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Orrery Software i NTF MppLab I Code

NOTE TO FILE:

Garvin H Boyle

Dated: 160510

Code for MppLab I, V1.09

Frontispiece

Orrery Software ii NTF MppLab I Code

Table of Contents 1 - References ................................................................................................................................. 1

2 - Background ................................................................................................................................ 1 3 - Purpose ...................................................................................................................................... 1 4 - Discussion .................................................................................................................................. 1 5 - Summary .................................................................................................................................... 1 6 - Yet-To-Do ................................................................................................................................. 1

7 - Code for MppLab I V1.09 ......................................................................................................... 2

Orrery Software 1 NTF Code for MppLab I

1 - References

A. MppLab_I_V1.09.nlogo

2 - Background

Ref A is a NetLogo program developed in 2015 that went undocumented for a while. This was

scooped out of the program for review as part of the after-the-fact effort to put some

documentation around the program.

3 - Purpose

To document the MppLab I code.

4 - Discussion

Nil

5 - Summary

Nil

6 - Yet-To-Do

Nil


7 - Code for MppLab I V1.09 ;;-----------------------------------------------------------------------------|

;; SECTION A – AUTHOR IDENTIFICATION AND CODE ABSTRACT

;;-----------------------------------------------------------------------------|

;;

;; File Name: MppLab_I_V1.09.nlogo

;; By Orrery Software

;; Dated: 2015-02-25

;; Author contact:

;; Garvin H Boyle

;; [email protected]

;; http://orrery-software.webs.com

;; As the author, I welcome questions, discussion of issues and suggestions

;; for improvements.

;;-----------------------------------------------------------------------------|

;; This MppLab I app is a laboratory in which students can study aspects

;; of the Maximum Power Principle (MPP) of H.T. Odum.

;;-----------------------------------------------------------------------------|

;; 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)

;; 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-mass ;; Initial mass of autotrophs on startup.

;; Biophyscial life function parameters, heterotrophs.

gb-h-heterotrophs-on ;; Creates heterotrophs

g-h-initial-mass ;; Initial 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-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-mass ;; 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-mass ;; 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 "Character Separated Values"

;; I use a space to separate values. This can be read by MS Excel.

g-recno-max ;; Maximum record number for all files.

;; Data Per Xaction

gb-dpx-on ;; Numeric Boolean switch

gs-dpx-status ;; Interpretation of gb-dpx-on


gs-dpx-file-name ;; The file name

g-dpx-recno ;; The number of the last record written.

;; Data Per Tick

gb-dpt-on ;; Numeric Boolean switch

gs-dpt-status ;; Interpretation of gb-dpt-on

gs-dpt-file-name ;; The file name

g-dpt-recno ;; The number of the last record written.

;;---------------

;; 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

;; gb-debug-show-steps ;; Switch, Native Boolean, show in command centre

]

;;-----------------------------------------------------------------------------|

;; 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

[


;; 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

mass ;; the 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

[


;; who ;; fixed id number

;; breed ;; to which breed this turtle belongs [heterotroph]

;; heading ;; 0 <= heading < 360, 0 = north




;; shape ;; a shape chosen from the shape library

;; color ;; color of this turtle ( 0 <= color < 140 )



;; hidden? ;; true or false

;; label ;; label of this turtle

;; label-color ;; color of this turtle's label ( 0 <= label-color < 140 )


;; 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

mass ;; the mass in this heterotroph (Atwood's Machine Ref).

lb-genetic-factor ;; gene to set lower bound on mass of prey.

ub-genetic-factor ;; gene to set upper bound on mass 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.


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 data capture is always off.

f-close-dpx-file

f-close-dpt-file

;; 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


;; 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_I_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.

;; Data capture to file feature.

;; The data capture files may be open, and the features, stored in switches,

;; may be on, as they are persistent. Ensure they are off.

f-close-dpx-file

f-close-dpt-file

;; Set the limit on the number of records in a CSV data file.

;; This applies to dpx and dpt files. (Debug log files?)

set g-recno-max 500000

;; 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-mass 128 ;; Initial 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-mass - " g-a-initial-mass )

LOG-TO-FILE ( "" )

LOG-TO-FILE ( " Do-set: HETEROTROPH POPULATION PARAMETERS:" )

;; Biophysical life function parameters, autotrophs.

set g-h-initial-mass 100 ;; Initial mass of heterotrophs on startup.

;; Biophysical life function parameters, heterotrophs.

set g-h-DAT 1600 ;; Death Age Threshold

;; g-h-mutation-factor ;; 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-mass - " g-h-initial-mass )

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 )


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


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.

