NetLogo 5.3 User Manual: Transition Guide

Many models created in earlier versions of NetLogo also work in NetLogo 5.0. However, some models will need changes. If an old model isn't working, this section of the User Manual may be able to help you.

What issues may arise depends on what version of NetLogo the model was created with.

This guide only covers changes most likely to cause issues for users. See the Release notes for more complete details on differences between versions.

Changes for NetLogo 5.0

Plotting

In 5.0, you don't have to put your plotting code in the Code tab anymore. Instead, you can put it inside the plots themselves, in the Interface tab.

Nonetheless, the old style and all of the existing plotting primitives are still supported. We recommend changing your model to use the new style, but if you don't, it should still work.

The following example shows how to change a model to use the new style. Suppose you have a typical NetLogo 4.1 model with one plot called "populations" and two pens called "robots" and "humans". The old code might look like:

to setup
  clear-all
  ...
  do-plotting
end

to go
  ...
  tick
  do-plotting
end

to do-plotting
  set-current-plot "populations"
  set-current-plot-pen "robots"
  plot count robots
  set-current-plot-pen "humans"
  plot count humans
end

Here are the steps to make the transition:

Copy the plot count robots command and paste it into the Update Commands field for the robots pen in the plot edit dialog. Remove it from the do-plotting procedure.
The plot count humans command can be moved in the same way for the humans pen.
After those lines are removed from the do-plotting procedure, it doesn't actually do anything anymore! Remove it.
The final step is to replace the do-plotting procedure calls in setup and go. In setup, the do-plotting call should be changed to reset-ticks. In go, the do-plotting call should be changed to tick. reset-ticks and tick will both cause plotting to happen automatically.

The resulting (much simpler) code looks like this:

to setup
  clear-all
  ...
  reset-ticks
end

to go
  ...
  tick
end

For more details on how plotting works in NetLogo 5.0, see the Plotting Sections of the Programming Guide and the Interface Guide. For details on how plotting interacts with the tick counter, read on.

Tick counter

The way the tick counter works has changed in 5.0. Instead of being initially set to 0, the tick counter is initially blank.

`reset-ticks`

You must use reset-ticks to start the tick counter at 0 before using ticks, tick or tick-advance for the first time.

reset-ticks should go at the end of your setup procedure. Putting it there will allow your model to work with 5.0's new plotting features.

`reset-ticks` and plotting

In 5.0, you don't have to put your plotting code in the Code tab anymore. Instead, you can put it inside the plots themselves, in the Interface tab. Code inside plots is triggered by reset-ticks and tick. Resetting the tick counter runs plot setup code, and then it also runs plot update code to plot the initial state of the model. The initial state of the model won't be in place until the end of setup, so that's why reset-ticks should go at the end.

`__clear-all-and-reset-ticks`

In order for models from previous NetLogo versions to work in 5.0 without changes, when an old model is opened in 5.0, any occurrences of clear-all (or ca) are automatically changed to __clear-all-and-reset-ticks, which combines the effects of clear-all and reset-ticks. The two underscores on the name indicate that this is not a normal primitive, but exists only for backwards compatibility.

You should remove __clear-all-and-reset-ticks from your code, replace it with clear-all, and put reset-ticks at the end of your setup procedure. (This doesn't happen automatically because the structure of NetLogo models is too free-form for an automatic converter to reliably make the change for you.)

Unicode characters

NetLogo 5.0 fully supports international characters cross-platform, using the Unicode character set. NetLogo 5.0 model files always represent Unicode characters using the UTF-8 encoding.

Previous versions of NetLogo allowed Unicode characters to be used in some contexts. However, model files were saved in the platform's default encoding, which on most systems was something other than UTF-8. Characters were handled correctly on the same platform (e.g. two Windows machines), but could be altered if the model was moved between platforms (e.g. from Windows to Mac or vice versa).

When opening an existing model in NetLogo 5.0, if the model contains international or other non-ASCII characters, the characters may be interpreted incorrectly, because they were originally written in a platform-specific encoding, but then read back in in UTF-8.

If only a few characters are affected, you might find it easiest just to fix them manually.

But if you expect a large number of characters to be affected, and you want them translated automatically, you can use a third party utility to re-encode your .nlogo file from its original encoding into UTF-8. After conversion, open the model in NetLogo 5.0 and all characters should be correct.

Info tabs

NetLogo 5.0 uses the Markdown markup language to allow you to format your Info tab, including headers, bold and italics, images, and so forth.

Earlier versions of NetLogo used a custom markup language with much more limited capabilities.

