[avida-cvs] avida CVS commits: /current/doc events.html
bdbaer
avida-cvs at alife.org
Sun Aug 24 05:40:09 PDT 2003
bdbaer Sat Aug 23 21:40:09 2003 EDT
Modified files:
/avida/current/doc events.html
Log:
Added documention for some existing events.
Changed format (added </li> and replaced <p> with <br> inside <menu>'s) so
file looks better with Safari web browser.
-------------- next part --------------
Index: avida/current/doc/events.html
diff -u avida/current/doc/events.html:1.7 avida/current/doc/events.html:1.8
--- avida/current/doc/events.html:1.7 Wed Jun 4 11:34:45 2003
+++ avida/current/doc/events.html Sat Aug 23 21:40:08 2003
@@ -88,61 +88,77 @@
See the last example above to see how this event can be put into use.
Note that this event will even create a detailed column legend at the top
of your file so you don't need to seperately keep track of what the
- columns mean.
-<p>
-<li><b>print_average_data</b><br>
+ columns mean.</li>
+<br>
+<li><b>print_average_data</b> [<font color="#008800">filename</font>]<br>
A print_data shortcut that will print all of the population averages to
- the file "average.dat".
-<p>
-<li><b>print_error_data</b><br>
+ the file "average.dat".</li>
+<br>
+<li><b>print_error_data</b> [<font color="#008800">filename</font>]<br>
A print_data shortcut that will print all of the standard errors of the
- population statistics to the file "error.dat".
-<p>
-<li><b>print_variance_data</b><br>
+ population statistics to the file "error.dat".</li>
+<br>
+<li><b>print_variance_data</b> [<font color="#008800">filename</font>]<br>
A print_data shortcut that will print all of the veriances of the
- population statistics to the file "variance.dat".
-<p>
-<li><b>print_dominant_data</b><br>
+ population statistics to the file "variance.dat".</li>
+<br>
+<li><b>print_dominant_data</b> [<font color="#008800">filename</font>]<br>
A print_data shortcut that will print all of the statistics relating
- to the dominant genotype to the file "dominant.dat".
-<p>
-<li><b>print_stats_data</b><br>
+ to the dominant genotype to the file "dominant.dat".</li>
+<br>
+<li><b>print_stats_data</b> [<font color="#008800">filename</font>]<br>
A print_data shortcut that will print all of the miscellanous population
- statistics to the file "stats.dat".
-<p>
-<li><b>print_counts_data</b><br>
+ statistics to the file "stats.dat".</li>
+<br>
+<li><b>print_counts_data</b> [<font color="#008800">filename</font>]<br>
A print_data shortcut that will print all of the statistics the keep
track of counts (such as the number of organisms in the population or
- the number of instructions executed) to the file "count.dat".
-<p>
-<li><b>print_totals_data</b><br>
+ the number of instructions executed) to the file "count.dat".</li>
+<br>
+<li><b>print_totals_data</b> [<font color="#008800">filename</font>]<br>
A print_data shortcut that will print the same information as the
previous event, but the counts will be the totals for the entire
length of the run (for example, the total number of organisms ever) to
- the file "totals.dat".
-<p>
-<li><b>print_time_data</b><br>
+ the file "totals.dat".</li>
+<br>
+<li><b>print_time_data</b> [<font color="#008800">filename</font>]<br>
A print_data shortcut that will print all of the timing related
- statistics to the file "time.dat".
-<p>
-<li><b>print_tasks_data</b><br>
+ statistics to the file "time.dat".</li>
+<br>
+<li><b>print_tasks_data</b> [<font color="#008800">filename</font>]<br>
Print the number of organisms that are able to perform each task to the
file "tasks.dat". This uses the environment configuration to determine
- what tasks are in use.
-<p>
-<li><b>print_resource_data</b><br>
+ what tasks are in use.</li>
+<br>
+<li><b>print_tasks_exe_data</b> [<font color="#008800">filename</font>]<br>
+ ???? prints to tasks_exe.dat</li>
+<br>
+<li><b>print_mutation_data</b> [<font color="#008800">filename</font>]<br>
+ ???? prints to mutation.dat</li>
+<br>
+<li><b>print_mutation_rate_data</b> [<font color="#008800">filename</font>]<br>
+ Output (regular and log) statistics about individual copy
+ mutation rates (aver, stdev, skew, cur) to mutation_rates.dat.<br>
+ Useful only when mutation rate is set per organism.</li>
+<br>
+<li><b>print_divide_mut_data</b> [<font color="#008800">filename</font>]<br>
+ Output (regular and log) statistics about individual, per site,
+ rates divide mutation rates (aver, stdev, skew, cur) to divide_mut.dat.<br>
+ Use with multiple divide instuction set.</li>
+<br>
+
+<li><b>print_resource_data</b> [<font color="#008800">filename</font>]<br>
Print the current counts of each resource available to the population
to the file "resource.dat". This uses the environment configuration to
determine what resources are in use. Also creates seperate files
"resource_<i>resource_name</i>.m" (in a format that is designed to
- be read into Matlab) for each spatial resource.
-<p>
+ be read into Matlab) for each spatial resource.</li>
+<br>
<li><b>print_dom</b> [<font color="#008800">filename</font>]<br>
Print the dominant organism's genome (and lots of information about it)
into the file specified. If no filename is given, just use the genotypes
- assigned name.