;;---------------------------------------------------------------------------|



;; 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-mass 0 ;; 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-mass 0 ;; 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 )

[






]

if( g-scenario-number = ge-scenario-omnivores )

[






]

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


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


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.


;; who ;; set automatically

set heading 0 ;; direction of motion






set color green


;; Associated with autotroph dynamics.

set mas-who -1 ;; serial number of parent autotroph

set default-colour green ;; distinctive colour for autotrophs

set mass g-a-initial-mass ;; the mass in this autotroph (Atwood's Machine

Ref).

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 mass.

f-set-mass-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 mass.

to f-set-mass-derived-autotroph-characters

;; This routine is to be executed by an autotroph.

set max-potential ( mass * g-acceleration * g-drop-distance )

LOG-TO-FILE ( word " Do-pre-tick: A(max-xrg) - (" floor max-potential ")" )

;; End of f-set-mass-derived-autotroph-characters

end

;;-----------------------------------------------------------------------------|

;; Initialize a population of heterotrophs.

to f-initialize-heterotrophs


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 ) )



;; 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.


;; who ;; set automatically

set heading 0






set color red


;; 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 mass g-h-initial-mass ;; the mass in this heterotroph.

set lb-genetic-factor g-h-lb-lower-bound ;; lower bound on prey mass.

set ub-genetic-factor g-h-ub-upper-bound ;; upper bound on prey mass.

set cause-of-death ge-cod-none ;; for statistical purposes

;; Compute value of controls scaled to mass.

f-set-mass-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



set cur-potential 0 ;; amount of gravitational potential energy


set b-is-in-oam ge-not-in-oam ;; 0=no; 1=RH-HOAM; 2=LH-HOAM


;; 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 mass.

to f-set-mass-derived-heterotroph-characters



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-mass-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

;;-----------------------------------------------

;; 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-mass; 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


;; 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 )

[

f-close-dpx-file

f-close-dpt-file

;; The Debug log file is handled differently elsewhere.

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


;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-move." ) ]

do-feed


;; [ LOG-TO-FILE ( word "Agents failed validity test: do-feed." ) ]

do-reproduce


;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-reproduce." ) ]

do-die


;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-die." ) ]

do-post-tick


;; [ LOG-TO-FILE ( word "Agents failed validity test: Do-post-tick." ) ]

end

;;-----------------------------------------------------------------------------|

;; D1 - do-pre-tick procedure( s )

;;-----------------------------------------------------------------------------|

to do-pre-tick



[

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 ]


]

;; 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.


set gl-causes-of-death-a-per-tick ( n-values 6 [0] )

set gl-causes-of-death-h-per-tick ( n-values 6 [0] )


set gl-causes-of-birth-a-per-tick ( n-values 2 [0] )

set gl-causes-of-birth-h-per-tick ( n-values 2 [0] )

;; Check to see if dpx file is full.

if( gb-dpx-on = 1 )

[

if( g-dpx-recno > g-recno-max )

[

f-reopen-dpx-file

]

]

;; 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

]


[

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


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



]

]

]

]

;; End f-stabilize-autotroph-population

end

;;-----------------------------------------------------------------------------|

;; D2 – do-move procedure(s)

;;-----------------------------------------------------------------------------|

to do-move



[

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 ]


]

;; 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 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.


[

;; 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 )


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


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 ]


ifelse( breedtype = autotrophs )

[


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 )


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

[


let old-count ( item codtype gl-causes-of-death-h-per-tick )


set gl-causes-of-death-h-per-tick

( replace-item codtype gl-causes-of-death-h-per-tick new-count )


set old-count ( item codtype gl-causes-of-death-h-cumulative )


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 ]


ifelse( breedtype = autotrophs )

[

;; show cobtype


let old-count ( item cobtype gl-causes-of-birth-a-per-tick )


set gl-causes-of-birth-a-per-tick

( replace-item cobtype gl-causes-of-birth-a-per-tick new-count )



set old-count ( item cobtype gl-causes-of-birth-a-cumulative )


set gl-causes-of-birth-a-cumulative

( replace-item cobtype gl-causes-of-birth-a-cumulative new-count )

]

;; Else breed is heterotrophs

[


let old-count ( item cobtype gl-causes-of-birth-h-per-tick )


set gl-causes-of-birth-h-per-tick

( replace-item cobtype gl-causes-of-birth-h-per-tick new-count )


set old-count ( item cobtype gl-causes-of-birth-h-cumulative )


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



[

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 ]


]


[

;; 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 )


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-mass mass

let lb-mass ( mass * lb-genetic-factor )

let ub-mass ( mass * 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 mass to act as an RH-HOAM when

;; forming an Open Atwood's Machine. I.e. mass > my-mass.