When opening a model from an older version, NetLogo 5.0 translates your old markup into Markdown. Most of the time this produces good results, but you may want to check the results yourself and make sure that your Info tab still looks good.

Model speed

In NetLogo 5.0 every model has a "target frame rate" which affects the default speed at which the model runs, when the speed slider is in the middle, on the "normal speed" setting.

The default target frame rate for new models, and for models that were created in earlier versions of NetLogo, is 30 frames per second. If you are using tick-based updates, as we recommend for most models, then that translates to 30 ticks per second.

If your model runs slower in 5.0 than it ran in 4.1, it's probably just because its speed is being limited by this rate. If you want, you can press the Settings button in the Interface tab and change the frame rate to a higher number.

Some old models used the every command to set a default speed. In most case this can be now removed from the code, and the target frame rate setting used instead.

List performance

The underlying data structure for NetLogo lists has changed.

In NetLogo 4.1, a NetLogo list was represented internally as a singly linked list. Some operations on singly linked lists are fast (such as first and butfirst) but others are slow because they could require traversing the whole list (such as item and last).

In NetLogo 5.0, lists are now actually trees internally. As a result, some operations are a little slower, but other operations are drastically faster on long lists. See the Lists section of the Programming Guide for details.

Some models may run a little slower with the new data structure, especially if you make heavy use of short lists. But other models will run faster -- perhaps dramatically faster.

Some special ways of writing list-processing code that were useful in NetLogo 4.1 are no longer needed in 5.0. For example, since in 4.1 fput was fast and lput was slow, modelers sometimes built up lists in reverse order using fput, perhaps calling reverse later to restore the intended order. In NetLogo 5.0, you don't need to code that way anymore. fput and lput are the same speed.

Extensions API

If you are the author of an extension, you will need to recompile it against the 5.0 NetLogo.jar and lib directory for it to work with 5.0.

You may also need to be aware of the following changes:

Syntax constants

The code for specifying the syntax of a primitive has changed slightly, for example Syntax.TYPE_STRING is now Syntax.StringType(). (From Java, the pair of parentheses at the end is required. In Scala, you can omit them.)

LogoList construction

One significant change is that org.nlogo.api.LogoList no longer has a public constructor. Instead, there are two new ways to construct a LogoList.

If you have a java.lang.Iterable, you can copy the contents into a fresh LogoList by passing it to the static method LogoList.fromJava(). See the array extension source code for a sample usage.

Or, to build up a new list one item a time, use org.nlogo.api.LogoListBuilder. The Extensions Guide has sample code showing the use of LogoListBuilder.

Primitive classes

In prior NetLogo versions, the extensions API required that each extension primitive have its own separate top-level class with a no-argument constructor. These limitations have now been lifted. Also, api.Primitive objects are now made only once, when the extension is loaded, instead of every time the Code tab was recompiled.

Changes for NetLogo 4.0

Who numbering

Prior to NetLogo 4.0, a dead turtle's who number (stored in the who turtle variable) could be reassigned to a later newborn turtle. In NetLogo 4.0, who numbers are never reused until who numbering is reset to 0 by the clear-all or clear-turtles command. This change in behavior may break a few old models.

Turtle creation: randomized vs. "ordered"

NetLogo 4.0 provides two different observer commands for creating turtles, create-turtles (crt) and create-ordered-turtles (cro).

crt gives the new turtles random colors and random integer headings. cro assigns colors sequentially and gives the turtles sequential equally spaced headings, with the first turtle facing north (heading of 0).

Prior to NetLogo 4.0, the crt command behaved the way cro does now. If your old model depends on the "ordered" behavior, you will need to change your code to use cro instead of crt.

It is common for old models that used crt to contain extra commands to randomize the new turtles' headings, for example rt random 360 or set heading random 360. These commands are no longer necessary when used inside crt.

Adding strings and lists

Prior to NetLogo 4.0, the + (addition) operator could be used to concatenate strings and join lists. In current NetLogo, + only works on numbers. To concatenate strings, use the word primitive; to join lists together, use the sentence primitive. This language change was made to increase the speed of code that uses +.

Old code:

print "There are " + count turtles + " turtles."

New code:

print (word "There are " count turtles " turtles.")

Likewise, if you need to concatenate lists, use SENTENCE.

This change is not handled automatically when converting old models; users will need to change their code by hand.

We know this change will be awkward for users who are used to the old syntax. We have made this change for efficiency and consistency. We can implement an addition operator that only adds numbers much more efficiently than one that handles several different data types. Because addition is such a common operation, NetLogo's overall speed is affected.

