## The Environment File

This is the setup file for the task/resource system in avida.

Two main keywords are used in this file, RESOURCE and REACTION. Their formats are:

RESOURCE name[:flow] {name ...}
REACTION name task [process:...] [requisite:...]

Where 'name' is a unique identifier. Resources can have additional flow information to indicate starting amounts, inflow and outflow. Reactions are further described by the task that triggers them, the processes they perform (including resources used and the results of using them), and requisites on when they can occur.

All entries on a resource line are names of individual resources. Resources have a global quantity depleatable by all organisms. The resource name "infinite" is used to refer to an undepleatable resource. The following chart specifies additional descriptions for resource initialization.

Table 1: Resource Specifications
(blue variables used for all resources while red variables are only used for spatial resources)

Argument | Description | Default
--- | --- | ---
inflow | The number of units of the resource that enter the population over the course of an update. For a global resource this inflow occurs evenly throughout the update, not all at once. For a spatial resource this inflow amount is added every update evenly to all grid cells in the rectangle described by the points (inflowx1,inflowy1) and (inflowx2,inflowy2). | 0
outflow | The fraction of the resource that will flow out of the population each update. As with inflow, this happens continuously over the course of the update for a global resource. In the case of a spatial resource the fraction is withdrawn each update from each cell in the rectangle described by the points (outflowx1,outflowy1) and (outflowx2,outflowy2). | 0.0
initial | The initial abundance of the resource in the population at the start of an experiment. For a spatial resource the initial amount is spread evenly to each cell in the world grid. | 0

geometry

The layout of the resource in space.
global -- the entire pool of a resource is available to all organisms
grid -- organisms can only access resources in their grid cell. Resource can not flow past the edges of the world grid. (resource will use spatial parameters)
torus -- organisms can only access resources in their grid cell. Resource can flow to the oposite edges of the world grid. (resource will use spatial parameters)

global

inflowx1 | Leftmost coordinate of the rectange where resource will flow into world grid. | 0
inflowx2 | Rightmost coordinate of the rectange where resource will flow into world grid. | 0
inflowy1 | Topmost coordinate of the rectange where resource will flow into world grid. | 0
inflowy2 | Bottommost coordinate of the rectange where resource will flow into world grid. | 0
outflowx1 | Leftmost coordinate of the rectange where resource will flow out of world grid. | 0
outflowx2 | Rightmost coordinate of the rectange where resource will flow out of world grid. | 0
outflowy1 | Topmost coordinate of the rectange where resource will flow out of world grid. | 0
outflowy2 | Bottommost coordinate of the rectange where resource will flow out of world grid. | 0
xdiffuse | How fast material will diffuse right and left. This flow depends on the amount of resources in a given cell and amount in the cells to the right and left of it. (0.0 - 1.0) | 1.0
xgravity | How fast material will move to the right or left. This movement depends only on the amount of resource in a given cell. (-1.0 - 1.0) | 0
ydiffuse | How fast material will diffuse up and down. This flow depends on the amount of resources in a given cell and amount in the cells above and below it. (0.0 - 1.0) | 1.0
ygravity | How fast material will move to the up or down. This movement depends only on the amount of resource in a given cell. (-1.0 - 1.0) | 0

An example of a RESOURCE statement that begins a run with a fixed amount of the (global) resource in the environment, but has no inflow or outflows is:

      RESOURCE  glucose:initial=10000

If you wanted to make this into a chemostat with a 10000 equilibrium concentration for unused resources, you could put:

      RESOURCE  maltose:initial=10000:inflow=100:outflow=0.01

If you want a resource that exists spatially where the resource enters from the top and flows towards the bottom where it exits the system, you could use:

      RESOURCE lactose:initial=100000:inflow=100:outflow=0.1:inflowx1=0:\
      inflowx2=100:inflowy1=0:inflowy2=0:outflowx1=0:outflowx2=100:\
      outflowy1=100:outflowy2=100:ygravity=0.5

Defining a resource with no parameters means that it will start at a zero quantity and have no inflow or outflow. This is sometimes desirable if you want that resource to only be present as a byproduct of a reaction. Remember, though, that you should still have an outflow rate if its in a chemostat.

