;; Setup Procedures globals [ke-change count-forward-reactions count-reverse-reactions forward-rate reverse-rate] turtles-own [KE] to setup ca cct bluemols [ set color blue randomize ] cct yellowmols [ set color yellow randomize ] cct greenmols [set color green randomize ] cct brownmols [set color brown randomize ] ;; adjust the y-range of the plot to fit the number of molecules set-current-plot "concentrations" set-plot-y-range 0 max (list yellowmols bluemols greenmols brownmols) set-current-plot "Temperature (kinetic energy)" set-plot-y-range 40 60 ask turtles [set KE (random-normal (initial-temp) (.4 * initial-temp))] let diff mean values-from turtles [ke] - initial-temp ask turtles [set ke ke - diff] set forward-rate [] set reverse-rate [] set-current-plot "KE distribution" set-plot-x-range 0 2 * int max values-from turtles [ke] set-plot-pen-interval 20 histogram-from turtles [ke] end to randomize set shape "circle" setxy random-float screen-size-x random-float screen-size-y rt random-float 360 end ;; Runtime Procedures ;; In GO, turtles move according to a number of different checks and ;; procedures. Note that all turtles must have executed the procedure ;; CHECK-FOR-SPACE before any turtle can continue with CHECK-FOR-REACTION ;; because they are broken up into two seperate ask blocks. This ensures ;; that every turtle will be on its own patch before any turtles checks for ;; a reaction. ;; In UPDATE-KE, the kinetic energy change from one cycle of the model ;; is distributed randomly to all turtles unless Hold-temp is switched on. ;; TALLY-FORWARD and TALLY-REVERSE tally the number of forward and reverse ;; reactions, respectively, in the most recent 20 turns of GO to GO update-plot set ke-change 0 set count-forward-reactions 0 set count-reverse-reactions 0 ask turtles [ fd 1 wiggle check-for-space ] ask turtles [ check-for-reaction ] if hold-temp = false [update-ke] TALLY-FORWARD TALLY-REVERSE end ;; In WIGGLE, turtles are given a slight random twist to their heading. to wiggle rt random-float 2 lt random-float 2 end ;; In CHECK-FOR-SPACE, each turtle moves forward until it is alone in its ;; own patch. Note that the procedure calls itself if the check is true. ;; This technique is called recursion. CHECK-FOR-SPACE is called in GO. to check-for-space if (count turtles-here > 1) [ fd 1 check-for-space ] end ;; In CHECK-FOR-REACTION, every turtle checks for a turtle it can react with within ;; a radius which approximates the eight patches surrounding it. Blue turtles can ;; react with yellow turtles, and brown turtles can react with green turtles. to check-for-reaction if color = blue and any? turtles in-radius 1 with [color = yellow] [ ke-forward random-one-of turtles in-radius 1 with [color = yellow] ] if color = brown and any? turtles in-radius 1 with [color = green] [ ke-reverse random-one-of turtles in-radius 1 with [color = green] ] end ;; In ke-forward and ke-reverse, the collision is checked for sufficient energy ;; and a reaction sector (chance of correctly oriented collision) is applied ;; For example, if the difficulty forward is set to 10, it means that only 1 ;; collision out of 10, with sufficient activation energy, will actually react. to ke-forward [t] if ke + ke-of t > Ea-forward and random (difficulty-forward - 1) = 0 [react-forward random-one-of turtles in-radius 1 with [color = yellow]] end to ke-reverse [t] if ke + ke-of t > Ea-reverse and random (difficulty-reverse - 1) = 0 [react-reverse random-one-of turtles in-radius 1 with [color = green]] end ;; In REACT-FORWARD and REACT-REVERSE, the turtle changes the its color and the color ;; of the turtle they are reacting with, sets a random heading, and jumps away to ;; avoid further interaction. They are the same except for their colors. ;; Also, the kinetic energy increases (exothermic direction) or decreases (endothermic). ;; The increase or decrease is stored temporarily in KE-change and, at ;; the end of a turn of GO, divided randomly among all turtles by UPDATE-KE, ;; unless the Hold-temp switch is on. ;; The procedures UPDATE-FORWARD and UPDATE-REVERSE count the number of forward and reverse ;; reactions in one turn of GO. TALLY-FORWARD and TALLY-REVERSE keep the data for the most ;; recent 20 turns in a list, which is used by the Rate plot to generate a "moving-window" ;; estimate of the rate of forward and reverse reactions. to react-forward [t] set color-of t brown set color green set ke-change ke-change + Ea-reverse - Ea-forward update-forward rt random-float 360 jump 2 end to react-reverse [t] set color-of t blue set color yellow set ke-change ke-change + Ea-forward - Ea-reverse update-reverse rt random-float 360 jump 2 end to UPDATE-KE let newtemp mean values-from turtles [ke] + (ke-change / count turtles) ask turtles [set ke (random-normal (newtemp) (.4 * newtemp))] let diff mean values-from turtles [ke] - newtemp ask turtles [set ke ke - diff ] end to UPDATE-FORWARD set count-forward-reactions count-forward-reactions + 1 end to UPDATE-REVERSE set count-reverse-reactions count-reverse-reactions + 1 end ;; In NEWT (new temperature) turtles are assigned a new random KE with mean ;; equal to the new temperature to NEWT [new-temp] ask turtles [set ke random-normal (new-temp) (new-temp / 2.5)] let diff mean values-from turtles [ke] - new-temp ask turtles [set ke ke - diff] end ;; In NEWBL, NEWBR, NEWY, and NEWG the existing turtles of the indicated color are killed and replace ;; by a new number of turtles chosen by the user, of the same color. KE's are reassigned by calling the ;; NEWT procedure with the old temperature so that the change in turtle number does not affect the ;; temperature. to NEWBL [num] let k mean values-from turtles [ke] ask turtles with [color = blue] [die] crt num ask turtles with [ke = 0] [set color blue randomize ] newt k end to NEWBR [num] let k mean values-from turtles [ke] ask turtles with [color = brown] [die] crt num ask turtles with [ke = 0] [set color brown randomize ] newt k end to NEWY [num] let k mean values-from turtles [ke] ask turtles with [color = yellow] [die] crt num ask turtles with [ke = 0] [set color yellow randomize ] newt k end to NEWG [num] let k mean values-from turtles [ke] ask turtles with [color = green] [die] crt num ask turtles with [ke = 0] [set color green randomize ] newt k end to TALLY-FORWARD set forward-rate fput count-forward-reactions forward-rate if length forward-rate = 21 [set forward-rate remove-item 20 forward-rate] end to TALLY-REVERSE set reverse-rate fput count-reverse-reactions reverse-rate if length reverse-rate = 21 [set reverse-rate remove-item 20 reverse-rate] end ;; In UPDATE-PLOT, each pen in "concentrations" plots its corresponding turtle count. ;; In the Temperature plot, the average KE of all the turtles is shown. ;; In the Rates plot, the number of successful collisions in the last 20 turns of GO is ;; plotted separately for the forward (blue pen) and reverse (red pen) reactions. ;; In the Reaction quotient plot, the current value of the reaction quotient is plotted. ;; In the KE distribution plot, histograms of the original KE distribution (black) and the ;; current one (blue) are shown. to update-plot set-current-plot "concentrations" set-current-plot-pen "Yellows" plot count turtles with [color = yellow] set-current-plot-pen "Blues" plot count turtles with [color = blue] set-current-plot-pen "Browns" plot count turtles with [color = brown] set-current-plot-pen "Greens" plot count turtles with [color = green] set-current-plot "Temperature (kinetic energy)" set-current-plot-pen "Temp" plot mean values-from turtles [ke] set-current-plot "Rates" set-current-plot-pen "Forward" if length forward-rate > 0 [plot (reduce [?1 + ?2] forward-rate) / (length forward-rate)] set-current-plot-pen "Reverse" if length reverse-rate > 0 [plot (reduce [?1 + ?2] reverse-rate) / (length reverse-rate)] set-current-plot "Reaction Quotient" set-current-plot-pen "Reaction quotient" plot count turtles with [color = green] * count turtles with [color = brown] / count turtles with [color = blue] / count turtles with [color = yellow] set-current-plot "KE distribution" set-current-plot-pen "current" set-plot-pen-interval 20 histogram-from turtles [ke] end ; *** NetLogo Model Copyright Notice *** ; ; This model was created as part of the project: CONNECTED MATHEMATICS: ; MAKING SENSE OF COMPLEX PHENOMENA THROUGH BUILDING OBJECT-BASED PARALLEL ; MODELS (OBPML). The project gratefully acknowledges the support of the ; National Science Foundation (Applications of Advanced Technologies ; Program) -- grant numbers RED #9552950 and REC #9632612. ; ; Copyright 1998 by Uri Wilensky. All rights reserved. ; ; Permission to use, modify or redistribute this model is hereby granted, ; provided that both of the following requirements are followed: ; a) this copyright notice is included. ; b) this model will not be redistributed for profit without permission ; from Uri Wilensky. ; Contact Uri Wilensky for appropriate licenses for redistribution for ; profit. ; ; This model was converted to NetLogo as part of the project: ; PARTICIPATORY SIMULATIONS: NETWORK-BASED DESIGN FOR SYSTEMS LEARNING IN ; CLASSROOMS. The project gratefully acknowledges the support of the ; National Science Foundation (REPP program) -- grant number REC #9814682. ; Converted from StarLogoT to NetLogo, 2001. Updated 2002. ; ; To refer to this model in academic publications, please use: ; Wilensky, U. (1998). NetLogo Chemical Equilibrium model. ; http://ccl.northwestern.edu/netlogo/models/ChemicalEquilibrium. ; Center for Connected Learning and Computer-Based Modeling, ; Northwestern University, Evanston, IL. ; ; In other publications, please use: ; Copyright 1998 by Uri Wilensky. All rights reserved. See ; http://ccl.northwestern.edu/netlogo/models/ChemicalEquilibrium ; for terms of use. ; ; *** End of NetLogo Model Copyright Notice *** @#$#@#$#@ GRAPHICS-WINDOW 459 10 774 346 30 30 5.0 1 10 1 1 1 0 CC-WINDOW 5 570 783 665 Command Center BUTTON 269 172 346 205 setup setup NIL 1 T OBSERVER T NIL BUTTON 368 173 458 206 go / pause go T 1 T OBSERVER T NIL SLIDER 9 73 121 106 yellowmols yellowmols 0 500 280 10 1 NIL SLIDER 9 106 121 139 bluemols bluemols 0 500 400 10 1 NIL MONITOR 72 155 122 204 blues count turtles with [color = blue] 3 1 MONITOR 20 155 70 204 yellows count turtles with [color = yellow] 3 1 MONITOR 129 156 179 205 greens count turtles with [color = green] 3 1 MONITOR 180 156 230 205 browns count turtles with [color = brown] 3 1 PLOT 13 207 237 373 Concentrations time molecules 0.0 100.0 0.0 200.0 true true PENS "Yellows" 1.0 0 -256 false "Blues" 1.0 0 -16776961 false "Greens" 1.0 0 -11352576 false "Browns" 1.0 0 -6524078 false SLIDER 123 74 239 107 greenmols greenmols 0 500 50 10 1 NIL SLIDER 123 107 239 140 brownmols brownmols 0 500 90 10 1 NIL SLIDER 262 73 362 106 Ea-forward Ea-forward 0 150 80 5 1 SLIDER 401 74 499 107 Ea-reverse Ea-reverse 0 150 30 5 1 NIL MONITOR 469 158 526 207 av. KE mean values-from turtles [ke] 3 1 PLOT 471 208 705 374 Temperature (kinetic energy) time KE 0.0 100.0 0.0 10.0 true false PENS "Temp" 1.0 0 -65281 true SLIDER 251 108 381 141 difficulty-forward difficulty-forward 1 50 1 1 1 NIL SLIDER 388 108 519 141 difficulty-reverse difficulty-reverse 1 50 1 1 1 NIL SWITCH 606 352 704 385 Hold-temp Hold-temp 1 1 -1000 PLOT 241 208 466 373 Rates time Rates 0.0 100.0 0.0 20.0 true false PENS "Forward" 1.0 0 -16776961 true "Reverse" 1.0 0 -65536 true MONITOR 12 405 122 454 Reaction-quotient count turtles with [color = green] * count turtles with [color = brown] / \ncount turtles with [color = blue] / count turtles with [color = yellow] 5 1 PLOT 130 406 330 556 Reaction quotient time NIL 0.0 101.0 0.0 2.0 true false PENS "Reaction quotient" 1.0 0 -16777216 false TEXTBOX 39 52 92 70 Reactants TEXTBOX 153 52 202 70 Products TEXTBOX 268 51 356 69 Forward Reaction TEXTBOX 409 50 497 68 Reverse reaction PLOT 374 406 574 556 KE distribution KE # of molecules 0.0 150.0 0.0 10.0 true false PENS "start" 1.0 0 -16777216 true "KE" 1.0 0 -16776961 true "current" 1.0 0 -16776961 true SLIDER 13 13 114 46 Initial-temp Initial-temp 0 200 40 10 1 NIL @#$#@#$#@ WHAT IS IT? ----------- This is a modification to the "Netlogo chemical equilibrium model" by Uri Wilensky. New features that have been added to the basic model include the following: 1. The individual molecules have a property designated ke (kinetic energy). During setup, the ke is assigned as a random-normal variable as described below. The ke can change as the simulation runs. 2. The system as a whole has a property designated temperature, calculated as the mean of the kinetic energies. In real life, temperature (of an ideal gas) is proportional to mean kinetic energy. Since we are using a proportionality constant of one, the energy and temperature should not be interpreted in conventional units. During setup, the user sets the initial temperature with a slider. The ke's are then assigned as random numbers from a normal distribution with mean = initial temperature and SD = .4 * initial temperature. (This approximates the Maxwell distribution, albeit imperfectly.) If, as usually happens, the random numbers do not have precisely the desired mean, all the ke's are adjusted up or down by the same amount to obtain the desired mean. A graph displays the distribution of kinetic energies as a histogram. 