The `-at` primitives

The observer may no longer use patch-at, turtles-at, and BREEDS-at. Use patch, turtles-on patch, and BREEDS-on patch instead. Note that patch now rounds its inputs (before it only accepted integer inputs).

Links

NetLogo 3.1 had supports for using links to connect turtles to make networks, graphs, and geometric figures. The links were themselves turtles.

In NetLogo 4.0, instead of links being turtles, links are now an independent fourth agent type, right alongside observer, turtles, patches. The primitives involving links are no longer considered experimental; they are now fully part of the language.

Models that use the old, experimental turtle-based link primitives will need to be updated to use link agents. The differences are not huge, but hand updating is required.

Links are documented in the Links section of the Programming Guide, and in the NetLogo Dictionary entries for the link primitives. See the Networks section of the Models Library for example models that use links. There are also some link-based Code Examples.

First you will need to remove any breeds called "links" if you are only using one type of links then you will not have to use breeds at all. If you are using multiple types of links see undirected-link-breed and directed-link-breed. Commands and reporters that contain the word "links" (like __create-links-with, etc.) will automatically be converted to the new form without underscores (create-links-with). However, primitives that use a different breed name (such as "edges") will not be converted. You will need to remove the underscores by hand and unless you are declaring a link breed with that name you will need to change the breed designation to "links".

The commands remove-link(s)-with/from/to no longer exist. Instead you should ask the links in question to die.

For example:

ask turtle 0 [ __remove-links-with link-neighbors ]

becomes

ask turtle 0 [ ask my-links [ die ] ]

Several of the layout commands have slightly different inputs, the first two inputs are generally a turtle agentset and a link agentset to perform the layout on. See the dictionary entries for details. layout-spring, layout-radial layout-tutte

You may also need to rearrange the declaration of turtles-own variables, since links were once actually turtles. Any variables that apply to links should be moved into a links-own block.

Since links are no longer turtles they no longer have the built-in turtle variables (though some of the link variables are the same such as color and label. If you formerly used the location of link turtles you will now need to calculate the midpoint of the link. This is fairly simple in a non-wrapping world.

to-report link-xcor
  report mean [xcor] of both-ends
end

to-report link-ycor
  report mean [ycor] of both-ends
end

it is a little bit trickier in a wrapping world but still fairly straightforward.

to-report link-xcor
  let other-guy end2
  let x 0
  ask end1
  [
    hatch 1
    [
      face other-guy
      fd [distance other-guy] of myself / 2
      set x xcor
      die
    ]
  ]
  report x
end

and similarly for ycor.

If you used either the size or heading of the link turtles you can use the reporters link-length and link-heading instead.

New "of" syntax

We have replaced three different language constructs, -of (with hyphen), value-from, and values-from with a single of construct (no hyphen).

old	new
`color-of turtle 0`	`[color] of turtle 0`
`value-from turtle 0 [size * size]`	`[size * size] of turtle 0`
`mean values-from turtles [size]`	`mean [size] of turtles`

When of is used with a single agent, it reports a single value. When used with an agentset, it reports a list of values (in random order, since agentsets are always in random order).

Note that when opening old models in the new version, -of, value-from, and values-from will automatically be converted to use "of" instead, but some nested uses of these constructs are too complex for the converter and must be converted by hand.

Serial `ask`

The ask command is now serial rather than concurrent. In other words, the asked agents will run one at a time. Not until one agent completely finishes the entire body of the ask does the next agent start.

Note that even the old ask was never truly concurrent; we simulated concurrent execution by interleaving execution among the agents using a turn-taking mechanism described in the NetLogo FAQ.

We have made this change because in our experience, users often wrote models that behaved in unexpected ways due to the simulated concurrency, but rarely wrote models that benefited from the simulated concurrency. Models exhibiting unexpected behavior could usually be fixed by adding the without-interruption command in the right places, but it was difficult for users to know whether that command was needed and if so, where.

In NetLogo 4.0, without-interruption is no longer necessary unless your model uses ask-concurrent (or a turtle or patch forever button containing code that depends on simulated concurrency). In most models, all uses of without-interruption can be removed.

The simulated concurrency formerly employed by "ask" is still accessible in three ways:

You may use the ask-concurrent primitive instead of ask to get the old simulated concurrency. (We don't recommend this, though.)
Commands issued in the Command Center directly to turtles, patches, or links have an implied ask-concurrent.
Turtle, patch, and link forever buttons have an implied ask-concurrent as well.

