Should be assigned a one. ge-lh-hoam ;; Should be assigned a two. ;;------------------------------------- ;; END OF MODEL PARAMETERS AND CONTROLS ;;------------------------------------- ;;------------------------------------- ;; DATA COLLECTION AND DISPLAY CONTROLS ;;------------------------------------- ;; The following global variables are not model controls or paramaters, ;; but, rather, are variables used to collect data about the model ;; for display in the user interface, in some fashion (monitors or plots), ;; or used to manage all of the debug routines and output. ;; SYSTEM-WIDE AGGREGATES ;; System of energy sinks. gl-sinks-per-tick gl-sinks-cumulative ;; Global enumeration (ge-) codes. ge-sinktype-source ;; Xrg in, from Sun, creation/injection of agents. ge-sinktype-unused-source ;; Unused after feeding. ge-sinktype-a-move ;; Autotrophs EPM ge-sinktype-h-move ;; Heterotrophs EPM ge-sinktype-a-fiss-exergy ;; 'Usable energy' transferred auto to D1/D2. ge-sinktype-h-fiss-exergy ;; 'Usable energy' transferred hetero to D1/D2. ge-sinktype-a-food-exergy ;; 'Usable energy' transferred auto to pred. ge-sinktype-h-food-exergy ;; 'Usable energy' transferred hetero to pred. ge-sinktype-a-food-excess ;; 'Excess food' exhausted by auto. ge-sinktype-h-food-excess ;; 'Excess food' exhausted by hetero. ge-sinktype-a-kinetic ;; 'Kinetic energy' exhausted by auto. ge-sinktype-h-kinetic ;; 'Kinetic energy' exhausted by hetero. ge-sinktype-a-die-fiss ;; Unused exergy of auto on fission. ge-sinktype-h-die-fiss ;; Unused exergy of hetero on fission. ge-sinktype-a-die-hunger ;; Remaining energy of auto on death. ge-sinktype-h-die-hunger ;; Remaining energy of hetero on death. ge-sinktype-a-die-oldage ;; Remaining energy of auto on death. ge-sinktype-h-die-oldage ;; Remaining energy of hetero on death. ge-sinktype-a-die-asprey ;; Remaining energy of auto on death. ge-sinktype-h-die-asprey ;; Remaining energy of hetero on death. ;;---------------------------------------------------------------------------| ;; The following agent sets, counts and averages are for data collection ;; and display in monitors and plots. ;; Agent sets ga-oams ;; Set of all turtles as lh-hoams ;; Counts g-no-of-autotrophs ;; count of all autotrophs g-no-of-heterotrophs ;; count of all heterotrophs g-no-of-oams ;; count of all Open Atwood Machines g-no-of-a-as-rh-hoams ;; count of all autotrophs in rh-hoams g-no-of-h-as-rh-hoams ;; count of all heterotrophs in rh-hoams ;; Averages g-a-ave-getf ;; getf (mass) of autotrophs g-a-ave-max-potential ;; max pot of autotrophs g-a-ave-cur-potential ;; current pot of autotrophs g-h-ave-age ;; age of heterotrophs g-h-ave-getf ;; getf (mass) of heterotrophs g-h-ave-lb-gene ;; gene controlling size of prey g-h-ave-ub-gene ;; gene controlling size of prey g-h-ave-RET ;; RET of heterotrophs g-h-ave-EPM ;; EPM of heterotrophs g-h-ave-max-potential ;; max pot of heterotrophs g-h-ave-cur-potential ;; current pot of heterotrophs g-h-ave-BITE-total ;; average bite of heterotrophs g-h-ave-BITE-xrg ;; portion to exergy g-h-ave-BITE-kinetic ;; portion to kinetic energy g-h-ave-Eu ;; Odum's efficiency of OAMs g-h-ave-max-dt ;; maximum drop time of OAMs g-h-ave-cur-dt ;; current drop time of OAMs g-h-ave-rem-dt ;; remaining drop time of OAMs g-h-ave-dt-ratio ;; ratio rem/max dt of OAMs ;; SWITCHES - These are declared in the switch itself, and so are ;; commented out here. They are all native Booleans, having values of ;; true or false. gb-stabilize-autotrophs ;; Enables additional autotrophs to be sprouted. ;; gb-plot-data ;; Enables plotting ;; Other - built-in or declared implicitly in plot interface items ;; See each plot design dialogue. ;;-------------------------- ;; DATA CAPTURE TO CSV FILES ;;-------------------------- ;; CSV means "Comma Separated Values" ;; ;;--------------- ;; DEBUG CONTROLS ;;--------------- gb-debug-on ;; Numeric Boolean, opens debug log file, 0 or 1. gs-debug-status ;; for monitor, '1 (On)' or '0 (Off)', ;; gs-debug-step-chooser ;; Chooser, used with gb-debug-flow-on gb-debug-flow-on ;; Numeric Boolean, in association with chooser, gs-log-file-name ;; name of the debug log file ;; opens flow to log file ] ;;-----------------------------------------------------------------------------| ;; Attributes of patches patches-own [ ;; BUILT-IN ATTRIBUTES ;; pxcor ;; min-pxcor <= pxcor < max-pxcor ;; pycor ;; min-pxcor <= pxcor < max-pxcor ;; pcolor ;; color of this patch ( 0 <= color < 140 ) ;; plabel ;; label of this patch ;; plabel-color ;; color of this patch's label ( 0 <= label-color < 140 ) ;; MppLab-DETERMINED ATTRIBUTES ;; Nil. ] ;;-----------------------------------------------------------------------------| ;; Attributes of links ;; nil ;; I don't understand links and did not use any. ;;-----------------------------------------------------------------------------| ;; Turtles and breeds breed [ autotrophs autotroph ] breed [ heterotrophs heterotroph ] ;;-----------------------------------------------------------------------------| ;; Attributes of autotrophs autotrophs-own [ ;; BUILT-IN ATTRIBUTES ;; who ;; fixed id number ;; breed ;; to which breed this turtle belongs [autotroph] ;; heading ;; 0 <= heading < 360, 0 = north ;; xcor ;; min-pxcor <= xcor < max-pxcor ;; ycor ;; min-pxcor <= xcor < max-pxcor ;; size ;; size relative to a patch, default is 1 ;; shape ;; a shape chosen from the shape library ;; color ;; color of this turtle ( 0 <= color < 140 ) ;; pen-mode ;; "up" or "down" ;; pen-size ;; in pixels ;; hidden? ;; true or false ;; label ;; label of this turtle ;; label-color ;; color of this turtle's label ( 0 <= label-color < 140 ) ;; USER-DETERMINED ATTRIBUTES ;; Associated with autotroph dynamics. mas-who ;; serial number of parent autotroph. default-colour ;; as it says ;; getf is short for genetic-energy-transfer-factor, proxy for mass in the AM. getf ;; the getf (mass) in this HOAM cause-of-death ;; for statistical purposes b-is-ready-to-die ;; old (in age) or starved (in exergy) ;; An autotroph can be unassociated, or in the role of prey in an OAM, ;; i.e. as an RH-HOAM. ;; Unassociated dynamics. max-potential ;; maximum potential energy cur-potential ;; amount of high-grade gravitational potential energy ;; Associated with RH-HOAM dynamics. b-is-in-oam ;; 0 = no; 1 = as RH-HOAM pred-who ;; the who number of the predator, i.e. the rh-haom trophic-level-floated ;; trophic level of this autotroph ] ;;-----------------------------------------------------------------------------| ;; Attributes of heterotrophs heterotrophs-own [ ;; BUILT-IN ATTRIBUTES ;; who ;; fixed id number ;; breed ;; to which breed this turtle belongs [heterotroph] ;; heading ;; 0 <= heading < 360, 0 = north ;; xcor ;; min-pxcor <= xcor < max-pxcor ;; ycor ;; min-pxcor <= xcor < max-pxcor ;; size ;; size relative to a patch, default is 1 ;; shape ;; a shape chosen from the shape library ;; color ;; color of this turtle ( 0 <= color < 140 ) ;; pen-mode ;; "up" or "down" ;; pen-size ;; in pixels ;; hidden? ;; true or false ;; label ;; label of this turtle ;; label-color ;; color of this turtle's label ( 0 <= label-color < 140 ) ;; USER-DETERMINED ATTRIBUTES ;; Associated with heterotroph. mas-who ;; serial number of parent heterotroph. heterotroph-sn ;; serial number of this heterotroph. age ;; age of this heterotroph default-colour ;; as it says ;; getf is short for genetic-energy-transfer-factor, proxy for mass in the AM. getf ;; the getf (mass) in this heterotroph lb-genetic-factor ;; gene to set lower bound on getf of prey. ub-genetic-factor ;; gene to set upper bound on getf of prey. cause-of-death ;; for statistical purposes RET ;; Reproductive Energy Threshold for this heterotroph EPM ;; Energy Per Move for this heterotroph b-is-ready-to-move ;; 0 = no; 1 = ready to move b-is-ready-to-reproduce ;; mature (in age) and healthy (in exergy) b-is-ready-to-die ;; old (in age) or starved (in exergy) ;; A heterotroph may be in a free-moving unassociated state (predator on the ;; hunt), in an OAM as an RH-HOAM (captured prey), or in an OAM as a ;; LH-HOAM (predatory eating prey). Variables are layed out here to address ;; four needs: ;; - unassociated heterotroph ;; - heterotroph in OAM as prey ;; - heterotroph in OAM as predator ;; - the OAM in which predator and prey are temporarily associated. ;; ;; Last two are used together. I.e. the OAM variables are stored in the ;; predator while the OAM exists. ;; Unassociated dynamics. max-potential cur-potential ;; amount of high-grade gravitational potential energy ;; Associated with OAM dynamics. b-is-in-oam ;; 0 = no; 1 = as RH-HOAM; 2 = as LH-HOAM prey-who ;; the who number of the prey, i.e. the rh-haom pred-who ;; the who number of the predator, i.e. the lh-hoam no-of-prey-eaten ;; the number of prey captured and eaten sum-of-t-plus-one ;; an aggregator for trophic level data trophic-level-floated ;; trophic level of this heterotroph trophic-level-rounded ;; trophic level of this heterotroph Eu-in-oam ;; Eu is H.T.Odum's efficiency (ML/MH) max-drop-time ;; Drop time for this OAM. cur-drop-time ;; Time since drop started. rem-drop-time ;; Remaining drop time. drop-time-ratio ;; Fraction of drop time remaining. ] ;;-----------------------------------------------------------------------------| ;; SECTION C – INITIALIZATION OR SETUP PROCEDURE( S ) ;;-----------------------------------------------------------------------------| ;;-----------------------------------------------------------------------------| ;; The 'autostart' startup routine to startup ;; This routine is to be executed by the observer. ;; The manual describes this routine as follows: ;; This procedure, if it exists, will be called when a model is first loaded in ;; the NetLogo application. Startup does not run when a model is run headless ;; from the command line, or by parallel BehaviorSpace. ;; On loading the model, the debug feature is always off. set gb-debug-on 0 set gs-debug-status "0 (Off)" ;; On loading the model, the model, the choosers, switches and sliders are ;; always reset to the values that are known to work. Only the chooser ;; for the scenario is not reset. The last saved ;; selection of scenario is persistant. This allows the 'Reset Defaults' ;; button to NOT reset the scenario. f-reset-default-parameters ;; Run the setup routine to initialize other globals. setup end ;;-----------------------------------------------------------------------------| ;; The setup button(s) to setup ;; This routine is to be executed by the observer. ;; NOTE: The contents of switches, sliders, and choosers seem to be ;; immune to these 'clear' commands. clear-ticks clear-turtles clear-patches clear-drawing clear-all-plots clear-output ;; clear-globals ;; Suppressed to make gb-debug-on value