3. Both the forward and reverse reactions are assigned an activation energy (which may be, and usually are, different), set by the user with sliders. When molecules of the correct colors collide, they can react only if their combined ke exceeds the activation energy. By setting temperature low relative to the activation energy, the frequency of the reaction will be decreased because many collisions will have too little energy. 4. Both the forward and reverse reactions are assigned another characteristic, which I've labeled "difficulty". Chemists will recognize this as the more familiar orientation factor. Most collisions fail because the molecules are not oriented properly to break old bonds and form new ones. The difficulty factor is used by the simulation as an attenuator. If the factor is set to 10, for example, then every time you have a potential reaction (right colors, enough kinetic energy), a random drawing is held, with a 1 in 10 chance of success, to see whether the reaction will be allowed to take place. The higher the difficulty setting, the lower the chances. 5. The simulation has a toggle switch called hold-temp. If this switch is ON, it is similar to conducting a real reaction in a temperature-controlled environment. Any heat produced or absorbed by the reaction is transferred to/absorbed from the environment and the temperature of the system remains constant. If the switch is OFF, it is similar to running the reaction in an insulated environment. In this case, heat changes are retained within the system, causing the temperature to change. The simulation keeps track of the energy changes as reactions occur. At the end of each turn of the simulation, the new temperature is calculated and new kinetic energies are assigned to all molecules (whether they participated in a productive collision or not), using the same procedure as during initial ke assignment in setup. 6. I've created "new" commands to facilitate playing with disturbances to equilibrium. These are entered in the command center (while the simulation is running or paused, but I think paused is easier to digest because you can take time to predict the effect, then restart the simulation and see if you were right). These commands all take a number as an argument (100 just for illustration purposes): newbl 100 changes the number of blue molecules to 100 newbr 100 changes the number of brown molecules to 100 newg 100 changes the number of green molecules to 100 newy 100 changes the number of yellow molecules to 100 newt 100 changes the temperature to 100 (can be used regardless of the hold-temp toggle) 7. Several additional graphs and monitors have been added to track new features. The rate graph tracks the average number of forward reactions per cycle (blue line) and the average number of reverse reactions per cycle (red line). For the first twenty turns of the simulation, it averages the reactions from all the turns since the beginning of the simulation; after that it averages the most recent 20 turns. The temperature graph shows the temperature (average ke) over time. The reaction quotient graph shows the evaluation of the equilibrium constant expression [GR][BR]/([BL][YE]). At equilibrium, this value should be independent of the initial concentrations, but is sensitive to temperature, activation energies, and difficulty settings. The ke distribution graph shows the initial distribution of kinetic energy (black line) as well as the current distribution (blue line). Note that as temperature increases, the distribution broadens; conversely, it narrows as temperature goes down. WHO MADE THESE MODIFICATIONS? ----------- Russ Maurer Hawken School PO Box 8002 Gates Mills, OH rmaur@hawken.edu Please send me your feedback or suggestions! The following is the description of the original model by Uri Wilensky: WHAT IS