Note that ask itself is always serial regardless of the context in which it is used, however.

In our own Models Library, models that make use of this concurrency are rare. A prominent example, though, is Termites, which uses a concurrent turtle forever button.

Tick counter

NetLogo now has a built-in tick counter for representing the passage of simulated time.

You advance the counter by one using the tick command. If you need to read its value, there's a reporter called ticks. The clear-all command resets the tick counter; so does reset-ticks.

In most models the tick counter will be integer-valued, but if you want to use smaller increments of time, you can use the tick-advance command to advance the tick counter by any positive amount, including fractional amounts. Some Models Library models that use tick-advance are Vector Fields and the GasLab models.

The value of the tick counter is displayed in the toolbar at the top of the Interface tab. (You can use the Settings... button in the toolbar to hide the tick counter, or change the word "ticks" to something else.)

View update modes

In the past, NetLogo always tried to update the view about 20 times a second. We're now calling that "continuous" view updates. The biggest problem with it was that you usually want updates to happen between model ticks, not in the middle of a tick, so we had a checkbox on buttons that (by default) forced a display update after every button iteration. That made sure updates happened between ticks, but it didn't get rid of the intermediate updates. You had to use no-display and display to lock them out.

We still support continuous updates. They are the default when you start up NetLogo. But most Models Library models now use tick-based updates. With tick-based updates, updates happen only when the tick counter advances. (The display command can be used to force additional updates; see below.)

The advantages of tick-based updates as we see them are as follows:

Consistent, predictable view update behavior which does not vary from computer to computer or from run to run.
Intermediate updates can confuse the user of your model by letting them see things they aren't supposed to see, which may be misleading.
Increased speed. Updating the view takes time, so if one update per tick is enough, then enforcing than there is only one update per tick will make your model faster.
Instead of having a "force view update" checkbox in every button like in NetLogo 3.1, we only need one choice which applies to the entire model.
Using the speed slider to slow down a model now just inserts pauses between ticks. So with tick-based updates, setup buttons are no longer affected by the speed slider. This was a real annoyance with the old speed slider. (The annoyance persists for models that use continuous updates, though.)

As mentioned above, most models in our Models Library now use tick-based updates.

Even for models that would normally be set to tick-based updates, it may be useful to switch to continuous updates temporarily for debugging purposes. Seeing what's going on within a tick, instead of only seeing the end result of a tick, could help with troubleshooting.

If you switch your model to use tick-based updates, you'll also need to add the tick command to your code, otherwise the view won't update. (Note that the view still always updates when a button pops up or a command entered in the command center finishes, though. So it's not like the view will just stay frozen indefinitely.)

How to make a model use ticks and tick-based updates

Here are the steps to follow to convert your model to use ticks and tick-based updates in NetLogo 4.0:

In the Interface tab toolbar, on the right hand side where it says "update view:", change the setting from "continuously" to "on ticks".
Add the tick command to your go procedure, at or near the end. In Models Library models we always put tick after the agents move but before any plotting commands. That's because the plotting commands might contain something like plotxy ticks ... and we want the new value of the tick counter used, not the old one. Most models don't refer to the tick counter in their plotting commands, but nonetheless, for consistency and to avoid mistakes we suggest always putting tick before the plotting commands.

Some models will require some additional changes:

If your model already has a global "ticks" or "clock" or "time" variable, get rid of it. Use the tick command and ticks reporter instead. (If your model uses fractional increments of time, use tick-advance instead of tick.) If you had a monitor for that variable, you can get rid of it; there's now a tick counter in the toolbar.
clear-all resets the tick counter to zero. If you don't use clear-all in your setup procedure, then you may need to add reset-ticks to reset the counter to zero.
If you used no-display and display to prevent view updates from happening in the middle of go, you can get rid of them.
If your model needs to update the view without advancing the tick counter (examples: Party, Dice Stalagmite, network models with animated layout, models with mouse interaction buttons), use the display command to force additional view updates so the user can see what is going on.

Speed slider

Previous versions of NetLogo had a speed slider that could be used to make models run slower, so you can see what's going on.

In NetLogo 4.0, the slider can be used to speed up models as well. It does this by updating the view less frequently. Updating the view takes time, so the fewer updates, the faster the model runs.

The default position of the slider is in the center. When you're at the center, the slider says "normal speed".

As you move the slider away from the center position, the model will gradually run faster or slower.

At very high speeds, view updates become very infrequent and may be separated by several seconds. It may feel like the model is actually running slower, since the updates are so infrequent. But watch the tick counter, or other indicators such as plots, and you'll see that yes, the model really is running faster. If the infrequent updates are disconcerting, don't push the slider so far over.