persistent. ;; NOTE: Instead of 'clear-globals', you must ensure all globals are ;; initialized properly in 'setup'. ;; import-drawing "01-B OrrSW.jpg" ;; The version should be coded in this global variable to be included in ;; output files. set gs-Version "MppLab_V1.09" ;; Debug features may be off or on depending on history. ;; - Perhaps 'Setup' was called by 'to Startup'. ;; - Perhaps 'setup' was called during a 'BehaviorSpace' run. ;; - Perhaps 'setup' was called by a user-pushed 'setup' button. ;; Setup needs to handle some quasi-persistant values correctly regardless of ;; the history. For gb-debug-on, in particular, I want it to be ;; persistant so I can have debug output from the 'setup' routine routed ;; to the debug log file, or to the command centre. ;; 'startup' automatically sets gb-debug-on to 0 when the application is first ;; loaded. I want to be able to (A) toggle debug on, then, (B) press ;; 'setup' and watch the debug output of the 'setup' command. The gb-debug-on ;; must be persistant through the above 'clear' commands. The debug log ;; file name and status, however, should not be persistent and must be ;; reset when setup runs, if appropriate. ifelse ( gb-debug-on = 1 ) [ ;; Debug is on due to user setting, so file name and status should be ;; reset. I do this by turn the feature off then on. ;; First toggle it off, closing any remnant log file, if needed. f-toggle-debug ;; Then toggle it back on, opening a new time-stamped log file. f-toggle-debug ] ;; else [ ;; Debug is off, possibly due to startup execution, possibly due to user ;; choice. ;; Ensure associated variables have compatible settings. set gb-debug-on 0 ;; Redundant but ensures consistency. set gs-debug-status "0 (Off)" ;; Redundant but ensures consistency. set gb-debug-flow-on 0 ;; Step-specific flow is off. file-close-all ;; Close the debug log file. set gs-log-file-name "dummyname" ] ;; Now, do the standard check that is done at the start of each debuggable ;; routine. This must follow the clear commands, which reset everything ;; except globals, switches, sliders and choosers. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "setup" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-setup: Debug on; tick = " 0 ] [ set gb-debug-flow-on 0 ] ] ;; g-use-this-seed comes from a slider, and is persistant. random-seed g-use-this-seed ;; Tells the PRNG to use this seed. ;; Declare values of hidden declarations from sliders. LOG-TO-FILE ( "" ) LOG-TO-FILE ( " Do-set: ATWOOD MACHINE PARAMETERS (Sliders):" ) LOG-TO-FILE ( word " Do-set: g-drop-distance - " g-drop-distance ) LOG-TO-FILE ( word " Do-set: g-acceleration - " g-acceleration ) LOG-TO-FILE ( "" ) LOG-TO-FILE ( " Do-set: AUTOTROPH POPULATION PARAMETERS (Sliders):" ) LOG-TO-FILE ( word " Do-set: g-a-target-population - " g-a-target-population ) LOG-TO-FILE ( "" ) ;; Biophysical life function parameters, autotrophs. set g-a-initial-getf 128 ;; Initial getf (mass) of autotrophs on startup. ;; g-a-target-population ;; The target carrying capacity [50, 10, 10000]. LOG-TO-FILE ( " Do-set: INTERNAL AUTOTROPH PARAMETERS:" ) LOG-TO-FILE ( word " Do-set: g-a-initial-getf - " g-a-initial-getf ) LOG-TO-FILE ( "" ) LOG-TO-FILE ( " Do-set: HETEROTROPH POPULATION PARAMETERS:" ) ;; Biophysical life function parameters, autotrophs. set g-h-initial-getf 100 ;; Initial getf (mass) of heterotrophs on startup. ;; Biophysical life function parameters, heterotrophs. set g-h-DAT 1600 ;; Death Age Threshold ;; g-h-mutation-factor ;; delta-getf (delta-mass); Slider [0,.01,1] ;; g-h-satiation-factor ;; feeding trigger; Slider [0,.01,1] ;; g-h-ub-upper-bound ;; Upper bound on the ub gene; Slider [2,.1,20] ;; g-h-lb-lower-bound ;; lower bound on the lb gene; Slider [1,.1,4] LOG-TO-FILE ( word " Do-set: g-h-initial-population - " g-h-initial-population ) LOG-TO-FILE ( word " Do-set: g-h-initial-getf - " g-h-initial-getf ) LOG-TO-FILE ( word " Do-set: g-h-DAT - " g-h-DAT ) LOG-TO-FILE ( word " Do-set: g-h-mutation-factor - " g-h-mutation-factor ) LOG-TO-FILE ( word " Do-set: g-h-satiation-factor - " g-h-satiation-factor ) LOG-TO-FILE ( word " Do-set: g-h-ub-upper-bound - " g-h-ub-upper-bound ) LOG-TO-FILE ( word " Do-set: g-h-lb-lower-bound - " g-h-lb-lower-bound ) ;; List to hold counts of cause of death. set gl-causes-of-death-a-per-tick ( n-values 6 [0] ) set gl-causes-of-death-a-cumulative ( n-values 6 [0] ) set gl-causes-of-death-h-per-tick ( n-values 6 [0] ) set gl-causes-of-death-h-cumulative ( n-values 6 [0] ) ;; Enumeration codes for cause of death. set ge-cod-none 0 set ge-cod-hunger 1 set ge-cod-fission 2 set ge-cod-old-age 3 set ge-cod-as-prey 4 set ge-cod-toggled 5 ;; List to hold counts of cause of birth. set gl-causes-of-birth-a-per-tick ( n-values 2 [0] ) set gl-causes-of-birth-a-cumulative ( n-values 2 [0] ) set gl-causes-of-birth-h-per-tick ( n-values 2 [0] ) set gl-causes-of-birth-h-cumulative ( n-values 2 [0] ) ;; Enumeration codes for cause of birth. set ge-cob-generated 0 set ge-cob-fission 1 ;; Control on type of participation in OAM (b-is-in-oam). ;; These are enumeration values, having no meaning beyond the name. set ge-not-in-oam 0 ;; Should be assigned a zero. set ge-rh-hoam 1 ;; Should be assigned a one. set ge-lh-hoam 2 ;; Should be assigned a two. ;; System of energy sinks. set gl-sinks-per-tick ( n-values 20 [0] ) set gl-sinks-cumulative ( n-values 20 [0] ) ;; Global enumeration (ge-) variables. set ge-sinktype-source 0 ;; Xrg in, from Sun, creation/injection of agents. set ge-sinktype-unused-source 1 ;; Unused after feeding. set ge-sinktype-a-move 2 ;; Autotrophs EPM set ge-sinktype-h-move 3 ;; Heterotrophs EPM set ge-sinktype-a-fiss-exergy 4 ;; 'Usable energy' transferred auto to D1/D2. set ge-sinktype-h-fiss-exergy 5 ;; 'Usable energy' transferred hetero to D1/D2. set ge-sinktype-a-food-exergy 6 ;; 'Usable energy' transferred auto to pred. set ge-sinktype-h-food-exergy 7 ;; 'Usable energy' transferred hetero to pred. set ge-sinktype-a-food-excess 8 ;; 'Excess food' transferred auto to pred. set ge-sinktype-h-food-excess 9 ;; 'Excess food' transferred hetero to pred. set ge-sinktype-a-kinetic 10 ;; 'Kinetic energy' exhausted by auto. set ge-sinktype-h-kinetic 11 ;; 'Kinetic energy' exhausted by hetero. set ge-sinktype-a-die-fiss 12 ;; Unused exergy of auto on fission. set ge-sinktype-h-die-fiss 13 ;; Unused exergy of hetero on fission. set ge-sinktype-a-die-hunger 14 ;; Remaining energy of auto on death. set ge-sinktype-h-die-hunger 15 ;; Remaining energy of hetero on death. set ge-sinktype-a-die-oldage 16 ;; Remaining energy of auto on death. set ge-sinktype-h-die-oldage 17 ;; Remaining energy of hetero on death. set ge-sinktype-a-die-asprey 18 ;; Remaining energy of auto on death. set ge-sinktype-h-die-asprey 19 ;; Remaining energy of hetero on death. ;;---------------------------------------------------------------------------| ;; The following agent sets, counts and averages are for data collection ;; and display in monitors and plots. ;; Agent sets set ga-oams turtles ;; Set of all turtles as lh-hoams ;; Counts set g-no-of-autotrophs 0 ;; count of all autotrophs set g-no-of-heterotrophs 0 ;; count of all heterotrophs set g-no-of-oams 0 ;; count of all Open Atwood Machines set g-no-of-a-as-rh-hoams 0 ;; count of all autotrophs in rh-hoams set g-no-of-h-as-rh-hoams 0 ;; count of all heterotrophs in rh-hoams ;; Averages - autotrophs set g-a-ave-getf 0 ;; getf (mass) of autotrophs set g-a-ave-max-potential 0 ;; max pot of autotrophs set g-a-ave-cur-potential 0 ;; current pot of autotrophs ;; Averages - heterotrophs set g-h-ave-age 0 ;; age of heterotrophs set g-h-ave-getf 0 ;; getf (mass) of heterotrophs set g-h-ave-lb-gene 0 ;; gene controlling size of prey set g-h-ave-ub-gene 0 ;; gene controlling size of prey set g-h-ave-RET 0 ;; RET of heterotrophs set g-h-ave-EPM 0 ;; EPM of heterotrophs set g-h-ave-max-potential 0 ;; max pot of heterotrophs set g-h-ave-cur-potential 0 ;; current pot of heterotrophs set g-h-ave-BITE-total 0 ;; average bite of heterotrophs set g-h-ave-BITE-xrg 0 ;; portion to exergy set g-h-ave-BITE-kinetic 0 ;; portion to kinetic energy ;; Averages - OAMs set g-h-ave-Eu 0 ;; Odum's efficiency of OAMs set g-h-ave-max-dt 0 ;; maximum drop time of OAMs set g-h-ave-cur-dt 0 ;; current drop time of OAMs set g-h-ave-rem-dt 0 ;; remaining drop time of OAMs set g-h-ave-dt-ratio 0 ;; ratio rem/max dt of OAMs ;; There are 3 scenarios possible set ge-scenario-herbivores 0 ;; Heterotrophs eat autotrophs set ge-scenario-omnivores 1 ;; Heterotrophs eat anything ;; Use the input from the chooser gs-scenario to invoke the selected scenario. f-set-scenario-number ;; For debugging the setup procedure, log the values of the globals. LOG-TO-FILE ( word " Do-set: Scenario number - " g-scenario-number ) LOG-TO-FILE ( word " Do-set: Scenario name - " gs-scenario ) LOG-TO-FILE ( word " Do-set: Random seed - " g-use-this-seed ) ;; For debugging the debug feature!!! Suppressed now. ;; show ( word "SETUP: Debug Is " gb-debug-on ) ;; show ( word "SETUP: Debug Status Is " gs-debug-status ) ;; show ( word "SETUP: Step Chooser Is " gs-debug-step-chooser ) ;; show ( word "SETUP: Flow Control Is " gb-debug-flow-on ) set-default-shape autotrophs "flower" ;; pulled from shapes library set-default-shape heterotrophs "arrow" ;; pulled from shapes library ask patches [ set pcolor brown ] reset-ticks ;; restarts tick counter and runs setup commands within plots ;; Set the switches to default setup values. set gb-plot-data true ;; Enables all plotting calls. set gb-stabilize-autotrophs true ;; Enables autotroph stabilization. set gb-h-heterotrophs-on 1 ;; Enables heterotrophs. set gb-h-ub-gene-active true ;; Activates ub gene for prey selection. set gb-h-lb-gene-active true ;; Activates lb gene for prey selection. if( g-scenario-number = ge-scenario-herbivores ) [ set gb-plot-data true ;; Enables all plotting calls. set gb-stabilize-autotrophs true ;; Enables autotroph stabilization. set gb-h-heterotrophs-on 1 ;; Enables heterotrophs. set gb-h-ub-gene-active true ;; Activates ub gene for prey selection. set gb-h-lb-gene-active true ;; Activates lb gene for prey selection. ] if( g-scenario-number = ge-scenario-omnivores ) [ set gb-plot-data true ;; Enables all plotting calls. set gb-stabilize-autotrophs true ;; Enables autotroph stabilization. set gb-h-heterotrophs-on 1 ;; Enables heterotrophs. set gb-h-ub-gene-active true ;; Activates ub gene for prey selection. set gb-h-lb-gene-active true ;; Activates lb gene for prey selection. ] f-initialize-autotrophs if( gb-h-heterotrophs-on = 1 ) [ f-initialize-heterotrophs ] ;; This call requires that 'reset-ticks' be called first. ;; Update the aggregates again, after energetics computed. f-update-aggregates ;; Totals and averages. ;; Clears