-
-<p>
+ assigned name.</li>
+<br>
<li><b>save_clone</b> [<font color="#008800">filename</font>]<br>
Save a clone of this organism to the file specified; if no filename is
given, use the name clone.update#. The update number allows regular
@@ -150,9 +166,8 @@
Running "avida -l filename" will start an avida population with the
saved clone. Note that a clone only consists of the genomes in
the population, and their current state is lost, so the run may not
- proceed identically as to if it had continued as it was going.
-
-<p>
+ proceed identically as to if it had continued as it was going.</li>
+<br>
<li><b>detail_pop</b> [<font color="#008800">filename</font>]<br>
Save the genotypes and lots of statistics about the population to the
file specified; if not filename is given, use the name
@@ -174,18 +189,17 @@
10) update born<br>
11) update deactivated<br>
12) depth<br>
- 13) genome (as a string)<br>
-
-<p>
+ 13) genome (as a string)</li>
+<br>
<li><b>dump_historic_pop</b> [<font color="#008800">filename</font>]<br>
This event is used to output all of the ancestors of the currently
living population to the file specified, of "historic_dump.update#".
- It uses the same format as the "detail_pop" event.
-<p>
-<li><b>print_genotype_map</b> [<fontcolor="#008800">filename</font>]<br>
+ It uses the same format as the "detail_pop" event.</li>
+<br>
+<li><b>print_genotype_map</b> [<font color="#008800">filename</font>]<br>
This event is used to ouput a map of the gentype IDs for the
population grid to a file that is suitable to be read into Matlab.
- Default file name: genotype_map.m
+ Default file name: genotype_map.m </li>
</menu>
<p>
@@ -203,12 +217,12 @@
Do a landscape analysis of the dominant genotype in the population and
write the results to "landscape.dat". This is a collection of
statistics obtained from examining all possible mutations at the distance
- specified. The default distance is one.
-<p>
+ specified. The default distance is one.</li>
+<br>
<li><b>task_snapshot</b> [<font color="#008800">filename</font>]<br>
Run all organisms in the population through test cpus and print out the
number of tasks each can perform. The default filename is
- "tasks_update#.dat".
+ "tasks_update#.dat".</li>
</menu>
<p>
@@ -224,26 +238,42 @@
Inject a single organisms into the population. Arguments must be
included from left to right; if all arguments are left out, the default
creature is the ancestral organism, and it will be injected into cell 0,
- have an uninitialized merit, and be marked as liniage id 0.
-
-<p>
+ have an uninitialized merit, and be marked as liniage id 0.</li>
+<br>
<li><b>inject_all</b> [<font color="#008800">filename</font>] [<font color="#008800">merit</font>] [<font color="#008800">lineage_id</font>]<br>
Same as inject, but no cell_id is specified and the organism is placed
- into <i>all</i> cells in the population.
-<p>
+ into <i>all</i> cells in the population.</li>
+<br>
<li><b>apocalypse</b> [<font color="#008800">kill_prob</font>]<br>
Using the specified probability, test each organism to see if it is killed
- off.
-<p>
+ off.</li>
+<br>
<li><b>serieal_transfer</b> [<font color="#008800">num_organisms</font>]<br>
Similar to apocalypse, but we specify the exact number of organisms to
- keep alive after the event.
-<p>
+ keep alive after the event.</li>
+<br>
<li><b>kill_rectanle</b> [<font color="#008800">X1</font>] [<font
color="#008800">Y1</font>] [<font color="#008800">X2</font>] [<font
color="#008800">Y2</font>]<br>
Kill off all organisms in a rectangle defined by the points (X1, Y1) and
- (X2, Y2).
+ (X2, Y2).</li>
+</menu>
+
+<p>
+<h3>Resource Events</h3>
+
+Events that allow user to change amounts of resources in the system.
+
+<menu>
+<li><b>inject_resource</b> [<font color="#008800">res_name</font>]
+[<font color="#008800">res_count</font>] <br>
+ Inject (add) a specified amount of a specified resource. <b>res_name</b> must
+ already exist as a resource in environment file.</li>
+<br>
+<li><b>set_resource</b> [<font color="#008800">res_name</font>]
+[<font color="#008800">res_count</font>] <br>
+ Set the resource amount to a specific level. <b>res_name</b> must
+ already exist as a resource in environment file.</li>
</menu>
<p>
@@ -255,11 +285,27 @@
<menu>
<li><b>echo</b> [<font color="#008800">message</font>]<br>
Print the message included when the event is triggered. This is mostly
- used for debugging.
+ used for debugging.</li>
-<p>
+<br>
<li><b>exit</b><br>
- Quit the current run.
+ Quit the current run.</li>
+<br>
+<li><b>exit_if_generation_greater_than</b> [<font color="#008800">max_generation</font>]<br>
+ Ends the Avida run when the current generation exceeds <b>max_generation</b>.</li>
+<br>
+<li><b>exit_if_update_greater_than</b> [<font color="#008800">max_update</font>]<br>
+ Ends the Avida run when the current generation exceeds <b>max_update</b>.</li>
+<br>
+ <li><b>exit_if_ave_lineage_label_smaller</b> [<font color="#008800">lineage_label_crit_value</font>]<br>
+ Halts the avida run if the current average lineage label is smaller
+ than <b>lineage_label_crit_value</b>.</li>
+<br>
+ <li><b>exit_if_ave_lineage_label_larger</b> [<font color="#008800">lineage_label_crit_value</font>]<br>
+ Halts the avida run if the current average lineage label is larger
+ than <b>lineage_label_crit_value</b>.</li>
+<br>
+
</menu>
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