Each reaction must have a task that triggers it. Currently, eighty tasks have been implemented, as summarized in the following table (in approximate order of complexity):

Table 2: Available Tasks

Task | Description
--- | ---
echo | This task is triggered when an organism inputs a single number and outputs it without modification.
add | This task is triggered when an organism inputs two numbers, sums them together, and outputs the result.
sub | This task is triggered when an organism inputs two numbers, subtracts one from the other, and outputs the result.
not | This task is triggered when an organism inputs a 32 bit number, toggles all of the bits, and outputs the result. This is typically done either by nanding (by use of the `nand` instruction) the sequence to itself, or negating it and subtracting one. The latter approach only works since numbers are stored in twos-complement notation.
nand | This task is triggered when two 32 bit numbers are input, the values are "nanded" together in a bitwise fashion, and the result is output. Nand stands for "not and". The nand operation returns a zero if and only if both inputs are one; otherwise it returns a one.
and | This task is triggered when two 32 bit numbers are input, the values are "anded" together in a bitwise fashion, and the result is output. The and operation returns a one if and only if both inputs are one; otherwise it returns a zero.
orn | This task is triggered when two 32 bit numbers are input, the values are "orn" together in a bitwise fashion, and the result is output. The orn operation stands for or-not. It is returns true if for each bit pair one input is one or the other one is zero.
or | This task is triggered when two 32 bit numbers are input, the values are "ored" together in a bitwise fashion, and the result is output. It returns a one if either the first input or the second input is a one, otherwise it returns a zero.
andn | This task is triggered when two 32 bit numbers are input, the values are "andn-ed" together in a bitwise fashion, and the result is output. The andn operation stands for and-not. It only returns a one if for each bit pair one input is a one and the other input is not a one. Otherwise it returns a zero.
nor | This task is triggered when two 32 bit numbers are input, the values are "nored" together in a bitwise fashion, and the result is output. The nor operation stands for not-or and returns a one only if both inputs are zero. Otherwise a zero is returned.
xor | This task is triggered when two 32 bit numbers are input, the values are "xored" together in a bitwise fashion, and the result is output. The xor operation stands for "exclusive or" and returns a one if one, but not both, of the inputs is a one. Otherwise a zero is returned.
equ | This task is triggered when two 32 bit numbers are input, the values are equated together in a bitwise fashion, and the result is output. The equ operation stands for "equals" and will return a one if both bits are identical, and a zero if they are different.
logic_3AA- logic_3CP | These tasks include all 68 possible unique 3-input logic operations, many of which don't have easy-to-understand human readable names.

When describing a reaction, the "process" portion determines consumption of resources, their byproducts, and the resulting bonuses. There are several arguments (separated by colons; example below) to detail the use of a resource. Default values are in brackets:

Table 3: Reaction Process Specifications

Argument | Description | Default
--- | --- | ---
resource | The name of the resource consumed. By default, no resource is being consumed, and the 'max' limit is the amount absorbed. | infinite
value | Multiply the value set here by the amount of the resource consumed to obtain the bonus. (0.5 may be inefficient, while 5.0 is very efficient.) This allows different reactions to make use of the same resource at different efficiency levels. | 1.0

type

Determines how to apply the bonus (i.e. the amount of the resource absorbed times the value of this process) to change the merit of the organism.
add: Directly add the bonus to the current merit.
mult: Multiply the current merit by the bonus (warning: if the bonus is ever less than one, this will be detrimental!)
pow: Multiply the current merit by 2bonus. this is effectively multiplicative, but positive bonuses are always beneficial, and negative bonuses are harmful.

add

max | The maximum amount of the resource consumed per occurrence. | 1.0
min | The minimum amount of resource required. If less than this quantity is available, the reaction ceases to proceed. | 0.0
frac | The maximum fraction of the available resource that can be consumed. | 1.0
product | The name of the by-product resource. At the moment, only a single by-product can be produced at a time. | none
conversion | The conversion rate to by-product resource | 1.0
lethal | Whether the cell dies after performing the process | 0

If no process is given, a single associated process with all default settings is assumed. If multiple process statements are given, all are acted upon when the reaction is triggered. Assuming you were going to set all of the portions of process to be their default values, this portion of the reaction statement would appear as:

      process:resource=infinite:value=1:type=add:max=1:min=0:frac=1:product=none:conversion=1

This statement has many redundancies; for example, it would indicate that the associated reaction should use the inifite resource, making 'frac' and 'min' settings irrelevant. Likewise, since 'product' is set to none, the 'conversion' rate is never considered.