unwanted zeros in plots. clear-all-plots setup-plots ;; Debug controls set gb-debug-flow-on 0 ;; Boolean, in association with chooser, turns debug LOG-TO-FILE on/off set g-halt-at-tick -1 ;; input variable to set a tick for stopping ;; ASSERT ( frb-EMgr-is-valid ) ( "EMgr validity check: D-Setup" ) -1 LOG-TO-FILE " Do-set: procedure completed" ;; end of to-setup end ;;-----------------------------------------------------------------------------| ;; Set the scenario number using the input from the chooser. to f-set-scenario-number ;; This routine is to be executed by the observer. set g-scenario-number ge-scenario-herbivores ;; default if( gs-scenario = "Omnivores" ) [ set g-scenario-number ge-scenario-omnivores ] ;; End f-set-scenario-number end ;;-----------------------------------------------------------------------------| ;; Initialize a population of autotrophs. to f-initialize-autotrophs ;; This routine is to be executed by the observer. create-autotrophs g-a-target-population [ f-initialize-new-autotroph set heading 0 ;; Stagger the amount of high-grade exergy from a ;; half load to a full load. let exergy floor( max-potential / 2 ) set cur-potential ( exergy + ( random exergy ) ) ;; Move each to a random point. setxy random-xcor random-ycor f-store-data-in-sink ge-sinktype-source cur-potential f-increment-cob-list breed ge-cob-generated ] ;; End f-initialize-autotrophs end ;;-----------------------------------------------------------------------------| ;; Initialize a single autotroph. to f-initialize-new-autotroph ;; This routine is to be executed by a autotroph. ;; BUILT-IN ATTRIBUTES ;; who ;; set automatically set heading 0 ;; direction of motion ;; xcor ;; min-pxcor <= xcor < max-pxcor ;; ycor ;; min-pxcor <= xcor < max-pxcor ;; pen-mode ;; "up" or "down" ;; pen-size ;; in pixels ;; size ;; size relative to a patch, default is 1 set color green ;; USER-DETERMINED ATTRIBUTES ;; Associated with autotroph dynamics. set mas-who -1 ;; serial number of parent autotroph set default-colour green ;; distinctive colour for autotrophs set getf g-a-initial-getf ;; the getf (mass) in this autotroph set cause-of-death ge-cod-none ;; for statistical purposes set b-is-ready-to-die 0 ;; old (in age) or starved (in exergy) ;; Recalculate the life function controls that are scaled to getf (mass). f-set-getf-derived-autotroph-characters ;; An autotroph can only be in the role of prey, i.e. RH-HOAM. set b-is-in-oam ge-not-in-oam ;; 0 = no; 1 = RH-HOAM set pred-who -1 ;; who number of predator haom. set trophic-level-floated 0 ;; trophic level of this autotroph ;; end f-initialize-new-autotroph end ;;-----------------------------------------------------------------------------| ;; Calculate all of the control variables that derive from getf. to f-set-getf-derived-autotroph-characters ;; This routine is to be executed by an autotroph. ;; getf is the genetic-energy-transfer-factor. In Atwood's Machine (the AM) ;; the mass of the two weights determine this. In organisms, some aspect ;; of the composition of the prey and the digestive system of the predator ;; determines this. E.g. Panda bears and bamboo go together well, but ;; panda bears and eucalyptis leaves do not. I call this the getf. ;; I use the mechanics of the AM to emulate the chemistry of digestion. This ;; affects both efficiency and duration of energy transfer. set max-potential ( getf * g-acceleration * g-drop-distance ) LOG-TO-FILE ( word " Do-pre-tick: A(max-xrg) - (" floor max-potential ")" ) ;; End of f-set-getf-derived-autotroph-characters end ;;-----------------------------------------------------------------------------| ;; Initialize a population of heterotrophs. to f-initialize-heterotrophs ;; This routine is to be executed by the observer. create-heterotrophs g-h-initial-population [ f-initialize-new-heterotroph let heading-list [ 0 45 90 135 180 225 270 315 ] let delta-heading 0 set delta-heading ( item ( random 8 ) heading-list ) set heading ( heading + delta-heading ) set age ( random g-h-DAT ) ;; Stagger the amount of high-grade exergy from a ;; half load to a full load. let exergy floor( max-potential / 2 ) set cur-potential ( exergy + ( random exergy ) ) f-store-data-in-sink ge-sinktype-source cur-potential f-increment-cob-list breed ge-cob-generated ;; Make one step forward - well back from prey, giving them a head start. forward 1 ] ;; End f-initialize-heterotrophs end ;;-----------------------------------------------------------------------------| ;; Initialize a single heterotroph. to f-initialize-new-heterotroph ;; This routine is to be executed by a heterotroph. ;; BUILT-IN ATTRIBUTES ;; who ;; set automatically set heading 0 ;; xcor ;; min-pxcor <= xcor < max-pxcor ;; ycor ;; min-pxcor <= xcor < max-pxcor ;; pen-mode ;; "up" or "down" ;; pen-size ;; in pixels ;; size ;; size relative to a patch, default is 1 set color red ;; USER-DETERMINED ATTRIBUTES ;; Associated with heterotroph. set mas-who -1 ;; serial number of parent heterotroph set age 0 ;; age of this heterotroph set default-colour red ;; distinctive colour for heterotrophs set getf g-h-initial-getf ;; the getf (mass) in this heterotroph. set lb-genetic-factor g-h-lb-lower-bound ;; lower bound on prey getf (mass). set ub-genetic-factor g-h-ub-upper-bound ;; upper bound on prey getf (mass). set cause-of-death ge-cod-none ;; for statistical purposes ;; Compute value of controls scaled to getf (scaled to mass). f-set-getf-derived-heterotroph-characters ;; Set the logic trigger flags. set b-is-ready-to-move 1 ;; i.e. true set b-is-ready-to-reproduce 0 ;; i.e. false set b-is-ready-to-die 0 ;; i.e. false ;; Unassociated dynamics. set max-potential ( getf * g-acceleration * g-drop-distance ) set cur-potential 0 ;; amount of gravitational potential energy ;; Associated with OAM dynamics. set b-is-in-oam ge-not-in-oam ;; 0=no; 1=RH-HOAM; 2=LH-HOAM ;; Associated with OAM dynamics. ;; These contain data for the OAM consisting of coupled predator/prey. set prey-who -1 ;; an invalid value; who number of prey haom. set pred-who -1 ;; an invalid value; who number of predator haom. set no-of-prey-eaten 0 ;; the number of prey captured and eaten set sum-of-t-plus-one 0 ;; an aggregator for trophic level data set trophic-level-floated 1 ;; trophic level of this heterotroph set trophic-level-rounded 1 ;; trophic level of this heterotroph set Eu-in-oam 1 ;; Eu is Odum's efficiency. set max-drop-time 0 ;; Drop time for this OAM. set cur-drop-time 0 ;; Time since drop started. set rem-drop-time 0 ;; Remaining drop time. set drop-time-ratio 0 ;; Fraction of drop time remaining. ;; end f-initialize-new-heterotroph end ;;-----------------------------------------------------------------------------| ;; Calculate all of the control variables that derive from getf (mass). to f-set-getf-derived-heterotroph-characters ;; This routine is to be executed by a heterotroph. ;; getf is the genetic-energy-transfer-factor. In Atwood's Machine (the AM) ;; the mass of the two weights determine this. In organisms, some aspect ;; of the composition of the prey and the digestive system of the predator ;; determines this. E.g. Panda bears and bamboo go together well, but ;; panda bears and eucalyptis leaves do not. I call this the getf. ;; I use the mechanics of the AM to emulate the chemistry of digestion. This ;; affects both efficiency and duration of energy transfer. set max-potential ( getf * g-acceleration * g-drop-distance ) set RET ( g-h-RET-factor * max-potential ) ;; Reproductive Energy Threshold set EPM ( g-h-EPM-factor * max-potential ) ;; Energy Per Move LOG-TO-FILE ( word " Do-xxx: H(max-xrg,RET,EPM) - (" floor max-potential "," floor RET "," floor EPM ")" ) ;; End of f-set-getf-derived-heterotroph-characters end ;;-----------------------------------------------------------------------------| ;; Reset the default values for the interface-declared items. to f-reset-default-parameters ;; The observer executes this routine. ;; Switches, sliders and choosers implicitly declare global variables. The ;; values in these variables are parameters for the model, and many ;; combinations of those parameters are not sustainable. However, the ;; values in those user interface devices are stored with the model and ;; are persistant across a save/load action. The default values must ;; be reset on load, or available to a user as a parameter set. The ;; purpose of this routine is to store at least one viable set of ;; parameter values. ;; Initialize the Pseudo Random Number Generator (PRNG). set g-use-this-seed 7 ;; Restore the values of the lb and ub switches. set gb-h-ub-gene-active true set gb-h-lb-gene-active true ;;----------------------------------------------- ;; BIOPHYSICAL SUB-SYSTEM CONTROLS AND PARAMETERS ;;----------------------------------------------- ;; Slider range settings are shown as (Min,Increment,Max) set g-drop-distance 100 ;; ( 50, 5, 200 ) meters set g-acceleration 1 ;; ( 1, 0.10, 12 ) m/s/s set g-a-target-population 500 ;; Target carrying capacity (50, 10, 10000). set g-h-initial-population 100 ;; # of heterotrophs (10,1,100) heterotrophs set g-h-RET-factor 0.95 ;; ( 0.10, 0.01, 1.00 ) Joules/Joule ifelse( g-scenario-number = ge-scenario-herbivores ) [ set g-h-EPM-factor 0.0050 ;; ( 0.00, 0.0001, 0.10 ) Joules/Joule ] ;; Else [ set g-h-EPM-factor 0.0125 ;; ( 0.00, 0.0001, 0.10 ) Joules/Joule ] set g-h-mutation-factor 0.10 ;; delta-getf; Slider (0,0.01,1) set g-h-satiation-factor 0.98 ;; feeding trigger; Slider (0,0.01,1) ;; NOTE: The satiation-factor must be greater than the RET-factor. set g-h-ub-upper-bound 4 ;; Upper bound on the ub gene; Slider (2,0.1,20) set g-h-lb-lower-bound 1 ;; lower bound on the lb gene; Slider (1,0.1,4) end ;;-----------------------------------------------------------------------------| ;; SECTION D – GO OR MAIN-LOOP PROCEDURE( S ) ;;-----------------------------------------------------------------------------| ;;-----------------------------------------------------------------------------| ;; The go button to go ;; This routine is to be executed by the observer. ;; Stop codes: ;; All stop decisions must be here in the 'go' procedure, as it causes an ;; exit from the current procdure only. if( g-halt-at-tick = ticks ) [ set g-halt-at-tick -1 stop ] let b-should-stop-now false if( count turtles <= 0 ) [ set b-should-stop-now true ] if( b-should-stop-now = true ) [ stop ] ;; MANUAL CHANGE FOR DEBUG ;; If needed, each check for validity can be enabled between steps. ;; They have been suppressed (turned into comments) for the sake ;; of speed of execution, but can be re-enabled if a bug has ;; somehow been re-introduced. ;; A single call to the validity check has been left active inside of the ;; Do-Post-Tick step. If it flags a problem, re-activate these