Changeset 3651

Timestamp:

02/25/10 15:49:25 (7 months ago)

Author:

blwalker

Message:

Added WRITE_CLONE, WRITE_INJECT_EVENTS, and WRITE_COMPETITION analyze commands to the documentation. (The commands already existed.)
Updated WRITE_INJECT_EVENTS and WRITE_COMPETITION to write current-style actions instead of deprecated ones.
Clarified the documentation of SaveClone? and LoadClone? actions somewhat.

Location:

development

Files:

• documentation/actions.html (modified) (3 diffs)
• documentation/analyze.html (modified) (1 diff)
• source/analyze/cAnalyze.cc (modified) (4 diffs)

development/documentation/actions.html

@@ -3645 +3645 @@
   </p>
   <p>
-  
+    Sets up a population based on a save file generated by <a href="#SaveClone">SaveClone</a>
+    or WRITE_CLONE (an analyze command).  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 it would have if it had continued as 
+    it was going.
   </p>
 </li>
@@ -3699 +3703 @@
   </p>
   <p>
-    Save a clone of this organism to the file specified; if no filename is
+    Save a clone of this population to the file specified; if no filename is
   given, use the name clone.<em>update</em>.  The update number allows regular
   clones with distinct filenames to be saved with the same periodic event.
@@ -3705 +3709 @@
   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.
-
+  proceed identically as it would have if it had continued as it was going.
   </p>
 </li>

development/documentation/analyze.html

@@ -524 +524 @@
 
 <p>&nbsp;</p>
+<h3>Building Input Files for Avida</h3>
+
+<p>
+These commands build input files for Avida, using the capabilities of analyze mode to 
+automate some tedium.
+</p>
+
+<dl>
+<dt><strong>
+  WRITE_CLONE [<span class="cmdargopt">file='clone.dat'</span>]
+  [<span class="cmdargopt">num_cells=-1</span>]
+</strong></dt>
+<dd>
+  Creates a clone population file (as <a href="actions.html#SaveClone">SaveClone</a>) 
+  from the current batch, suitable for loading with <a href="actions.html#LoadClone">LoadClone</a>.  
+  The starting update is 0 and the archive is empty.  num_cells should be the number 
+  of cells in the world -- the default value of -1 will not be accepted by LoadClone, 
+  so be sure to specify the correct number.
+  <br />
+  <strong>Warning:</strong> Unlike SaveClone, WRITE_CLONE does not preserve location.  
+  Any spatial structure the population had is lost.
+</dd>
+<dt><strong>
+  WRITE_INJECT_EVENTS [<span class="cmdargopt">file='events_inj.cfg'</span>]
+  [<span class="cmdargopt">start_cell=0</span>] [<span class="cmdargopt">lineage=0</span>]
+</strong></dt>
+<dd>
+  Creates an <a href="events.html">events file</a> which injects all the genotypes of the current 
+  batch at update 0.  Injection starts at the given start_cell id and increments 
+  upward.  All injected organisms are assigned the given lineage label and start 
+  with the relevant merit; num_cpus copies of each genotype are injected.
+  <br />
+  <strong>Warning:</strong> injection is in order that the genotypes appear in the batch.  
+  This will break any spatial structure your population may have had.
+</dd>
+<dt><strong>
+  WRITE_COMPETITION [<span class="cmdargopt">join_UD=0</span>]
+  [<span class="cmdargopt">start_merit=50000</span>] [<span class="cmdargopt">file='events_comp.cfg'</span>]
+  [<span class="cmdargopt">batch_A=cur_batch-1</span>] 
+  [<span class="cmdargopt">file=batch_B=cur_batch</span>] [<span class="cmdargopt">grid_side=-1</span>]
+  [<span class="cmdargopt">lineage=0</span>]
+</strong></dt>
+<dd>
+  Creates an <a href="events.html">events file</a> which acts much like the one produced 
+  by WRITE_INJECT_EVENTS, but injects two populations (from the given batches), separates 
+  the populations at update 0 (via SeverGridRow grid_side), and joins them at the given 
+  join_UD.  Organisms from batch_A are injected starting at cell id 0; organisms from 
+  batch_B are injected starting at cell id grid_side*grid_side.    (If grid_side is negative, 
+  an attempt will be made to infer it from the number of organisms in the population.)
+  <br />
+  Each population should be square, of grid_side x grid_side dimensions.  (You will have 
+  to set up the world in avida.cfg to have WORLD_X of grid_side and WORLD_Y of 2*grid_side.)  
+  Each population may not be larger than 10,000 organisms.  Organisms from batch_A will 
+  be assigned the given lineage label; organisms from batch_B will be assigned the given 
+  lineage label + 1.
+  <br />
+  <strong>Warning:</strong> Like WRITE_INJECT_EVENTS, WRITE_COMPEITITIONS will destroy any 
+  spatial structure the populations may have had.  Also, since it severs/joins only the grid_side 
+  row, it is not suitable for use with WORLD_GEOMETRY values other than 1 (bounded grid).
+</dd>
+</dl>
+
+
+<p>&nbsp;</p>
 <h2><a name="USING_RESOURCES">Using Test CPU Resources Summary</a></h2>
 

development/source/analyze/cAnalyze.cc

@@ -6572 +6572 @@
     const cGenome & genome = genotype->GetGenome();
     
-    fp << "u 0 inject_sequence "
+    fp << "u 0 InjectSequence "
       << genome.AsString() << " "
       << start_cell << " "
@@ -6656 +6656 @@
     double cur_merit = start_merit;
     if (cur_merit < 0) cur_merit = genotype->GetMerit();
-    fp << "u 0 inject_sequence "
+    fp << "u 0 InjectSequence "
       << genome.AsString() << " "
       << inject_pos << " "
@@ -6672 +6672 @@
     double cur_merit = start_merit;
     if (cur_merit < 0) cur_merit = genotype->GetMerit();
-    fp << "u 0 inject_sequence "
+    fp << "u 0 InjectSequence "
       << genome.AsString() << " "
       << inject_pos << " "
@@ -6682 +6682 @@
   }
   
-  fp << "u 0 sever_grid_row" << grid_side << endl;
-  fp << "u " << join_UD << " join_grid_row " << grid_side << endl;
+  fp << "u 0 SeverGridRow" << grid_side << endl;
+  fp << "u " << join_UD << " JoinGridRow " << grid_side << endl;
 }