;; 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 mass of the prey must be > lb-mass.

;; - If the ub gene is active, the mass of the prey must be < ub-mass.

;; 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

( mass > my-mass ) ] )

;; Test the lb gene.

if( ( any? prey-list ) and ( gb-h-lb-gene-active = true ) )

[ set prey-list ( prey-list with [mass > lb-mass] ) ]

;; Test the ub gene.

if( ( any? prey-list ) and ( gb-h-ub-gene-active = true ) )

[ set prey-list ( prey-list with [mass < ub-mass] ) ]


;; 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

( mass > my-mass ) ] )

;; Test the lb gene.

if( ( any? prey-list ) and ( gb-h-lb-gene-active = true ) )

[ set prey-list ( prey-list with [mass > lb-mass] ) ]

;; Test the ub gene.

if( ( any? prey-list ) and ( gb-h-ub-gene-active = true ) )

[ set prey-list ( prey-list with [mass < ub-mass] ) ]

;; Select the most energetic of available prey.


[

set prey-list ( prey-list with

[cur-potential = ( max [cur-potential] of prey-list ) ] )

]

]

;; End else Herbivores


[

;; These two HOAMs (Halves of an Open Atwood's Machine) are now coupled

;; together as an Open Atwood's Machine (OAM). 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.

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 )

let heavy-mass ( [mass] of rh-hoam )

let light-mass ( [mass] 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 expell 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.

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



[

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 ]


]

;; Autotrophs come from forcible maintenance of population.

;; The population is topped up with sufficient fully energized

;; autotrophs in the 'do-pre-tick' function.


[

ask heterotrophs

[

f-set-heterotroph-repro-flag

f-reproduce-heterotroph

]

]


LOG-TO-FILE " Do-reproduce: procedure completed"

end

;;-----------------------------------------------------------------------------|

;; f-set-heterotroph-repro-flag

to f-set-heterotroph-repro-flag


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.


[ 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


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-mass ( [mass] 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 mass of this heterotroph to mutate.

;; Note, mass in this application is NOT to be considered an explicit

;; reference to mass, but rather, an analogue for 'ability to store

;; exergy'. This application implements a generalized Atwood's machine.

LOG-TO-FILE ( word " Do-reproduce: Heterotroph Dx - " who )

;; Copy the mass, then mutate it.

set mass mothers-mass


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 mass downwards.

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 mass that controls the ability to store exergy.

;; Determine whether it mutates upwards or downwards.

let old-mass mass

let sign ( -1 + 2 * ( random 2 ) ) ;; either a -1 or a 1.

let delta-mass ( g-h-mutation-factor * mass * sign )

set delta-mass ( delta-mass * ( random-float 1 ) )

set mass ( mass + delta-mass )

LOG-TO-FILE ( word " Do-reproduce: Mutate mass - H(old,delta,new) - ("

floor old-mass "," floor delta-mass "," floor mass ")" )

;; Recalculate the life function controls that are scaled to mass.

f-set-mass-derived-heterotroph-characters

;; Next, mutate the gene that controls the minimum mass of prey.


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 mass of prey.


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]


LOG-TO-FILE ( word " Do-reproduce: endowment-offered - " endowment-offered )

let endowment-remaining 0

;; Calculate the maximum energy charge allowed for this heterotroph.

let max-exergy ( mass * 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



[

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 ]



]

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

]

]


LOG-TO-FILE " Do-die: procedure completed"

end

;;-----------------------------------------------------------------------------|

;; f-set-autotroph-death-flag

to f-set-autotroph-death-flag


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


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.


[

let predator ( turtle pred-who )

ask predator

[


]

]

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


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.


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 cause-of-death ge-cod-hunger



]

if( age > g-h-DAT )

[


set cause-of-death ge-cod-old-age



]

;; 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




]

;; End f-set-heterotroph-death-flag

end

;;-----------------------------------------------------------------------------|

;; f-heterotroph-dies

to f-heterotroph-dies


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 )

[


]

;; 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.


[

let predator ( turtle pred-who )

ask predator

[


]

]

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 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



[

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 ]


]

;; 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." ) ]

;; Write "Data Per Tick" (dpt) macro data to CSV file, if it is turned on.

DPT-DUMP


;; 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


;; 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.