The "requisite" entry limits when this reaction can be triggered. The following requisites (in any combination) are possible:

Table 4: Reaction Requisite Specifications

Argument | Description | Default
--- | --- | ---
reaction | This limits this reaction from being triggered until the other reaction specified here has been triggered first. With this, the user can force organisms to perform reactions in a specified order. | none
noreaction | This limits this reaction from being triggered if the reaction specified here has already been triggered. This allows the user to make mutually exclusive reactions, and force organisms to "choose" their own path. | none
min_count | This restriction requires that the task used to trigger this reaction must be performed a certain number of times before the trigger will actually occur. This (along with max_count) allows the user to provide different reactions depending on the number of times an organism has performed a task. | 0
max_count | This restriction places a cap on the number of times a task can be done and still trigger this reaction. It allows the user to limit the number of times a reaction can be done, as well as (along with min_count) provide different reactions depending on the number of times an organism as performed a task. | INT_MAX

No restrictions are present by default. If there are multiple requisite entries, only *one* of them need be satisfied in order to trigger the reaction. Note though that a single requisite entry can have as many portions as needed.

EXAMPLES:

We could simulate the pre-environment system (in which no resources were present and task performace was rewarded with a fixed bonus) with a file including only lines like:

REACTION AND logic:2a process:type=mult:value=4.0 requisite:max_count=1
REACTION EQU logic:2h process:type=mult:value=32.0 requisite:max_count=1

No RESOURCE statements need be included since only the infinite resource is used (by default, since we don't specify another resources' name) # To create an environment with two resources that are converted back and forth as tasks are performed, we might have:

RESOURCE yummyA:initial=1000
RESOURCE yummyB:initial=1000
REACTION AtoB gobbleA process:resource=yummyA:frac=0.001:product=yummyB
REACTION BtoA gobbleB process:resource=yummyB:frac=0.001:product=yummyA

A value of 1.0 per reaction is default. Obviously "gobbleA" and "gobbleB" would have to be tasks described within avida.

A requisite against the other reaction being performed would prevent a single organism from garnering both rewards in equal measure.

As an example, to simulate a chemostat, we might have:

RESOURCE glucose:inflow=100:outflow=0.01

This would create a resource called "glucose" that has a fixed inflow rate of 10000 units where 20% flows out every update. (Leaving a steady state of 50,000 units if no organism-consumption occurs).

Limitations to this system:

- Resources are currently all global; at some point soon we need to implement local resources.
- Only a single resource can be required at a time, and only a single by-product can be produced.
- Events to affect resources have not yet been implemented.

  The default setup is:

        REACTION  NOT  not   process:value=1.0:type=pow  requisite:max_count=1
        REACTION  NAND nand  process:value=1.0:type=pow  requisite:max_count=1
        REACTION  AND  and   process:value=2.0:type=pow  requisite:max_count=1
        REACTION  ORN  orn   process:value=2.0:type=pow  requisite:max_count=1
        REACTION  OR   or    process:value=3.0:type=pow  requisite:max_count=1
        REACTION  ANDN andn  process:value=3.0:type=pow  requisite:max_count=1
        REACTION  NOR  nor   process:value=4.0:type=pow  requisite:max_count=1
        REACTION  XOR  xor   process:value=4.0:type=pow  requisite:max_count=1
        REACTION  EQU  equ   process:value=5.0:type=pow  requisite:max_count=1

  This creates an environment where the organisms get a bonus for performing any of nine tasks. Since none of the reactions are associated with a resource, the infinite resource is assumed, which is non-depeleatable. The max_count of one means they can only get the bonus from each reaction a single time.

  A similar setup that has 9 resources, one corresponding to each of the nine possible tasks listed above is:

        RESOURCE  resNOT:inflow=100:outflow=0.01   resNAND:inflow=100:outflow=0.01
        RESOURCE  resAND:inflow=100:outflow=0.01   resORN:inflow=100:outflow=0.01
        RESOURCE  resOR:inflow=100:outflow=0.01    resANDN:inflow=100:outflow=0.01
        RESOURCE  resNOR:inflow=100:outflow=0.01   resXOR:inflow=100:outflow=0.01
        RESOURCE  resEQU:inflow=100:outflow=0.01

        REACTION  NOT  not   process:resource=resNOT:value=1.0:frac=0.0025
        REACTION  NAND nand  process:resource=resNAND:value=1.0:frac=0.0025
        REACTION  AND  and   process:resource=resAND:value=2.0:frac=0.0025
        REACTION  ORN  orn   process:resource=resORN:value=2.0:frac=0.0025
        REACTION  OR   or    process:resource=resOR:value=4.0:frac=0.0025
        REACTION  ANDN andn  process:resource=resANDN:value=4.0:frac=0.0025
        REACTION  NOR  nor   process:resource=resNOR:value=8.0:frac=0.0025
        REACTION  XOR  xor   process:resource=resXOR:value=8.0:frac=0.0025
        REACTION  EQU  equ   process:resource=resEQU:value=16.0:frac=0.0025

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