When using tick-based updates, slowing the model down does not cause additional view updates. Rather, NetLogo simply pauses after each tick.

When using continuous updates, slowing the model down means view updates become more closely spaced. If you push the speed slider more than halfway to the left, the model will be running so slowly that you can watch turtles moving one at a time! This is new in NetLogo 4.0; in previous NetLogo versions, no matter how slowly you ran a model, you would never see the agents in an ask moving one at a time; all the agents in an ask always appeared to move together.

Numbers

NetLogo no longer maintains an internal distinction between integers and floating point numbers. So for example:

Old:

observer> print 3
3
observer> print 3.0
3.0
observer> print 1 + 2
3
observer> print 1.5 + 1.5
3.0
observer> print 3 = 3.0
true

(The last line shows that although the distinction between integer 3 and floating point 3.0 was maintained, the two numbers were still considered equal.)

New:

observer> print 3
3
observer> print 3.0
3
observer> print 1 + 2
3
observer> print 1.5 + 1.5
3
observer> print 3 = 3.0
true

We expect that only rare models will be negatively impacted by this change.

A benefit of this change is that NetLogo now supports a much larger range of integers. The old range was -2,147,483,648 to 2,147,483,647 (around +/- 2 billion); the new range is +/-9,007,199,254,740,992 (around +/- 9 quadrillion).

Agentset building

NetLogo 3.1 (and some earlier versions) included primitives called turtles-from and patches-from that were occasionally useful for building agentsets. In NetLogo 4.0, these primitives have been replaced with new primitives called turtle-set and patch-set that are much more flexible and powerful. (link-set exists as well.) See the entries for these primitives in the NetLogo Dictionary. Models that use the old turtles-from and patches-from will need to be altered by hand to use the new primitives.

RGB Colors

In NetLogo 3.1 RGB and HSB colors could be approximated as NetLogo colors using the rgb and hsb primitives. These have been renamed to approximate-rgb and approximate-hsb and now expect inputs in the range 0-255, not 0-1.

The full RGB spectrum is now available in NetLogo so it may no longer be necessary to use these primitives at all. You can set any color variable to a three-item RGB list, with values in the 0-255 range, and get that exact color. See the Color section of the Programming Guide for details.

Tie

In previous versions __tie was provided as an experimental feature. As of NetLogo 4.0 links have a tie-mode variable which can be set to "none", "free", or "fixed". In 4.0 tie is now a link-only primitive. This means that to tie turtle 1 to turtle 0 you write:

  ask turtle 0 [ create-link-to turtle 1 [ tie ] ]

See the Tie section of the programming guide for details.

Transition Guide

Changes for NetLogo 5.2

hsb primitives

GoGo extension

Changes for NetLogo 5.0

Plotting

Tick counter

`reset-ticks`

`reset-ticks` and plotting

`__clear-all-and-reset-ticks`

Unicode characters

Info tabs

Model speed

List performance

Extensions API

Syntax constants

LogoList construction

Primitive classes

Changes for NetLogo 4.1

Combining `set` and `of`

Changes for NetLogo 4.0

Who numbering

Turtle creation: randomized vs. "ordered"

Adding strings and lists

The `-at` primitives

Links

New "of" syntax

Serial `ask`

Tick counter

View update modes

How to make a model use ticks and tick-based updates

Speed slider

Numbers

Agentset building

RGB Colors

Tie

Changes for NetLogo 3.1

Agentsets

Wrapping

Random turtle coordinates

Transition Guide

Changes for NetLogo 5.2

hsb primitives

GoGo extension

Changes for NetLogo 5.0

Plotting

Tick counter

reset-ticks

reset-ticks and plotting

__clear-all-and-reset-ticks

Unicode characters

Info tabs

Model speed

List performance

Extensions API

Syntax constants

LogoList construction

Primitive classes

Changes for NetLogo 4.1

Combining set and of

Changes for NetLogo 4.0

Who numbering

Turtle creation: randomized vs. "ordered"

Adding strings and lists

The -at primitives

Links

New "of" syntax

Serial ask

Tick counter

View update modes

How to make a model use ticks and tick-based updates

Speed slider

Numbers

Agentset building

RGB Colors

Tie

Changes for NetLogo 3.1

Agentsets

Wrapping

Random turtle coordinates

`reset-ticks`

`reset-ticks` and plotting

`__clear-all-and-reset-ticks`

Combining `set` and `of`

The `-at` primitives

Serial `ask`