;;---------------------------------------------------------------------------|



;; 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-mass 0

set g-a-ave-max-potential 0

set g-a-ave-cur-potential 0

]

;; Else

[

set g-a-ave-mass ( sum [mass] 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-mass 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-mass ( sum [mass] 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


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


let answer "Non-phenotypic"

if( gb-h-ub-gene-active = true )

[ set answer "phenotypic" ]

report answer

end

;;--------------------------

;; DATA CAPTURE TO CSV FILES

;;--------------------------

;;-----------------------------------------------------------------------------|

;; Open a dpx file.

to f-open-dpx-file


;; DPX stands for 'Data Per Xaction'

;; Ensure previous dpx file is closed.

f-close-dpx-file

set gb-dpx-on 1

set gs-dpx-status "1 (On)"

set gs-dpx-file-name ( fr-construct-file-name "dpx" )

set g-dpx-recno 0

file-open gs-dpx-file-name

;; Write the mast autotroph for the file.

file-show "Data Per Transaction (DPX) File for a MppLab (NetLogo) Model."

file-show word "File Name: " gs-dpx-file-name

file-show ( word "Application Version Number: "gs-Version )

file-show ""

ifelse ( file-exists? gs-dpx-file-name )

[

;; Send a message directly to the command centre.

show word gs-dpx-file-name " opened."

;; Write the system parameter settings to the file.

f-write-system-settings

f-write-dpx-headers

]

;; else

[


show word gs-dpx-file-name " not opened."

set gb-dpx-on 0

set gs-dpx-status "0 (Off)"

set gs-dpx-file-name "DpxDummyName"

]

end

;;-----------------------------------------------------------------------------|

;; Write header recordS to the dpx data file.

to f-write-dpx-headers


;; Select the file


;; Write a header record for mutation data.

let line-out "DPX-A, "

set line-out ( word line-out "RecNo, " )

set line-out ( word line-out "Tick, " )

set line-out ( word line-out "Ma's Serial #, " )

set line-out ( word line-out "Serial #, " )

set line-out ( word line-out "HOAM #, " )

set line-out ( word line-out "Mass Was, " )

set line-out ( word line-out "Mass Is now, " )

file-print line-out

;; Write a header record for a mutated chain.

set line-out "DPX-C, "



;; Head of chain

set line-out ( word line-out "X-Action, " )

set line-out ( word line-out "Ma's Serial #, " )

set line-out ( word line-out "Serial #, " )

set line-out ( word line-out "Chain-time-to-drop, " )

set line-out ( word line-out "Chain-Eu, " )

set line-out ( word line-out "Chain-Mt, " )

set line-out ( word line-out "Chain-Mu, " )

set line-out ( word line-out "Chain-Mj, " )

set line-out ( word line-out "Who #, " )


set line-out ( word line-out "HOAM-mass, " )

set line-out ( word line-out "OAM-time-to-drop, " )


set line-out ( word line-out "OAM-rh-exergy, " )

set line-out ( word line-out "OAM-waste-heat, " )

set line-out ( word line-out "OAM-Eu, " )

set line-out ( word line-out "OAM-Mt, " )

set line-out ( word line-out "OAM-Mu, " )

set line-out ( word line-out "OAM-Mj, " )

;; Bodies within chain.

;; let hoam-index 1

;; while [ hoam-index < ( g-length-of-chains - 1 ) ] ;; Exclude auto and tail.

;; [

;; set line-out ( word line-out "Who #, " )

;; set line-out ( word line-out "HOAM #, " )

;; set line-out ( word line-out "HOAM-mass, " )

;; set line-out ( word line-out "OAM-time-to-drop, " )

;; set line-out ( word line-out "OAM-rh-exergy, " )

;; set line-out ( word line-out "OAM-waste-heat, " )

;; set line-out ( word line-out "OAM-Eu, " )

;; set line-out ( word line-out "OAM-Mt, " )

;; set line-out ( word line-out "OAM-Mu, " )

;; set line-out ( word line-out "OAM-Mj, " )

;; set hoam-index ( hoam-index + 1 )

;; ]

set line-out ( word line-out "Who #, " )


set line-out ( word line-out "HOAM-mass " )

file-print line-out

end

;;-----------------------------------------------------------------------------|

;; Write the data record type B (mutation event) for the dpx data file.

to WRITE-DPX-RECORD-B [ this-record ]


;; Select the file


;; Write a data record for X-Action.

set g-dpx-recno ( g-dpx-recno + 1 )

;; Record type

let line-out "DPX-B, "

;; Record number

set line-out ( word line-out g-dpx-recno ", " )

set line-out ( word line-out ticks ", " )

set line-out ( word line-out ( item 0 this-record ) ", " ) ;; Ma's Serial #

set line-out ( word line-out ( item 1 this-record ) ", " ) ;; Serial #

set line-out ( word line-out ( item 2 this-record ) ", " ) ;; HOAM #

set line-out ( word line-out ( item 3 this-record ) ", " ) ;; Mass was

set line-out ( word line-out ( item 4 this-record ) ", " ) ;; Mass is now

file-print line-out

end

;;-----------------------------------------------------------------------------|

;; Write a record to the DPX file, if appropriate.

to WRITE-DPX-D-RECORD [ index-of-chain action ]

;; The observer executes this routine.