to ;; narrow down where the problem starts. ;; Major steps or functions, done once per tick, in order of execution. do-pre-tick ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-pre-tick." ) ] do-move ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-move." ) ] do-feed ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: do-feed." ) ] do-reproduce ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-reproduce." ) ] do-die ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-die." ) ] do-post-tick ;; if( frb-agents-are-all-valid = false ) ;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-post-tick." ) ] end ;;-----------------------------------------------------------------------------| ;; D1 - do-pre-tick procedure( s ) ;;-----------------------------------------------------------------------------| to do-pre-tick ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "pre-tick" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-pre-tick: Debug on.; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; Enter all commands that need to be done before a tick begins. ;; Supressed. f-update-aggregates ;; Advance the tick counter by 1 tick. ifelse( gb-plot-data = true ) [ ;; Advance the ticks by one and update the plots. tick ;; 'tick' is exactly the same as 'update-plots' except that the tick counter ;; is incremented before the plot commands are executed. ] ;; else [ ;; Advance ticks by one but do not update the plots. tick-advance 1 ] ;; End else ;; Once the data is plotted, the per-tick counts can be cleared. ;; List to hold counts of cause of death. set gl-causes-of-death-a-per-tick ( n-values 6 [0] ) set gl-causes-of-death-h-per-tick ( n-values 6 [0] ) ;; List to hold counts of cause of birth. set gl-causes-of-birth-a-per-tick ( n-values 2 [0] ) set gl-causes-of-birth-h-per-tick ( n-values 2 [0] ) ;; Reset the scenario number, in case the chooser has been changed. f-set-scenario-number ;; Clear the per-tick data for energy sinks. ;; This call must happen before the autotroph population is stabilized. set gl-sinks-per-tick ( n-values 20 [0] ) ;; Stabilize the autotroph population at the target population size. f-stabilize-autotroph-population ;; Re-set g-h-satiation-factor in case g-h-RET-factor has changed. ;; Hunger must set in at or above the cost of reproduction. if( g-h-satiation-factor < g-h-RET-factor ) [ set g-h-satiation-factor ( 0.01 + precision g-h-RET-factor 2 ) ] if( g-h-satiation-factor >= 0.99 ) [ set g-h-satiation-factor 0.99 set g-h-RET-factor 0.98 ] if( gb-h-heterotrophs-on = 1 ) [ ask heterotrophs [ set age ( age + 1 ) ] LOG-TO-FILE ( word " Do-pre-tick: heterotrophs aged." ) ] LOG-TO-FILE ( word " Do-pre-tick: Halt at tick - " g-halt-at-tick ) LOG-TO-FILE ( word " Do-pre-tick: Current tick - " ticks ) LOG-TO-FILE " Do-pre-tick: Routine completed." end ;;-----------------------------------------------------------------------------| ;; Stabilize the autotroph population ;;-----------------------------------------------------------------------------| to f-stabilize-autotroph-population ;; This routine is to be executed by the observer. if( gb-stabilize-autotrophs = true ) [ let current-a-population ( count autotrophs ) if( current-a-population < g-a-target-population ) [ let add-this-many ( g-a-target-population - current-a-population ) let this-patch patch 0 0 ask this-patch [ sprout-autotrophs add-this-many [ f-initialize-new-autotroph set heading 0 ;; Set the amount of high-grade exergy at a full load. set cur-potential max-potential ;; Move each to a random point. setxy random-xcor random-ycor f-store-data-in-sink ge-sinktype-source cur-potential f-increment-cob-list breed ge-cob-generated ] ] ] ] ;; End f-stabilize-autotroph-population end ;;-----------------------------------------------------------------------------| ;; D2 – do-move procedure(s) ;;-----------------------------------------------------------------------------| to do-move ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "move" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-move: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; Implement 'arrow' behaviour from PSoup application. I.e. a strong ;; probability of movement directly forward, and small probability of a ;; slight turn. This represents the most effective search pattern for ;; an arena that is wrapped on all sides. Of course, it doesn't matter for ;; the autotrophs that get energy from the sun, but it will matter ;; for the heterotrophs. let heading-list [ -45 0 0 0 0 0 0 0 0 45 ] ;; Autotrophs are plants, and normally would not move, but I don't want ;; bias to leak in due to plants being stationary. In order to ensure that ;; plants are equally accessible to all heterotrophs regardless of their ;; parentage or location of birth I want them to roam far from parents and ;; circumstances of birth. They must be independently discovered and eaten. ;; Then the heterotrophs move. if( gb-h-heterotrophs-on = 1 ) [ ;; Heterotrophs move later. Same 'arrow' search pattern. ask heterotrophs [ if( b-is-ready-to-move = 1 ) [ let delta-heading ( item ( random length heading-list ) heading-list ) set heading ( heading + delta-heading ) forward 1 ;; The heterotroph converts some exergy to waste kinetic energy as it moves. f-heterotroph-expends-EPM ] ;; End if( b-is-ready-to-move = 1 ) ] ;; End ask autotrophs ;; A heterotroph which is acting as lh-hoam (predator, eating) does not move ;; but nevertheless expends energy on life functions. let feeding-predator-agentset ( heterotrophs with [b-is-in-oam = ge-lh-hoam] ) if( count feeding-predator-agentset > 0 ) [ ask feeding-predator-agentset [ ;; Exact the price of living from this predator. ;; The heterotroph converts some exergy to waste kinetic energy as it moves. f-heterotroph-expends-EPM ] ;; End ask feeding-predator-agentset ] ;; End if( count feeding-predator-agentset > 0 ) ] ;; End if( gb-h-heterotrophs-on = 1 ) ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-move: procedure completed" end ;;-----------------------------------------------------------------------------| ;; A heterotroph expends EPM of energy from the appropriate pool to the sink. to f-heterotroph-expends-EPM ;; This routine is to be executed by a heterotroph. if( ( b-is-in-oam = ge-not-in-oam ) or ( b-is-in-oam = ge-lh-hoam ) ) [ ;; When a heterotroph moves it expends energy out of the pool of exergy. ;; Determine if this heterotroph has sufficient energy. ifelse ( cur-potential >= EPM ) [ f-store-data-in-sink ge-sinktype-h-move EPM set cur-potential ( cur-potential - EPM ) ] ;; Else [ f-store-data-in-sink ge-sinktype-h-move cur-potential set cur-potential 0 set cause-of-death ge-cod-hunger ] ;; End else LOG-TO-FILE ( word " Do-move: H(heading,xrg,die-flag) - (" heading "," floor cur-potential "," b-is-ready-to-die ")" ) ] if( b-is-in-oam = ge-rh-hoam ) [ ;; When a heterotroph is associated with a heterotroph as prey in an OAM ;; then it expends energy out of the "rh" pool of exergy (-una-). ;; This would only take action in parasite mode. ;; - In predator mode the autotroph is not able to move or function, ;; and essentially behaves as dead until all of the exergy is removed. ;; this is the dedault mode. ;; - In parasite mode the autotroph is not able to move, but still functions ;; and expends exergy during each move. ;; TODO: Leave empty until parasite mode implemented. ] ;; End of f-heterotroph-expends-EPM end ;;-----------------------------------------------------------------------------| ;; Store data in the lists of sinks. to f-store-data-in-sink [ sinktype value ] ;; This routine is to be executed by anyone. ;; Record it in the per-tick list. let old-value ( item sinktype gl-sinks-per-tick ) let new-value ( old-value + value ) set gl-sinks-per-tick ( replace-item sinktype gl-sinks-per-tick new-value ) ;; Record it in the cumulative list. set old-value ( item sinktype gl-sinks-cumulative ) set new-value ( old-value + value ) set gl-sinks-cumulative ( replace-item sinktype gl-sinks-cumulative new-value ) end ;;-----------------------------------------------------------------------------| ;; Increment the count in the lists of causes of death. to f-increment-cod-list [ breedtype codtype ] ;; This routine is to be executed by anyone. ifelse( breedtype = autotrophs ) [ ;; Record it in the per-tick list. let old-count ( item codtype gl-causes-of-death-a-per-tick ) let new-count ( old-count + 1 ) set gl-causes-of-death-a-per-tick ( replace-item codtype gl-causes-of-death-a-per-tick new-count ) ;; Record it in the cumulative list. set old-count ( item codtype gl-causes-of-death-a-cumulative ) set new-count ( old-count + 1 ) set gl-causes-of-death-a-cumulative ( replace-item codtype gl-causes-of-death-a-cumulative new-count ) ] ;; Else breed is heterotrophs [ ;; Record it in the per-tick list. let old-count ( item codtype gl-causes-of-death-h-per-tick ) let new-count ( old-count + 1 ) set gl-causes-of-death-h-per-tick ( replace-item codtype gl-causes-of-death-h-per-tick new-count ) ;; Record it in the cumulative list. set old-count ( item codtype gl-causes-of-death-h-cumulative ) set new-count ( old-count + 1 ) set gl-causes-of-death-h-cumulative ( replace-item codtype gl-causes-of-death-h-cumulative new-count ) ] ;; End else end ;;-----------------------------------------------------------------------------| ;; Increment the count in the lists of causes of birth. to f-increment-cob-list [ breedtype cobtype ] ;; This routine is to be executed by anyone. ifelse( breedtype = autotrophs ) [ ;; show cobtype ;; Record it in the per-tick list. let old-count ( item cobtype gl-causes-of-birth-a-per-tick ) let new-count ( old-count + 1 ) set gl-causes-of-birth-a-per-tick ( replace-item cobtype gl-causes-of-birth-a-per-tick new-count ) ;; Record it in the cumulative list. set old-count ( item cobtype gl-causes-of-birth-a-cumulative ) set new-count ( old-count + 1 ) set gl-causes-of-birth-a-cumulative ( replace-item cobtype gl-causes-of-birth-a-cumulative new-count ) ] ;; Else breed is heterotrophs [ ;; Record it in the per-tick list. let old-count ( item cobtype gl-causes-of-birth-h-per-tick ) let new-count ( old-count + 1 ) set gl-causes-of-birth-h-per-tick ( replace-item cobtype gl-causes-of-birth-h-per-tick new-count ) ;; Record it in the cumulative list. set old-count ( item cobtype gl-causes-of-birth-h-cumulative ) set new-count ( old-count + 1 ) set gl-causes-of-birth-h-cumulative ( replace-item cobtype gl-causes-of-birth-h-cumulative new-count ) ] ;; End else end ;;-----------------------------------------------------------------------------| ;; D3 – do-feed procedure(s) ;;-----------------------------------------------------------------------------| to do-feed ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "feed" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-feed: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] if( gb-h-heterotrophs-on = 1 ) [ ;; Heterotrophs feed on other HOAMs. ;; Heterotrophs feed second. ask heterotrophs [ ASSERT ( breed = heterotrophs ) ( "Is not heterotroph." ) who ;; This predator may be in one of three states: ;; - Currently hunting for prey. ;; - Currently eating prey. ;; - Currently being eaten by another predator. ifelse( b-is-in-oam = ge-not-in-oam ) [ f-hunt-for-prey ] ;; Else - is in oam already. [ f-eat-or-be-eaten ] ;; End Else ] ;; End of ask heterotrophs ] ;; End of if( gb-h-heterotrophs-on = 1 ) ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-feed: procedure completed" end ;;-----------------------------------------------------------------------------| ;; Heterotrophs hunt for prey. to f-hunt-for-prey ;; This routine is to be executed by an heterotroph. ;; This heterotroph is not in an oam. It is not feeding. It is not being ;; fed upon. It will check whether suitable prey is within reach, and, ;; if yes, will form an oam as the lh-hoam, and begin feeding upon such ;; prey. ;; Is this heterotroph already satiated? Is it hungry? let satiation-level ( cur-potential / max-potential ) ;; TODO: put satiation-factor in slider. ifelse( satiation-level < g-h-satiation-factor ) [ ;; It is hungry. LOG-TO-FILE ( " Do-feed: Hunting." ) ;; Establish which patch it is in. let my-who who let my-getf getf let lb-getf ( getf * lb-genetic-factor ) let ub-getf ( getf * ub-genetic-factor ) ;; Establish a list of potential prey. ;; Potential prey must be mobile (i.e. not already part of an immobile ;; predator-prey feeding pair, an OAM). ;; Potential prey must be within reach, in this patch or an immediately ;; neighbouring patch. ;; Potential prey must have sufficient getf (proxy-mass) to act as an ;; RH-HOAM when forming an Open Atwood's Machine. I.e. getf > my-getf. ;; Organism is not a potential prey for itself. ;; Within the above restrictions, some switches or operational choices ;; restrict the prey list further. ;; - If the scenario allows onmivores, heterotrophs may eat heterotrophs. ;; - If the lb gene is active, the getf of the prey must be > lb-getf. ;; - If the ub gene is active, the getf of the prey must be < ub-getf. ;; A dummy let statement. let prey-list [] ifelse( g-scenario-number = ge-scenario-omnivores ) [ ;; Heterotrophs can feed on other heterotrophs or autotrophs ;; (i.e. all turtles). set prey-list ( ( turtles-on neighbors ) with [ ( b-is-in-oam = ge-not-in-oam ) and ( who != my-who ) and ( getf > my-getf ) ] ) ;; Test the lb gene. if( ( any? prey-list ) and ( gb-h-lb-gene-active = true ) ) [ set prey-list ( prey-list with [getf > lb-getf] ) ] ;; Test the ub gene. if( ( any? prey-list ) and ( gb-h-ub-gene-active = true ) ) [ set prey-list ( prey-list with [getf < ub-getf] ) ] ;; Select the most energetic of available prey. if( any? prey-list ) [ set prey-list ( prey-list with [cur-potential = ( max [cur-potential] of prey-list ) ] ) ] ] ;; Else herbivores [ ;; Heterotrophs feed on autotrophs only. set prey-list ( ( autotrophs-on neighbors ) with [ ( b-is-in-oam = ge-not-in-oam ) and ( who != my-who ) and ( getf > my-getf ) ] ) ;; Test the lb gene. if( ( any? prey-list ) and ( gb-h-lb-gene-active = true ) ) [ set prey-list ( prey-list with [getf > lb-getf] ) ] ;; Test the ub gene. if( ( any? prey-list ) and ( gb-h-ub-gene-active = true ) ) [ set prey-list ( prey-list with [getf < ub-getf] ) ] ;; Select the most energetic of available prey. if( any? prey-list ) [ set prey-list ( prey-list with [cur-potential = ( max [cur-potential] of prey-list ) ] ) ] ] ;; End else Herbivores if( any? prey-list ) [ ;; These two HOAMs (Halves of an Open Atwood's Machine) are now coupled ;; together as an Open Atwood's Machine (OAM). Using the terminology ;; of the AM, the exergy in the RH-HOAM is transformed into: ;; (a) kinetic energy that will be exhausted as waste heat; and ;; (b) gravitational potential energy as the mass of the LH-HOAM ;; is raised. ;; The two HOAMs are so linked and immobile until the consumption of ;; the RH-HOAM (i.e. the prey) is completed, at which time the predator ;; will continue the hunt and the prey is removed from the model. let prey one-of prey-list ;; The hunt is successful. set prey-who ( [who] of prey ) let predator-who ( [who] of self ) ask prey [ ;; Mark this HOAM as captured prey. if( breed = heterotrophs ) [ set b-is-ready-to-move 0 ] set b-is-in-oam ge-rh-hoam set color violet set pred-who predator-who ] ;; Mark this HOAM as predator. set b-is-ready-to-move 0 set b-is-in-oam ge-lh-hoam set color yellow face turtle prey-who LOG-TO-FILE ( word " Do-feed: Captured - " prey ) ;; Adjust the trophic level data for this predator. set no-of-prey-eaten ( no-of-prey-eaten + 1 ) set sum-of-t-plus-one ( sum-of-t-plus-one + ( 1 + ( [trophic-level-floated] of prey ) ) ) set trophic-level-floated ( sum-of-t-plus-one / no-of-prey-eaten ) set trophic-level-rounded round( trophic-level-floated ) ;; The predator/prey pair are now locked in an OAM. ;; The predator takes a first bite. f-effect-per-tick-xrg-xfer-in-oam ] ] ;; End of if( g-h-satiation-factor ) ;; Else [ LOG-TO-FILE ( word " Do-feed: Satiated! Not hunting." ) ] ;; End Else ;; End of f-hunt-for-prey end ;;-----------------------------------------------------------------------------| ;; Effect the exergy transfer within the OAM associated with one tick of time. to f-effect-per-tick-xrg-xfer-in-oam ;; This routine is to be executed by a heterotroph, in the role of lh-hoam. ASSERT ( b-is-in-oam = ge-lh-hoam ) ( "Not an lh-hoam." ) who let rh-hoam ( turtle prey-who ) let prey-breed ( [breed] of rh-hoam ) ;; getf stands for genetic-energy-transfer-factor, and is a proxy for ;; mass in an AM. So "heavy" and "light" are in reference to mass. let heavy-mass ( [getf] of rh-hoam ) let light-mass ( [getf] of self ) set Eu-in-oam ( light-mass / heavy-mass ) let mass-total ( heavy-mass + light-mass ) let mass-diff ( heavy-mass - light-mass ) LOG-TO-FILE ( word " Do-feed: self - " self ) LOG-TO-FILE ( word " Do-feed: rh-hoam - " rh-hoam ) LOG-TO-FILE ( word " Do-feed: light-mass - " light-mass ) LOG-TO-FILE ( word " Do-feed: heavy-mass - " heavy-mass ) LOG-TO-FILE ( word " Do-feed: Eu-in-oam - " Eu-in-oam ) LOG-TO-FILE ( word " Do-feed: mass-total - " mass-total ) LOG-TO-FILE ( word " Do-feed: mass-diff - " mass-diff ) let max-rh-potential ( [max-potential] of rh-hoam ) let cur-rh-potential ( [cur-potential] of rh-hoam ) let numerator ( max-rh-potential - cur-rh-potential ) LOG-TO-FILE ( word " Do-feed: max-rh-potential - " max-rh-potential ) LOG-TO-FILE ( word " Do-feed: cur-rh-potential - " cur-rh-potential ) LOG-TO-FILE ( word " Do-feed: numerator - " numerator ) let mass-assembly-ratio ( mass-diff / mass-total ) let factor ( heavy-mass * g-acceleration * g-acceleration / 2 ) let denominator ( mass-assembly-ratio * factor ) LOG-TO-FILE ( word " Do-feed: mass-assembly-ratio - " mass-assembly-ratio ) LOG-TO-FILE ( word " Do-feed: factor - " factor ) LOG-TO-FILE ( word " Do-feed: denominator - " denominator ) let time ( ( numerator / denominator ) ^ 0.5 ) let time-plus-one ( time + 1 ) let time-plus-two ( time + 2 ) LOG-TO-FILE ( word " Do-feed: time - " time ) LOG-TO-FILE ( word " Do-feed: time-plus-one - " time-plus-one ) set max-drop-time ( ( ( 2 * g-drop-distance ) / ( g-acceleration * mass-assembly-ratio ) ) ^ 0.5 ) ;; Drop time for this OAM. set cur-drop-time time ;; Effective time since drop started. set rem-drop-time ( max-drop-time - cur-drop-time ) set drop-time-ratio ( rem-drop-time / max-drop-time ) ;; Fraction of drop time remaining. ;; The variable 'time' is the effective time, as if this OAM had started to ;; drop with current rh potential equal to its maximum. ;; Now, I need to calculate, using the discrete time OAM formulae, the ;; amount of potential that is transferred/transformed in the next tick. let delta-rh-potential ( -1 * denominator * ( ( time ^ 2 ) - ( time-plus-one ^ 2 ) ) ) ;; The sign has been reversed to make this a positive value. let next-delta-rh-potential ( -1 * denominator * ( ( time-plus-one ^ 2 ) - ( time-plus-two ^ 2 ) ) ) LOG-TO-FILE ( word " Do-feed: delta-rh-potential - " delta-rh-potential ) ;; I cannot remove more potential energy than is currently there. if( delta-rh-potential > cur-rh-potential ) [ set delta-rh-potential cur-rh-potential ] LOG-TO-FILE ( word " Do-feed: delta-rh-potential - " delta-rh-potential ) ;; Use the efficiency to break this into potential and kinetic. let delta-lh-potential ( Eu-in-oam * delta-rh-potential ) let delta-oam-kinetic ( delta-rh-potential - delta-lh-potential ) LOG-TO-FILE ( word " Do-feed: delta-lh-potential - " delta-lh-potential ) LOG-TO-FILE ( word " Do-feed: delta-oam-kinetic - " delta-oam-kinetic ) LOG-TO-FILE ( word " Do-feed: (ticks,epm,bite) - (" ticks "," epm "," floor delta-lh-potential ")" ) ;; Now, I need to transfer the appropriate potential energy to the lh-hoam. let available-room ( max-potential - cur-potential ) let excess-potential 0 LOG-TO-FILE ( word " Do-feed: available-room - " available-room ) LOG-TO-FILE ( word " Do-feed: excess-potential - " excess-potential ) if( available-room < delta-lh-potential ) [ ;; To maintain the rate of transformation of energy from the OAM I do not ;; want to pro-rate the amount taken from the RH-HOAM down, nor do I ;; want to reduce the kinetic energy exhausted. I only want to reduce ;; the amount received by the predator, and send the rest to two sinks, ;; one sink for kinetic, and one for excess exergy. set excess-potential ( delta-lh-potential - available-room ) set delta-lh-potential available-room ] ;; Transfer the energy and expel the exhaust of both types. ;; Store energy in the predator. set cur-potential ( cur-potential + delta-lh-potential ) ask rh-hoam [ ;; Remove the energy from the prey. set cur-potential ( cur-potential - delta-rh-potential ) ] ;; Send the kinetic energy to the sink now. In a normal OAM the kinetic energy is ;; not expelled to sink until MH hits the floor. However, because I want to ;; put new potential in and take it out whenever it is appropriate, so I don't ;; want to hold kinetic energy for a moment that may not come in a long while. ;; So, I expel it immediately. ;; Exhaust kinetic energy and excess potential to appropriate sinks. ifelse( prey-breed = autotrophs ) [ ;; Prey is an autotroph. f-store-data-in-sink ge-sinktype-a-food-exergy delta-lh-potential f-store-data-in-sink ge-sinktype-a-kinetic delta-oam-kinetic f-store-data-in-sink ge-sinktype-a-food-excess excess-potential ] ;; Else [ ;; Prey is a heterotroph. f-store-data-in-sink ge-sinktype-h-food-exergy delta-lh-potential f-store-data-in-sink ge-sinktype-h-kinetic