environment.html

有趣的模拟进化的程序 由国外一生物学家开发 十分有趣

        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.
<tr><td><font color="#0000AA">equ   </font>
    <td>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.
<tr><td><font color="#0000AA">logic_3AA-<br> logic_3CP</font>
    <td>These tasks include all 68 possible unique 3-input logic operations,
        many of which don't have easy-to-understand human readable names.
</table>

<p>
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:

<p>
<p align=center><b>Table 3: <font color="#004400">Reaction Process Specifications</font></b>
<table cellpadding=4 border=2>
<tr><th>Argument <th>Description <th>Default
<tr><td><font color="#0000AA">resource</font>
    <td>The name of the resource consumed.  By default, no resource is being
        consumed, and the 'max' limit is the amount absorbed.
    <td>infinite
<tr><td><font color="#0000AA">value</font>
    <td>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.
    <td>1.0
<tr><td><font color="#0000AA">type</font>
    <td>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.<br>
        <b>add</b>: Directly add the bonus to the current merit.<br>
        <b>mult</b>: Multiply the current merit by the bonus (warning: if
           the bonus is ever less than one, this will be detrimental!)<br>
        <b>pow</b>: Multiply the current merit by 2<sup>bonus</sup>.
           this is effectively multiplicative, but positive bonuses are
           always beneficial, and negative bonuses are harmful.<br>
    <td>add
<tr><td><font color="#0000AA">max</font>
    <td>The maximum amount of the resource consumed per occurrence.
    <td>1.0
<tr><td><font color="#0000AA">min</font>
    <td>The minimum amount of resource required.  If less than this quantity
        is available, the reaction ceases to proceed.
    <td>0.0
<tr><td><font color="#0000AA">frac</font>
    <td>The maximum fraction of the available resource that can be consumed.
    <td>1.0
<tr><td><font color="#0000AA">product</font>
    <td>The name of the by-product resource.  At the moment, only a single
        by-product can be produced at a time.
    <td>none
<tr><td><font color="#0000AA">conversion</font>
    <td>The conversion rate to by-product resource
    <td>1.0
</table>

<p>
If no process is given, a single associated process with all default
settings is assumed.  If multiple process statements are given, <i>all</i> 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:

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

<p>
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.

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

<p>
<p align=center><b>Table 4: <font color="#004400">Reaction Requisite Specifications</font></b>
<table cellpadding=4 border=2>
<tr><th>Argument <th>Description <th>Default
<tr><td><font color="#0000AA">reaction</font>
    <td>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.
    <td>none
<tr><td><font color="#0000AA">noreaction</font>
    <td>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.
    <td>none
<tr><td><font color="#0000AA">min_count</font>
    <td>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.
    <td>0
<tr><td><font color="#0000AA">max_count</font>
    <td>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.
    <td>INT_MAX
</table>

<p>
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.

<p>
EXAMPLES:

<p>
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:

<p>
&nbsp;&nbsp;&nbsp;REACTION AND logic:2a process:type=mult:value=4.0   requisite:max_count=1<br>
&nbsp;&nbsp;&nbsp;REACTION EQU logic:2h process:type=mult:value=32.0  requisite:max_count=1<br>

<p>
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:

<p>
&nbsp;&nbsp;&nbsp;RESOURCE  yummyA:initial=1000<br>
&nbsp;&nbsp;&nbsp;RESOURCE  yummyB:initial=1000<br>
&nbsp;&nbsp;&nbsp;REACTION  AtoB  gobbleA  process:resource=yummyA:frac=0.001:product=yummyB<br>
&nbsp;&nbsp;&nbsp;REACTION  BtoA  gobbleB  process:resource=yummyB:frac=0.001:product=yummyA<br>

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

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

<p>
As an example, to simulate a chemostat, we might have:<br>
<p>
&nbsp;&nbsp;&nbsp;RESOURCE glucose:inflow=100:outflow=0.01

<p>
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).

<p>
Limitations to this system:
<menu>
<li>Resources are currently all global; at some point soon we need to
    implement local resources.
<li>Only a single resource can be required at a time, and only a single
    by-product can be produced.
<li>Events to affect resources have not yet been implemented.
</menu>

<p>
The default setup is:

<pre>
  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
</pre>

<p>
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.

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

<pre>
  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
</pre>