;; Only execute if "data per event" is toggled on.

;; if ( gb-dpx-on = 1 )

;; [

;; Select the file

;; file-open gs-dpx-file-name

;; Increment the record number.

;; set g-dpx-recno ( g-dpx-recno + 1 )

;; Unpack the chain.

;; let this-chain ( item index-of-chain gl-chains-lib )

;; let this-value 0 ;; Dummy declaration

;; Record type

;; let line-out "DPX-D, "

;; set line-out ( word line-out g-dpx-recno ", " )

;; set line-out ( word line-out ticks ", " )

;; set line-out ( word line-out action ", " )

;; Unpack the auto of chain

;; let this-hoam ( item 0 this-chain )

;; Write data from the auto.

;; set this-value ( item 0 [mas-sn] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; Ma's serial number

;; set this-value ( item 0 [autotroph-sn] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; Serial number

;; set this-value ( item 0 [chain-time-to-drop] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; Chain-time-to-drop

;; set this-value ( item 0 [Eu-useful-energy-measure] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; Chain-Eu

;; set this-value ( item 0 [who] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; Who #

;; set this-value ( item 0 [index-into-chain] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; HOAM #

;; set this-value ( item 0 [mass] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; HOAM-mass

;; set this-value ( item 0 [oam-time-to-drop] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-time-to-drop

;; set this-value ( item 0 [rh-exergy] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-rh-exergy

;; set this-value ( item 0 [waste-heat] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-waste-heat

;; set this-value ( item 0 [Eu-in-oam] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-Eu


;; set this-value ( item 0 [Mt-in-oam] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-Mt

;; set this-value ( item 0 [Mu-in-oam] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-Mu

;; set this-value ( item 0 [Mj-in-oam] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-Mj

;; Bodies within chain.

;; let hoam-index 1

;; while [ hoam-index < ( g-length-of-chains - 1 ) ] ;; Exclude auto and tail.

;; [

;; set this-hoam ( item hoam-index this-chain )


;; set line-out ( word line-out this-value ", " ) ;; Who#





;; set this-value ( item 0 [oam-time-to-drop] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-time-to-drop

;; set this-value ( item 0 [rh-exergy] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-rh-exergy

;; set this-value ( item 0 [waste-heat] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-waste-heat

;; set this-value ( item 0 [Eu-in-oam] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-Eu

;; set this-value ( item 0 [Mt-in-oam] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-Mt

;; set this-value ( item 0 [Mu-in-oam] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-Mu

;; set this-value ( item 0 [Mj-in-oam] of this-hoam )

;; set line-out ( word line-out this-value ", " ) ;; OAM-Mj


;; ] ;; End while [ hoam-index < ( g-length-of-chains - 1 ) ]

;; The tail of the chain.


;; set this-hoam ( item hoam-index this-chain )


;; set line-out ( word line-out this-value ", " ) ;; Who #





;; file-print line-out

;; ] ;; End if ( gb-dpx-on = 1 )

end

;;-----------------------------------------------------------------------------|

;; Close the dpx file.

to f-close-dpx-file


;; DPX stands for 'Data Per Xaction'

if ( Is-string? gs-dpx-file-name )

[

if ( file-exists? gs-dpx-file-name )

[

;; Select the file


;; Close it.

file-close

]

]

set gb-dpx-on 0

set gs-dpx-status "0 (Off)"

set gs-dpx-file-name "DpxDummyName"

set g-dpx-recno 0

end

;;-----------------------------------------------------------------------------|

;; Close and reopen the dpx file, it is too full.

to f-reopen-dpx-file


f-close-dpx-file

f-open-dpx-file

end

;;-----------------------------------------------------------------------------|

;; Write a pair of records for the system settings.

to f-write-system-settings


;; A file must already be selected.

;; These system setting records are meant to be writtin right after the

;; mast auto lines.