delta-oam-kinetic f-store-data-in-sink ge-sinktype-h-food-excess excess-potential ] ;; End else ;; Finally, if the prey is almost emptied, such that it is inefficient ;; for the predator to continue eating, and it would be more efficient ;; to release this prey and start eating another, then the prey is ;; released. The real reason for this little piece of logic is to ;; ensure that there is no noise or bias introduced due to a mismatch ;; of bite size and energy available in the prey. I want every energy ;; transfer, in every tick, to perfectly represent a transfer consistent ;; with the dynamics of the AM. So partial bites are not allowed. if( next-delta-rh-potential > ( [cur-potential] of rh-hoam ) ) [ f-predator-releases-prey ] ;; End of f-effect-per-tick-xrg-xfer-in-oam end ;;-----------------------------------------------------------------------------| ;; Heterotrophs eat or are eaten to f-eat-or-be-eaten ;; This routine is to be executed by a heterotroph in an OAM. ;; The heterotroph is in an OAM. ifelse( b-is-in-oam = ge-lh-hoam ) [ ;; Access the prey. let rh-hoam ( turtle prey-who ) let cur-rh-potential ( [cur-potential] of rh-hoam ) ;; The heterotroph is in predator mode. if( cur-rh-potential > 0 ) [ ;; And there is food on the table. f-effect-per-tick-xrg-xfer-in-oam ] ] ;; Else [ ;; Heterotroph is prey. No action required. LOG-TO-FILE ( word " Do-feed: Heterotroph is prey." ) ] ;; End else. ;; End of f-eat-or-be-eaten end ;;-----------------------------------------------------------------------------| ;; D4 – do-reproduce procedure(s) ;;-----------------------------------------------------------------------------| to do-reproduce ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "reproduce" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-reproduce: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; Autotrophs come from forcible maintenance of population. ;; The population is topped up with sufficient fully energized ;; autotrophs in the 'do-pre-tick' function. if( gb-h-heterotrophs-on = 1 ) [ ask heterotrophs [ f-set-heterotroph-repro-flag f-reproduce-heterotroph ] ] ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-reproduce: procedure completed" end ;;-----------------------------------------------------------------------------| ;; f-set-heterotroph-repro-flag to f-set-heterotroph-repro-flag ;; This routine is to be executed by a heterotroph. set b-is-ready-to-reproduce 1 ;; i.e. true if( cur-potential < RET ) [ set b-is-ready-to-reproduce 0 ] ;; i.e. false due to lack of health. ;; TODO: if( age < g-h-RAT ) ;; TODO: [ set b-is-ready-to-reproduce 0 ] ;; i.e. false due to lack of maturity. if( b-is-in-oam = ge-rh-hoam ) [ set b-is-ready-to-reproduce 0 ] ;; i.e. false due to being eaten. if( b-is-ready-to-reproduce = 1 ) [ LOG-TO-FILE ( word " Do-reproduce: H(age,xrg,oam-flag,rep-flag) - (" age "," floor cur-potential "," b-is-in-oam "," b-is-ready-to-reproduce ")" ) ] ;; End f-set-heterotroph-repro-flag end ;;-----------------------------------------------------------------------------| ;; A heterotroph reproduces via fission, one mother having two daughters. to f-reproduce-heterotroph ;; This routine is to be executed by a heterotroph. if( b-is-ready-to-reproduce = 1 ) ;; 1 = true [ LOG-TO-FILE ( word " Do-reproduce: Heterotroph Ma - " who ) ;; If this heterotroph is in the process of eating prey at the moment that ;; it reproduces, the prey is set free, with a total exergy equal to the ;; unexpended exergy plus associated kinetic energy. if( b-is-in-oam = ge-lh-hoam ) [ f-predator-releases-prey ] let my-who who let my-exergy cur-potential let one-share-of-exergy floor( my-exergy / 2 ) let excess-exergy ( my-exergy - ( 2 * one-share-of-exergy ) ) let my-patch patch-here let mothers-getf ( [getf] of self ) let mothers-lb-gene ( [lb-genetic-factor] of self ) let mothers-ub-gene ( [ub-genetic-factor] of self ) ask my-patch [ sprout-heterotrophs 2 [ f-initialize-new-heterotroph ;; Note the mother of this daughter. set mas-who my-who ;; Cause the getf of this heterotroph to mutate. ;; Remember that getf is a proxy for mass in the AM. LOG-TO-FILE ( word " Do-reproduce: Heterotroph Dx - " who ) ;; Copy the getf, then mutate it. ;; Remember that getf is a proxy for mass in the AM. set getf mothers-getf set lb-genetic-factor mothers-lb-gene set ub-genetic-factor mothers-ub-gene f-mutate-new-heterotroph ;; In rare cases a mother may be full of exergy and a daughter may be ;; unable to accept a full share, due to mutation of getf downwards. ;; getf scales the maximum amount of energy that can be held because ;; it is analogous to mass in the AM. let endowment-rejected ( fr-heterotroph-accepts-endowment one-share-of-exergy ) LOG-TO-FILE ( word " Do-reproduce: endowment-rejected - " endowment-rejected ) set excess-exergy ( excess-exergy + endowment-rejected ) f-increment-cob-list breed ge-cob-fission ] ] f-store-data-in-sink ge-sinktype-h-die-fiss excess-exergy set cause-of-death ge-cod-fission ;; die ;; The mother disappears after fission, leaving two daughters. ] ;; End f-reproduce-heterotroph end ;;-----------------------------------------------------------------------------| ;; An new heterotroph mutates, chainging the ability to store exergy or attack ;; suitable prey. to f-mutate-new-heterotroph ;; This routine is to be executed by an heterotroph. ;; First, mutate the getf (mass) that controls the ability to store exergy. ;; Remember that getf is a proxy for mass in the AM. ;; Determine whether it mutates upwards or downwards. let old-getf getf let sign ( -1 + 2 * ( random 2 ) ) ;; either a -1 or a 1. let delta-getf ( g-h-mutation-factor * getf * sign ) set delta-getf ( delta-getf * ( random-float 1 ) ) set getf ( getf + delta-getf ) LOG-TO-FILE ( word " Do-reproduce: Mutate getf - H(old,delta,new) - (" floor old-getf "," floor delta-getf "," floor getf ")" ) ;; Recalculate the life function controls that are scaled to getf (mass). ;; Remember that getf is a proxy for mass in the AM. f-set-getf-derived-heterotroph-characters ;; Next, mutate the gene that controls the minimum getf (mass) of prey. ;; Remember that getf is a proxy for mass in the AM. ;; Determine whether it mutates upwards or downwards. let old-gene lb-genetic-factor set sign ( -1 + 2 * ( random 2 ) ) ;; either a -1 or a 1. let delta-gene ( g-h-mutation-factor * 2.5 * sign ) ;; 2.5 = scaling factor set delta-gene ( delta-gene * ( random-float 1 ) ) set lb-genetic-factor ( lb-genetic-factor + delta-gene ) ;; If its less than one, reflect the overage above one. if( lb-genetic-factor < g-h-lb-lower-bound ) [ set lb-genetic-factor ( ( 2 * g-h-lb-lower-bound ) - lb-genetic-factor ) ] LOG-TO-FILE ( word " Do-reproduce: Mutate lb gene - H(old,delta,new) - (" precision old-gene 4 "," precision delta-gene 4 "," precision lb-genetic-factor 4 ")" ) ;; Last, mutate the gene that controls the maximum getf (mass) of prey. ;; Remember that getf is a proxy for mass in the AM. ;; Determine whether it mutates upwards or downwards. set old-gene ub-genetic-factor set sign ( -1 + 2 * ( random 2 ) ) ;; either a -1 or a 1. set delta-gene ( g-h-mutation-factor * 2.5 * sign ) ;; 2.5 = scaling factor set delta-gene ( delta-gene * ( random-float 1 ) ) set ub-genetic-factor ( ub-genetic-factor + delta-gene ) ;; If its more than four, reflect the overage below four. if( ub-genetic-factor > g-h-ub-upper-bound ) [ set ub-genetic-factor ( ( 2 * g-h-ub-upper-bound ) - ub-genetic-factor ) ] LOG-TO-FILE ( word " Do-reproduce: Mutate ub gene - H(old,delta,new) - (" precision old-gene 4 "," precision delta-gene 4 "," precision ub-genetic-factor 4 ")" ) ;; End of f-mutate-new-heterotroph end ;;-----------------------------------------------------------------------------| ;; An new heterotroph accepts what exergy it can. to-report fr-heterotroph-accepts-endowment [endowment-offered] ;; This routine is to be executed by a heterotroph. LOG-TO-FILE ( word " Do-reproduce: endowment-offered - " endowment-offered ) let endowment-remaining 0 ;; Calculate the maximum energy charge allowed for this heterotroph. ;; Remember that getf is a proxy for mass in the AM. let max-exergy ( getf * g-acceleration * g-drop-distance ) ;; Determine how much of the endowment this heterotroph can accept. let energy-to-reject ( endowment-offered - max-exergy ) ;; If there is too much energy offered, reject some. Otherwise, store all ;; of it. ifelse( energy-to-reject > 0 ) [ set cur-potential ( max-exergy ) f-store-data-in-sink ge-sinktype-h-fiss-exergy cur-potential set endowment-remaining energy-to-reject LOG-TO-FILE ( word " Do-reproduce: energy accepted - " max-exergy ) LOG-TO-FILE ( word " Do-reproduce: energy-to-reject - " energy-to-reject ) ] ;; Else [ set cur-potential ( endowment-offered ) f-store-data-in-sink ge-sinktype-h-fiss-exergy cur-potential LOG-TO-FILE ( word " Do-reproduce: energy accepted - " endowment-offered ) set endowment-remaining 0 ] ;; End else report endowment-remaining ;; End of fr-heterotroph-accepts-endowment end ;;-----------------------------------------------------------------------------| ;; D5 – do-die procedure(s) ;;-----------------------------------------------------------------------------| to do-die ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "die" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-die: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] if( ( count autotrophs ) > 0 ) [ ask autotrophs [ f-set-autotroph-death-flag f-autotroph-dies ] ] if( ( count heterotrophs ) > 0 ) [ ask heterotrophs [ f-set-heterotroph-death-flag f-heterotroph-dies ] ] ;; Supressed. f-update-aggregates LOG-TO-FILE " Do-die: procedure completed" end ;;-----------------------------------------------------------------------------| ;; f-set-autotroph-death-flag to f-set-autotroph-death-flag ;; This routine is to be executed by a autotroph. set b-is-ready-to-die 0 ;; i.e. false, default. ;; If a cause of death has already been noted, it dies. if( cause-of-death > ge-cod-none ) [ ;; A cause of death has been previously flagged. set b-is-ready-to-die 1 LOG-TO-FILE ( WORD " Do-die: A(xrg,cod) - (" floor cur-potential "," cause-of-death ")" ) ] ;; End f-set-autotroph-death-flag end ;;-----------------------------------------------------------------------------| ;; f-autotroph-dies to f-autotroph-dies ;; This routine is to be executed by a autotroph. if( b-is-ready-to-die = 1 ) [ ;; If this autotroph is in the process of being eaten as prey at the ;; moment that it dies it must be released from the oam. if( b-is-in-oam = ge-rh-hoam ) [ let predator ( turtle pred-who ) ask predator [ f-predator-releases-prey ] ] LOG-TO-FILE ( word " Do-die: A(xrg,die-flag,cod) - (" floor cur-potential "," b-is-ready-to-die "," cause-of-death ")" ) ;; Record the cause