IT? ----------- This project shows how a simple chemical system comes to different equilibrium states depending on the concentrations of the initial reactants. Equilibrium is the term we use to describe a system in which there are no macroscopic changes. This means that the system "looks" like nothing is happening. In fact, in all chemical systems microscopic processes continue but in a balance that yields no changes at the macroscopic level. This model simulates two simple reactions of four molecules. The reactions can be written A + B yields C + D. And at the same time, of course, C + D yields A + B. A classic real-life example that would illustrate such reactions is the reactions of carbon monoxide with nitrous dioxide to produce carbon dioxide and nitrous monoxide. The reverse is also possible. All the reactants are gases. We could watch such an equilibrium system because NO2 is a reddish colored gas which is visible. However, the combining of nitrous dioxide (NO2) with carbon monoxide (CO) results in the colorless products nitrous monoxide (NO) and carbon dioxide (CO2), and so the system loses its reddish color. And yet, not all the color is lost. Ultimately the system comes to equilibrium with some of the "reactants" and some of the "products" present. How much "reactant" and "product" a system ends up with depends on a number of factors. The inherent kinetics of the reaction are of vital concern: For instance, some reactions tend to go in a particular direction because energy is released in that direction. A system's equilibrium is also affected by the concentrations of the reactants -- this is modeled here -- and by the system's temperature. HOW TO USE IT ------------- As stated above, this model simulates a chemical system of four different molecules. They are represented on the graphics screen as turtles of four different colors. In this simulation, yellow molecules react with blue molecules to produce brown molecules and green molecules. The model is setup by first adjusting the YELLOWMOLS and BLUEMOLS sliders and pushing the SETUP button. YELLOWMOLS sets how many yellow molecules the simulation starts with, while BLUEMOLS sets how many blue molecules the simulation starts with. The GO button sets the simulation in motion. Molecules move randomly and react with each other, changing color to represent rearrangement of atoms into different molecular structures. The system soon comes into equilibrium. Four monitors show how many of each kind of molecule are present in the system. There is also a plot which plots the number of each kind of molecule present versus time. THINGS TO NOTICE ---------------- Notice that the number of product molecules is limited by the smallest amount of reactant product. Notice that there are always the same number of reactant products since they are formed in a one-to-one correspondence with each other. THINGS TO TRY ------------- How do different amounts of the two reactants affect the final equilibrium. Are absolute amounts important, is it the difference between the amounts, or is it a ratio of the two reactants that matters? Try setting the YELLOWMOLS slider to 400 and the BLUEMOLS slider to 20, 40, 100, 200, and 400 in five successive simulations. What sort of equilibrium state do you predict in each case? Are certain ratios predictable? EXTENDING THE MODEL ------------------- What if the forward and reverse reaction rates were the variables controlled instead of initial concentrations. You could compare such a simulation with the one in this model and see if concentration and reaction rates act independently of each other, as measured by the final equilibrium state. You could also extend the program by allowing the user to introduce new molecules into the simulation while it is running. How would the addition of fifty blue molecules affect a system that was already at equilibrium? CREDITS AND REFERENCES ---------------------- To refer to this model in academic publications, please use: Wilensky, U. (2002). NetLogo Chemical Equilibrium model. http://ccl.northwestern.edu/netlogo/models/ChemicalEquilibrium. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL. In other publications, please use: Copyright 2002 by Uri Wilensky. All rights reserved. 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