;; Write a header record for system parameters.

let line-out "SYS-A, "

set line-out ( word line-out "Version, " )

set line-out ( word line-out "Scenario, " )

set line-out ( word line-out "PRNG-Seed, " )

set line-out ( word line-out "g-drop-distance, " )

set line-out ( word line-out "g-acceleration, " )

set line-out ( word line-out "gb-mutate-autos, " )

set line-out ( word line-out "gb-mutate-tails " )

file-print line-out


;; Write a data record for system parameters.

set line-out "SYS-B, "

set line-out ( word line-out gs-Version ", " )

set line-out ( word line-out gs-scenario ", " )

set line-out ( word line-out g-use-this-seed ", " )

set line-out ( word line-out g-drop-distance ", " )

set line-out ( word line-out g-acceleration ", " )

file-print line-out

;; Now, write instructions on how to process the data.

set line-out ( word "INSTRUCTIONS:" )

file-print line-out

set line-out ( word " - Copy the above rows of meta-data to a fresh sheet." )

file-print line-out

set line-out ( word " - Then delete the rows of meta-data and instructions." )

file-print line-out

set line-out ( word " - Then sort all columns and all rows of headers and data

using Column A as sort key." )

file-print line-out

end

;;-----------------------------------------------------------------------------|

;; Dump "Data Per Tick" data to dpt file, if open.

to DPT-DUMP


;; Activate only if the dpt file is open and ready to receive data.

if( gb-dpt-on = 1 )

[

;; If the file is full, close it. MS Excel can handle 1,048,000 records.

;; Terminate the file before 1,000,000 records.

ifelse( g-dpt-recno > g-recno-max ) [ f-reopen-dpt-file ]

[

;; Activate once per tick. Take a reading.

;; This collects macro-economic data of various kinds.

f-write-dpt-macro-data

]

]

end

;;-----------------------------------------------------------------------------|

;; Open a dpt file.

to f-open-dpt-file


;; DPT stands for 'Data Per Tick'

;; Ensure previous dpt file is closed.

f-close-dpt-file

set gb-dpt-on 1

set gs-dpt-status "1 (On)"

set gs-dpt-file-name ( fr-construct-file-name "dpt" )

set g-dpt-recno 0

file-open gs-dpt-file-name

;; Write the mast auto for the file.

file-show "Data Per Transaction (dpt) File for a MppLab (NetLogo) Model."

file-show ( word "Application Version Number: "gs-Version )

file-show word "File opened at:" date-and-time

file-show ""

ifelse ( file-exists? gs-dpt-file-name )

[


show word gs-dpt-file-name " opened."

;; Write the system parameter settings to the file.

f-write-system-settings

;; Write header records to the file.

f-write-dpt-headers

]

;; else

[


show word gs-dpt-file-name " not opened. Writing dpt data cancelled."

set gb-dpt-on 0

set gs-dpt-status "0 (Off)"

set gs-dpt-file-name "DptDummyName"

]

end

;;-----------------------------------------------------------------------------|

;; Write the header records for the dpt data file.

to f-write-dpt-headers


;; Select the file


;; Write a header record for general macro-level data.

f-write-dpt-a-header

;; Write headers for data collected per HOAM.

f-write-dpt-x-hoam-header "DPT-C" "Ave Mass per HOAM"

f-write-dpt-x-hoam-header "DPT-E" "Ave Low-grade energy per HOAM"

f-write-dpt-x-hoam-header "DPT-G" "Ave Hg energy transferred"

f-write-dpt-x-hoam-header "DPT-I" "Ave Lg energy exhausted"

;; Write headers for data collected per OAM.

f-write-dpt-x-oam-header "DPT-K" "Ave High-grade energy per OAM"

f-write-dpt-x-oam-header "DPT-M" "Ave Eu"

f-write-dpt-x-oam-header "DPT-O" "Ave Mt"

f-write-dpt-x-oam-header "DPT-Q" "Ave Mu"

f-write-dpt-x-oam-header "DPT-S" "Ave Mj"

;; Write header for data associated with switches that may be flipped.

f-write-dpt-u-header

end

;;-----------------------------------------------------------------------------|

;; Write the header record, the DPT-A record type.

to f-write-dpt-a-header



;; Select the file



let line-out "DPT-A, "



set line-out ( word line-out "g-no-of-chains, " )

set line-out ( word line-out "Ave age of chains, " )

set line-out ( word line-out "Ave drop time of chains, " )

set line-out ( word line-out "AofG Ave Eu, " )

set line-out ( word line-out "AofG Ave Mt, " )

set line-out ( word line-out "AofG Ave Mu, " )

set line-out ( word line-out "AofG Ave Mj " )

file-print line-out

end

;;-----------------------------------------------------------------------------|

;; Write the header record, the DPT-X record type, per HOAM.

to f-write-dpt-x-hoam-header [ s-rtype s-rname ]


;; Select the file


;; Write a header record for averages by HOAM type.

let line-out ( word s-rtype ", " )



set line-out ( word line-out s-rname " " )

;; let hoam-index 0

;; while [ hoam-index < g-length-of-chains ]

;; [

;; set line-out ( word line-out ", HOAM " hoam-index " " )


;; ]


end

;;-----------------------------------------------------------------------------|

;; Write the header record, the DPT-X record type, per OAM.