of death in the statistics. if( cause-of-death > 0 ) [ if( cause-of-death = ge-cod-as-prey ) [ f-store-data-in-sink ge-sinktype-a-die-asprey cur-potential ] f-increment-cod-list breed cause-of-death ] die ;; The autotroph disappears from the system. ] ;; End f-autotroph-dies end ;;-----------------------------------------------------------------------------| ;; f-set-heterotroph-death-flag to f-set-heterotroph-death-flag ;; This routine is to be executed by a heterotroph. set b-is-ready-to-die 0 ;; i.e. false, default. ;; If a cause of death has already been noted, it dies. if( cause-of-death > ge-cod-none ) [ ;; A cause of death has been previously flagged. set b-is-ready-to-die 1 LOG-TO-FILE ( WORD " Do-die: A(age,xrg,oam,cod) - (" age "," floor cur-potential "," b-is-in-oam "," cause-of-death ")" ) ] ;; No cause of death has been set yet. Check basic vital signs. if( cur-potential <= EPM ) ;; Effectively, this is g-h-DET. [ set b-is-ready-to-die 1 set cause-of-death ge-cod-hunger LOG-TO-FILE ( WORD " Do-die: A(age,xrg,oam,cod) - (" age "," floor cur-potential "," b-is-in-oam "," cause-of-death ")" ) ] if( age > g-h-DAT ) [ set b-is-ready-to-die 1 set cause-of-death ge-cod-old-age LOG-TO-FILE ( WORD " Do-die: A(age,xrg,oam,cod) - (" age "," floor cur-potential "," b-is-in-oam "," cause-of-death ")" ) ] ;; If it dies as prey, that over-rides all other causes of death. if( ( b-is-in-oam = ge-rh-hoam ) and ( b-is-ready-to-die = 1 ) ) [ set cause-of-death ge-cod-as-prey LOG-TO-FILE ( WORD " Do-die: A(age,xrg,oam,cod) - (" age "," floor cur-potential "," b-is-in-oam "," cause-of-death ")" ) ] ;; End f-set-heterotroph-death-flag end ;;-----------------------------------------------------------------------------| ;; f-heterotroph-dies to f-heterotroph-dies ;; This routine is to be executed by a heterotroph. if( b-is-ready-to-die = 1 ) [ ;; If this heterotroph is in the process of eating prey at the moment that ;; it dies, the prey is set free. if( b-is-in-oam = ge-lh-hoam ) [ f-predator-releases-prey ] ;; If this heterotroph is in the process of being eaten as prey at the ;; moment that it dies it must be released from the oam. if( b-is-in-oam = ge-rh-hoam ) [ let predator ( turtle pred-who ) ask predator [ f-predator-releases-prey ] ] LOG-TO-FILE ( word "Do-die: H(xrg,die-flag,cod) - (" floor cur-potential "," b-is-ready-to-die "," cause-of-death ")" ) ;; TODO debug cause of death. ;; Record the cause of death in the statistics. if( cause-of-death > 0 ) [ if( cause-of-death = ge-cod-hunger ) [ f-store-data-in-sink ge-sinktype-h-die-hunger cur-potential ] if( cause-of-death = ge-cod-old-age ) [ f-store-data-in-sink ge-sinktype-h-die-oldage cur-potential ] if( cause-of-death = ge-cod-as-prey ) [ f-store-data-in-sink ge-sinktype-h-die-asprey cur-potential ] f-increment-cod-list breed cause-of-death ] die ;; The heterotroph disappears from the system. ] ;; End f-heterotroph-dies end ;;-----------------------------------------------------------------------------| ;; f-predator-releases-prey to f-predator-releases-prey ;; This routine is to be executed by a heterotroph. ;; This heterotroph is currently eating prey. The prey is released. let prey turtle prey-who ask prey [ set color default-colour if( breed = heterotrophs ) [ set b-is-ready-to-move 1 ;; true ] set b-is-in-oam ge-not-in-oam set cause-of-death ge-cod-as-prey ] set color default-colour set b-is-ready-to-move 1 ;; true set b-is-in-oam ge-not-in-oam ;; Return OAM-related variables to defaults. ;; These contain data for the OAM consisting of coupled predator/prey. set prey-who -1 ;; an invalid value; who number of prey haom. set pred-who -1 ;; an invalid value; who number of predator haom. set Eu-in-oam 1 ;; Eu is Odum's efficiency. set max-drop-time 0 ;; Drop time for this OAM. set cur-drop-time 0 ;; Time since drop started. set rem-drop-time 0 ;; Remaining drop time. set drop-time-ratio 0 ;; Fraction of drop time remaining. ;; End f-predator-releases-prey end ;;-----------------------------------------------------------------------------| ;; D6 - do-post-tick procedure(s) ;;-----------------------------------------------------------------------------| to do-post-tick ;; This routine is to be executed by the observer. if( gb-debug-on = 1 ) [ ifelse( ( gs-debug-step-chooser = "all" ) or ( gs-debug-step-chooser = "post-tick" ) ) [ set gb-debug-flow-on 1 LOG-TO-FILE "" LOG-TO-FILE word "Do-Post-tick: Debug on; tick = " ticks ] [ set gb-debug-flow-on 0 ] ] ;; MANUAL CHANGE FOR DEBUG. ;; This is a call to a debug routine which could be suppressed if all is okay. ;; This is one of a group of such calls, most of which are between steps in ;; the 'Go' routine. They are suppressed there, but can be enabled again. ;; I have decided to leave this one active, for now. ;; It checks all agents, every tick, to ensure that all values are greater than ;; or equal to zero. if( frb-agents-are-all-valid = false ) [ LOG-TO-FILE ( word "Agents failed validity test." ) ] ;; Update the aggregates for display in the monitors. f-update-aggregates display LOG-TO-FILE " Do-post-tick: procedure completed." end ;;-----------------------------------------------------------------------------| ;; SECTION E – DRAWING AND MAINTENANCE PROCEDURE(S) ;;-----------------------------------------------------------------------------| ;;-----------------------------------------------------------------------------| ;; Update the values of global aggregate numbers. to f-update-aggregates ;; This routine is to be executed by the observer. ;; Although this is a display-only routine, it may implicitly call the PRNG and ;; so may have an effect on the trajectory of the model. In a standard 'go' ;; run it is called only once per tick, before graphs are updated. If you ;; use the one-step debug buttons, it is called once after each step, so ;; debug runs that use those buttons will not replicate a real run. ;;---------------------------------------------------------------------------| ;; The following agent sets, counts and averages are for data collection ;; and display in monitors and plots. ;; Agent sets ;; Set of all turtles as lh-hoams set ga-oams ( heterotrophs with [b-is-in-oam = ge-lh-hoam] ) ;; Counts set g-no-of-autotrophs ( count autotrophs ) ;; count of all autotrophs set g-no-of-heterotrophs ( count heterotrophs ) ;; count of all heterotrophs set g-no-of-oams ( count ga-oams ) ;; count of all Open Atwood Machines set g-no-of-a-as-rh-hoams ( count autotrophs with [b-is-in-oam = ge-rh-hoam] ) set g-no-of-h-as-rh-hoams ( count heterotrophs with [b-is-in-oam = ge-rh-hoam] ) ;; Averages - autotrophs ifelse( g-no-of-autotrophs = 0 ) [ set g-a-ave-getf 0 set g-a-ave-max-potential 0 set g-a-ave-cur-potential 0 ] ;; Else [ set g-a-ave-getf ( sum [getf] of autotrophs ) / g-no-of-autotrophs set g-a-ave-max-potential ( sum [max-potential] of autotrophs ) / g-no-of-autotrophs set g-a-ave-cur-potential ( sum [cur-potential] of autotrophs ) / g-no-of-autotrophs ] ;; End else ;; Averages - heterotrophs ifelse( g-no-of-heterotrophs = 0 ) [ set g-h-ave-age 0 set g-h-ave-getf 0 set g-h-ave-lb-gene 0 set g-h-ave-ub-gene 0 set g-h-ave-RET 0 set g-h-ave-EPM 0 set g-h-ave-max-potential 0 set g-h-ave-cur-potential 0 ] ;; Else [ set g-h-ave-age ( sum [age] of heterotrophs ) / g-no-of-heterotrophs set g-h-ave-getf ( sum [getf] of heterotrophs ) / g-no-of-heterotrophs set g-h-ave-lb-gene ( sum [lb-genetic-factor] of heterotrophs ) / g-no-of-heterotrophs set g-h-ave-ub-gene ( sum [ub-genetic-factor] of heterotrophs ) / g-no-of-heterotrophs set g-h-ave-RET ( sum [RET] of heterotrophs ) / g-no-of-heterotrophs set g-h-ave-EPM ( sum [EPM] of heterotrophs ) / g-no-of-heterotrophs set g-h-ave-max-potential ( sum [max-potential] of heterotrophs ) / g-no-of-heterotrophs set g-h-ave-cur-potential ( sum [cur-potential] of heterotrophs ) / g-no-of-heterotrophs ] ;; End else ;; Averages - OAMs ifelse( g-no-of-oams = 0 ) [ set g-h-ave-Eu 0 set g-h-ave-max-dt 0 set g-h-ave-cur-dt 0 set g-h-ave-rem-dt 0 set g-h-ave-dt-ratio 0 set g-h-ave-BITE-total 0 set g-h-ave-BITE-xrg 0 set g-h-ave-BITE-kinetic 0 ] ;; Else [ set g-h-ave-Eu ( sum [Eu-in-oam] of ga-oams ) / g-no-of-oams set g-h-ave-max-dt ( sum [max-drop-time] of ga-oams ) / g-no-of-oams set g-h-ave-cur-dt ( sum [cur-drop-time] of ga-oams ) / g-no-of-oams set g-h-ave-rem-dt ( sum [rem-drop-time] of ga-oams ) / g-no-of-oams set g-h-ave-dt-ratio ( sum [drop-time-ratio] of ga-oams ) / g-no-of-oams set g-h-ave-BITE-xrg ( ( item ge-sinktype-a-food-exergy gl-sinks-per-tick ) + ( item ge-sinktype-h-food-exergy gl-sinks-per-tick ) ) / g-no-of-oams set g-h-ave-BITE-kinetic ( ( item ge-sinktype-a-kinetic gl-sinks-per-tick ) + ( item ge-sinktype-h-kinetic gl-sinks-per-tick ) ) / g-no-of-oams set g-h-ave-BITE-total ( g-h-ave-BITE-xrg + g-h-ave-BITE-kinetic ) ] ;; End else ;;-----------------------------------------------------------------------------| ;; To ensure that the PRNG is called whether or not plots are displayed, the ;; calculations needed for the histogram plots which invoke the PRNG ;; implicitly should be carried out here where they will happen every tick. ;;-----------------------------------------------------------------------------| ;; Setup for Plot "AAAAAA" ;; This log entry may come from any step during debug operations. LOG-TO-FILE " Do-xxx: All aggregates updated." end ;;-----------------------------------------------------------------------------| ;; Report the status of a switch. to-report fr-h-lb-switch-status ;; This routine is to be executed by the observer. let answer "Non-phenotypic" if( gb-h-lb-gene-active = true ) [ set answer "phenotypic" ] report answer end ;;-----------------------------------------------------------------------------| ;; Report the status of a switch. to-report fr-h-ub-switch-status ;; This routine is to be executed by the observer. let answer "Non-phenotypic" if( gb-h-ub-gene-active = true ) [ set answer "phenotypic" ] report answer end ;;-------------------------- ;; DATA CAPTURE TO CSV FILES ;;-------------------------- ;;-----------------------------------------------------------------------------| ;; Record the data is several selected plots to CSV files to f-record-selected-plots ;; This routine is to be executed by the observer. ;; The template for the export command is: ;; export-plot plotname filename ;; Get a common timestamp for all plots. let timestamp fr-get-time-stamp ;; Plot 01 let plotname "Populations" let plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl01_POPS.CSV" ) export-plot plotname plot-filename ;; Plot 02 set plotname "Ave Eu of OAMs" set plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl02_OAMS.CSV" ) export-plot plotname plot-filename ;; Plot 03 set plotname "Prey Numbers" set plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl03_PREY.CSV" ) export-plot plotname plot-filename ;; Plot 04 set plotname "Counts By T-Level" set plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl04_TCNTS.CSV" ) export-plot plotname plot-filename ;; Plot 05 set plotname "Eu By T-Level" set plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl05_EUBYTL.CSV" ) export-plot plotname plot-filename ;; Plot 06 set plotname "Max Trophic Level" set plot-filename ( word timestamp "_Sc" g-scenario-number "_Se" g-use-this-seed "_Pl06_MAXTL.CSV" ) export-plot plotname plot-filename ;; End f-record-selected-plots end ;;-----------------------------------------------------------------------------| ;; Construct a time stamp for a file name for data in CSV format. to-report fr-get-time-stamp ;; This routine is to be executed by the observer. ;; ;; Date-string format "01:19:36.685 PM 19-Sep-2002" let date-string date-and-time let time-stamp "" ;; Append the year as yy. set time-stamp word time-stamp ( substring date-string 25 27 ) ;; Append the month as Mmm. set time-stamp word time-stamp fr-convert-mmm-mm ( substring date-string 19 22 ) ;; Append the day as dd. set time-stamp word time-stamp ( substring date-string 16 18 ) ;; Append a dash. set time-stamp word time-stamp "_" ;; Append the hour as hh. set time-stamp word time-stamp fr-convert1224 ( substring date-string 0 2 ) ( substring date-string 13 15 ) ;; Append the minute as mm. set time-stamp word time-stamp ( substring date-string 3 5 ) ;; Append the second as ss. set time-stamp word time-stamp ( substring date-string 6 8 ) report time-stamp ;; End fr-get-time-stamp end ;;-----------------------------------------------------------------------------| ;; DEBUG AND DEBUG LOG FILE MANAGEMENT FUNCTIONS ;;-----------------------------------------------------------------------------| ;;-----------------------------------------------------------------------------| ;; Open a log file for debug output. to f-open-log-file ;; This routine is to be executed by the observer. ;; Ensure previous log file is closed. if ( is-string? gs-log-file-name ) [ if ( file-exists? gs-log-file-name ) [ file-close-all ] ] ;; Date-string format "01:19:36.685 PM 19-Sep-2002" let date-string date-and-time set gs-log-file-name "MppLab_Log_" ;; Append the year as yy. set gs-log-file-name word gs-log-file-name ( substring date-string 25 27 ) ;; Append the month as Mmm. set gs-log-file-name word gs-log-file-name fr-convert-mmm-mm ( substring date-string 19 22 ) ;; Append the day as dd. set gs-log-file-name word gs-log-file-name ( substring date-string 16 18 ) ;; Append a dash. set gs-log-file-name word gs-log-file-name "_" ;; Append the hour as hh. set gs-log-file-name word gs-log-file-name fr-convert1224 ( substring date-string 0 2 ) ( substring date-string 13 15 ) ;; Append the minute as mm. set gs-log-file-name word gs-log-file-name ( substring date-string 3 5 ) ;; Append the second as ss. set gs-log-file-name word gs-log-file-name ( substring date-string 6 8 ) ;; Append the .txt extension. set gs-log-file-name word gs-log-file-name ".txt" file-open gs-log-file-name file-show "Log File for a MppLab (NetLogo) Model." file-show word "File Name: " gs-log-file-name file-show word "File opened at:" date-and-time file-show "" ;; Send a message directly to the command centre. ifelse ( file-exists? gs-log-file-name ) [ show word gs-log-file-name " opened." ] [ show word gs-log-file-name " not opened." ] end ;;-----------------------------------------------------------------------------| ;; Convert month in text form to digital form. to-report fr-convert-mmm-mm [ mmm ] ;; This routine is to be executed by the observer. ;; It converts a string in the form mmm ( alpha text ) to the form mm ( digit-text ). let mm "00" if( mmm = "Jan" ) [ set mm "01" ] if( mmm = "Feb" ) [ set mm "02" ] if( mmm = "Mar" ) [ set mm "03" ] if( mmm = "Apr" ) [ set mm "04" ] if( mmm = "May" ) [ set mm "05" ] if( mmm = "Jun" ) [ set mm "06" ] if( mmm = "Jul" ) [ set mm "07" ] if( mmm = "Aug" ) [ set mm "08" ] if( mmm = "SeP" ) [ set mm "09" ] if( mmm = "Oct" ) [ set mm "10" ] if( mmm = "Nov" ) [ set mm "11" ] if( mmm = "Dec" ) [ set mm "12" ] report mm end ;;-----------------------------------------------------------------------------| ;; Convert hour in 12 format to 24 hour format. to-report fr-convert1224 [ hh ampm ] ;; This routine is to be executed by the observer. ;; It converts a string in 12 hour format to 24 hour format. let hour read-from-string hh if( ampm = "PM" ) [ set hour ( hour + 12 ) ] let dd ( word "00" hour ) let d2 last dd set dd but-last dd let d1 last dd set dd ( word d1 d2 ) report dd end ;;-----------------------------------------------------------------------------| ;; Close a log file for debug output. to f-close-log-file ;; This routine is to be executed by the observer. let b-filename-exists 0 if ( is-string? gs-log-file-name ) [ if ( file-exists? gs-log-file-name ) [ set b-filename-exists 1 ] ] ifelse( b-filename-exists = 1 ) [ ;; Ensure the file is selected. file-open gs-log-file-name ;; Stanp it. LOG-TO-FILE word "File closed at: " date-and-time ;; Flush the buffers. file-flush ;; Close it. file-close-all ;; Note sent to command centre. show word gs-log-file-name " closed." ;; Revert to dummy name. set gs-log-file-name "dummyname" ] [ if( gs-log-file-name = "dummyname" ) [ show "No log file is open. Cannot close it." ] ] end ;;-----------------------------------------------------------------------------| ;; Select an already opened log file. to f-select-log-file ;; This routine is to be executed by the observer. ifelse ( file-exists? gs-log-file-name ) [ ;; Ensure the file is selected. file-open gs-log-file-name ;; Ensure it is open for writing. LOG-TO-FILE "" LOG-TO-FILE "SELECTED" ] [ show word gs-log-file-name " is not open. Cannot select it." ] end ;;-----------------------------------------------------------------------------| ;; Change the debug mode from on to off, or vice versa. to f-toggle-debug ;; This routine is to be executed by the observer, and is activated by a ;; button. ifelse( gb-debug-on = 1 ) [ ;; Debug is On, turn it Off. ;; Close the file before turning debug logging off. f-close-log-file set gs-debug-status "0 (Off)" ;; This appears in the monitor. set gb-debug-on 0 ;; But this controls the debug feature. ] [ ;; Debug is Off, turn it On. set gs-debug-status "1 (On)" ;; This appears in the monitor. set gb-debug-on 1 ;; But this controls the debug feature. ;; The switches, if needed, are reset manually by the user. ;; Open the log file after turning debug logging on. f-open-log-file ] end ;;-----------------------------------------------------------------------------| ;; 'Show' a string in a debug log. to LOG-TO-FILE [ log-this-string ] ;; This routine may be executed by observer, autotroph, or heterotroph. ;; It should be invoked as a debug routine only, and would not be used for ;; normal output. It sends output to the debug log file, or, optionally, ;; also to the command centre. ;; gb-debug-on is a global Boolean and has value 1 (true) or 0 (false). if( gb-debug-on = 1 ) [ ;; gb-debug-flow-on is declared as a global Boolean variable, and its value ;; is 0 ( false ) or 1 ( true ) and is set on or off at the beginning of each ;; function ( each do-step ). It is controlled by the chooser that selects 'all' ;; or a specific do-function. ;; ;; When it is 'on' you can assume the debug log file exists and is open for ;; write. if( gb-debug-flow-on = 1 ) [ file-show log-this-string show log-this-string ] ] end ;;-----------------------------------------------------------------------------| ;; This replicates the effect of an 'ASSERTION' in C++ to ASSERT [ error-test error-string error-who ] ;; This routine can be run by observer, autotroph or heterotroph (I think). if( error-test = false ) [ show ( word error-test " " error-string " " error-who ) ;; Cause a run-time error and display a message. error ( word "Agent: " error-who " - " error-string ) ] end ;;-----------------------------------------------------------------------------| ;; Check whether the agents are all valid. to-report frb-agents-are-all-valid ;; This routine can be run by the observer. let b-agents-are-all-valid true if( gb-debug-on = 1 ) [ ;; Do the check only if debug is on. ;; Check the autotrophs. ask autotrophs [ if( frb-autotroph-is-valid = false ) [ set b-agents-are-all-valid false ] ] ;; Check the heterotrophs. ask heterotrophs [ if( frb-heterotroph-is-valid = false ) [ set b-agents-are-all-valid false ] ] ] report b-agents-are-all-valid end ;;-----------------------------------------------------------------------------| ;; Check whether a autotroph is valid. to-report frb-autotroph-is-valid ;; This routine can be run by a autotroph. let b-autotroph-is-valid true report b-autotroph-is-valid end ;;-----------------------------------------------------------------------------| ;; Check whether a heterotroph is valid. to-report frb-heterotroph-is-valid ;; This routine can be run by a heterotroph. let b-heterotroph-is-valid true if( getf < 0 ) [ set b-heterotroph-is-valid false LOG-TO-FILE ( word "getf = " getf "; at tick = " ticks ) ] report b-heterotroph-is-valid end
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Attached files
File | Type | Description | Last updated | |
---|---|---|---|---|
03 MppLab V1.09.png | preview | Preview for '03 MppLab V1.09' | over 7 years ago, by Garvin Boyle | Download |
141129 NTF - NetLogo Stds for OrrerySW R2.pdf | Prepared standards for Orrery Software for NetLogo projects. | over 7 years ago, by Garvin Boyle | Download | |
150101 NTF Atwood's Machine R4.pdf | An analysis of the functioning of Atwood's Machine. | over 7 years ago, by Garvin Boyle | Download | |
150105 NTF AM Shape Study R1.pdf | A study of the shape of the power vs efficiency curve of Atwood's Machine. | over 7 years ago, by Garvin Boyle | Download | |
150113 NTF Atwoods Machine Revisited R4.pdf | More thoughts on the operations of Atwood's Machine as a model for energy transfers. | over 7 years ago, by Garvin Boyle | Download | |
150418 NTF Three Shapes of AM Revisited R2.pdf | A more detailed study of the power vs efficiency curves associated with Atwood's Machine. | over 7 years ago, by Garvin Boyle | Download | |
160509 NTF Video of MppLab - Trophic Levels - On Youtube.pdf | A document with a link to a youtube video produced using MppLab. | over 7 years ago, by Garvin Boyle | Download | |
170324 NTF MppLab Change Diary R4.pdf | The most recent change diary. | over 7 years ago, by Garvin Boyle | Download | |
170326 NTF High-Level Design - MppLab R2.pdf | A high-level technical description of the model. | over 7 years ago, by Garvin Boyle | Download |
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