to f-write-dpt-x-oam-header [ s-rtype s-rname ]


;; Select the file


let GofA-list [ "DPT-M" "DPT-O" "DPT-Q" "DPT-S" ]

let b-is-GofA 0

if ( member? s-rtype GofA-list ) [ set b-is-GofA 1 ]

;; Write a header record for averages by OAM type.

let line-out ( word s-rtype ", " )



set line-out ( word line-out s-rname " " )

;; let oam-index 0

;; while [ oam-index < ( g-length-of-chains - 1 ) ]

;; [

;; set line-out ( word line-out ", OAM " oam-index " " )

;; set oam-index ( oam-index + 1 )

;; ]

if( b-is-GofA = 1 )

[ set line-out ( word line-out ", GofA Ave " ) ]

file-print line-out

end

;;-----------------------------------------------------------------------------|

;; Write the header record, the DPT-U record type.

to f-write-dpt-u-header


;; Select the file



let line-out "DPT-U, "



;;

set line-out ( word line-out "g-no-of-chains-max, " )

set line-out ( word line-out "g-length-of-chains, " )

set line-out ( word line-out "g-drop-distance, " )

set line-out ( word line-out "g-acceleration, " )

set line-out ( word line-out "gb-mutate-autos, " )

set line-out ( word line-out "gb-mutate-tails " )

file-print line-out

end

;;-----------------------------------------------------------------------------|

;; Write the data records for the dpt data file.

to f-write-dpt-macro-data


;; Select the file


;; Write a data record for general macro-level data.

;; f-write-dpt-a-data

;; Write data collected per HOAM.

;; f-write-dpt-x-hoam-data "DPT-D" "Ave Mass per HOAM" gl-ttl-mass-per-hoam

;; f-write-dpt-x-hoam-data "DPT-F" "Ave Low-grade energy per HOAM" gl-ttl-lg-nrg-

per-hoam

;; f-write-dpt-x-hoam-data "DPT-H" "Ave Hg energy transferred" gl-ttl-hg-nrg-per-

tick


;; f-write-dpt-x-hoam-data "DPT-J" "Ave Lg energy exhausted" gl-ttl-lg-nrg-per-

tick

;; Write data collected per OAM.

;; f-write-dpt-x-oam-data "DPT-L" "Ave High-grade energy per OAM" gl-ttl-hg-nrg-

per-oam

;; f-write-dpt-x-oam-data "DPT-N" "Ave Eu" gl-ttl-Eu-per-oam

;; f-write-dpt-x-oam-data "DPT-P" "Ave Mt" gl-ttl-Mt-per-oam

;; f-write-dpt-x-oam-data "DPT-R" "Ave Mu" gl-ttl-Mu-per-oam

;; f-write-dpt-x-oam-data "DPT-T" "Ave Mj" gl-ttl-Mj-per-oam

;; Write data associated with switches that may be flipped.

;; f-write-dpt-u-data

end

;;-----------------------------------------------------------------------------|

;; Write the data record, the dpt-a data record.

to f-write-dpt-a-data


;; Select the file

;; file-open gs-dpt-file-name


;; set g-dpt-recno ( g-dpt-recno + 1 )

;; Write a data record for general macro-level data.

;; let line-out "DPT-B, "

;; set line-out ( word line-out g-dpt-recno ", " )


;; let value-out 0

;; set line-out ( word line-out g-no-of-chains ", " )

;; set value-out ( g-ttl-age-of-autotrophs / g-no-of-chains )

;; set line-out ( word line-out value-out ", " )

;; set value-out ( g-ttl-dt-of-chains / g-no-of-chains )


;; set value-out ( g-ttl-Eu / g-no-of-chains )


;; set value-out ( g-ttl-Mt / g-no-of-chains )


;; set value-out ( g-ttl-Mu / g-no-of-chains )


;; set value-out ( g-ttl-Mj / g-no-of-chains )



end

;;-----------------------------------------------------------------------------|

;; Write the data record, the DPT-X record type, per HOAM.

to f-write-dpt-x-hoam-data [ s-rtype s-rname this-list ]


;; Select the file




;; Write a data record for averages per HOAM.

;; let line-out ( word s-rtype ", " )



;; set line-out ( word line-out s-rname " " )

;; let value-out 0 ;; Dummy declaration

;; let hoam-index 0

;; while [ hoam-index < g-length-of-chains ]

;; [

;; set value-out ( item hoam-index this-list )

;; set value-out ( value-out / g-no-of-chains )

;; set line-out ( word line-out ", " value-out " " )


;; ]


end

;;-----------------------------------------------------------------------------|

;; Write the data record, the DPT-X record type, per OAM.

to f-write-dpt-x-oam-data [ s-rtype s-rname this-list ]


;; Select the file




;; let GofA-list [ "DPT-N" "DPT-P" "DPT-R" "DPT-T" ]

;; let b-is-GofA 0

;; if ( member? s-rtype GofA-list ) [ set b-is-GofA 1 ]

;; let this-GofA 1

;; Write a header record for averages by OAM type.

;; let line-out ( word s-rtype ", " )



;; set line-out ( word line-out s-rname " " )

;; let value-out 0 ;; Dummy declaration.

;; let oam-index 0

;; while [ oam-index < ( g-length-of-chains - 1 ) ]

;; [

;; set value-out ( item oam-index this-list )

;; set value-out ( value-out / g-no-of-chains )


;; if( b-is-GofA = 1 ) [ set this-GofA ( this-GofA * value-out ) ]

;; set oam-index ( oam-index + 1 )

;; ]


;; if ( b-is-GofA = 1 )

;; [

;; set value-out ( this-GofA ^ ( 1 / g-length-of-chains ) )


;; ]


end

;;-----------------------------------------------------------------------------|

;; Write the data record, the DPT-V record type.

to f-write-dpt-u-data


;; Select the file




;; Write a data record for quasi-variable switches.

;; let line-out "DPT-V, "



;; set line-out ( word line-out g-no-of-chains-max ", " )

;; set line-out ( word line-out g-length-of-chains ", " )

;; set line-out ( word line-out g-drop-distance ", " )

;; set line-out ( word line-out g-acceleration ", " )

;; set line-out ( word line-out gb-mutate-autotrophs ", " )

;; set line-out ( word line-out gb-mutate-tails " " )


end

;;-----------------------------------------------------------------------------|

;; Close the dpt file.

to f-close-dpt-file


;; DPT stands for 'Data Per Tick'

if ( Is-string? gs-dpt-file-name )

[

if ( file-exists? gs-dpt-file-name )

[

;; Select the file


;; Close it.

file-close

]

]

set gb-dpt-on 0

set gs-dpt-status "0 (Off)"

set gs-dpt-file-name "DptDummyName"

set g-dpt-recno 0

end

;;-----------------------------------------------------------------------------|

;; Close and reopen the dpt file, it is too full.

to f-reopen-dpt-file


f-close-dpt-file

f-open-dpt-file

end

;;-----------------------------------------------------------------------------|

;; Construct a CSV data file name.

to-report fr-construct-file-name [ type-string ]


;;

;; Date-string format "01:19:36.685 PM 19-Sep-2002"

let date-string date-and-time

let file-name ( word "MppLab_" type-string "_" )

;; Append the year as yy.

set file-name word file-name ( substring date-string 25 27 )

;; Append the month as Mmm.

set file-name word file-name fr-convert-mmm-mm ( substring date-string 19 22 )

;; Append the day as dd.


;; Append a dash.

set file-name word file-name "_"

;; Append the hour as hh.

set file-name word file-name fr-convert1224 ( substring date-string 0 2 ) (

substring date-string 13 15 )

;; Append the minute as mm.


;; Append the second as ss.


;; Append the .csv extension.

set file-name word file-name ".csv"

report file-name

end

;;-----------------------------------------------------------------------------|

;; DEBUG AND DEBUG LOG FILE MANAGEMENT FUNCTIONS

;;-----------------------------------------------------------------------------|

;;-----------------------------------------------------------------------------|

;; Open a log file for debug output.

to f-open-log-file


;; 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.


;; 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.


;; Append the second as ss.


;; 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 ""


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 ]


;; 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 ]


;; 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


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.


;; 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



ifelse ( file-exists? gs-log-file-name )

[

;; Ensure the file is selected.


;; 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

;;-----------------------------------------------------------------------------|

to f-regulate-debug-switches

;; This routine is to be performed by the observer.

;; There are certain combinations of debug switch settings which are meaning-

;; less when in debug mode. Rather than placing this logic here and there

;; throughout the application, this routine has the logic to ensure that

;; the debug switches remain in a meaningful configuration.

if(gb-debug-on = 0 )

[

;; The debug feature is turned off. All switches should be set to default

;; positions, which is 'Off', or zero, or false.

set gb-debug-show-steps false

]

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.

f-regulate-debug-switches

;; gb-debug-on is a global Boolean and has value 1 (true) or 0 (false).


[

;; 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

if( gb-debug-show-steps = true )

[

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


[

;; 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( mass < 0 )

[

set b-heterotroph-is-valid false

LOG-TO-FILE ( word "mass = " mass "; at tick = " ticks )

]

report b-heterotroph-is-valid

end

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