[Avida-SVN] r2077 - in stable: . Avida.xcodeproj documentation source/actions source/analyze source/cpu source/main tests/energy_deme_level_res tests/energy_deme_level_res/expected tests/energy_deme_level_res/expected/data
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Sat Sep 8 16:11:33 PDT 2007
Author: brysonda
Date: 2007-09-08 19:11:33 -0400 (Sat, 08 Sep 2007)
New Revision: 2077
Added:
stable/documentation/energy_model.html
stable/source/main/cDemeCellEvent.cc
stable/source/main/cDemeCellEvent.h
stable/tests/energy_deme_level_res/expected/
stable/tests/energy_deme_level_res/expected/data/
stable/tests/energy_deme_level_res/expected/data/average.dat
stable/tests/energy_deme_level_res/expected/data/count.dat
stable/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m
stable/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m
stable/tests/energy_deme_level_res/expected/data/deme_donor.dat
stable/tests/energy_deme_level_res/expected/data/deme_fitness.dat
stable/tests/energy_deme_level_res/expected/data/deme_gest_time.dat
stable/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat
stable/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat
stable/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat
stable/tests/energy_deme_level_res/expected/data/deme_merit.dat
stable/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat
stable/tests/energy_deme_level_res/expected/data/deme_receiver.dat
stable/tests/energy_deme_level_res/expected/data/deme_resources.dat
stable/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m
stable/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m
stable/tests/energy_deme_level_res/expected/data/deme_task.dat
stable/tests/energy_deme_level_res/expected/data/dominant.dat
stable/tests/energy_deme_level_res/expected/data/instruction.dat
stable/tests/energy_deme_level_res/expected/data/instruction_histogram.dat
stable/tests/energy_deme_level_res/expected/data/resource.dat
stable/tests/energy_deme_level_res/expected/data/sleep.dat
stable/tests/energy_deme_level_res/expected/data/stats.dat
stable/tests/energy_deme_level_res/expected/data/tasks.dat
stable/tests/energy_deme_level_res/expected/data/tasks_exe.dat
stable/tests/energy_deme_level_res/expected/data/time.dat
Removed:
stable/tests/energy_deme_level_res/expected/
stable/tests/energy_deme_level_res/expected/data/
stable/tests/energy_deme_level_res/expected/data/average.dat
stable/tests/energy_deme_level_res/expected/data/count.dat
stable/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m
stable/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m
stable/tests/energy_deme_level_res/expected/data/deme_donor.dat
stable/tests/energy_deme_level_res/expected/data/deme_fitness.dat
stable/tests/energy_deme_level_res/expected/data/deme_gest_time.dat
stable/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat
stable/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat
stable/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat
stable/tests/energy_deme_level_res/expected/data/deme_merit.dat
stable/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat
stable/tests/energy_deme_level_res/expected/data/deme_receiver.dat
stable/tests/energy_deme_level_res/expected/data/deme_resources.dat
stable/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m
stable/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m
stable/tests/energy_deme_level_res/expected/data/deme_task.dat
stable/tests/energy_deme_level_res/expected/data/dominant.dat
stable/tests/energy_deme_level_res/expected/data/instruction.dat
stable/tests/energy_deme_level_res/expected/data/instruction_histogram.dat
stable/tests/energy_deme_level_res/expected/data/resource.dat
stable/tests/energy_deme_level_res/expected/data/sleep.dat
stable/tests/energy_deme_level_res/expected/data/stats.dat
stable/tests/energy_deme_level_res/expected/data/tasks.dat
stable/tests/energy_deme_level_res/expected/data/tasks_exe.dat
stable/tests/energy_deme_level_res/expected/data/time.dat
Modified:
stable/Avida.xcodeproj/project.pbxproj
stable/CMakeLists.txt
stable/documentation/analyze.html
stable/documentation/index.html
stable/source/actions/EnvironmentActions.cc
stable/source/actions/PopulationActions.cc
stable/source/actions/PrintActions.cc
stable/source/analyze/cAnalyze.cc
stable/source/analyze/cAnalyzeGenotype.h
stable/source/cpu/cHardwareBase.cc
stable/source/cpu/cHardwareCPU.cc
stable/source/cpu/cHardwareCPU.h
stable/source/main/avida.cc
stable/source/main/cAvidaConfig.h
stable/source/main/cDeme.cc
stable/source/main/cDeme.h
stable/source/main/cOrganism.cc
stable/source/main/cPhenotype.cc
stable/source/main/cPhenotype.h
stable/source/main/cPopulation.cc
stable/source/main/cPopulationCell.cc
stable/source/main/cPopulationCell.h
Log:
Merge in energe model changes from development branch.
Modified: stable/Avida.xcodeproj/project.pbxproj
===================================================================
--- stable/Avida.xcodeproj/project.pbxproj 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/Avida.xcodeproj/project.pbxproj 2007-09-08 23:11:33 UTC (rev 2077)
@@ -176,6 +176,7 @@
70DCAC9C097AF7C0002F8733 /* primitive.cc in Sources */ = {isa = PBXBuildFile; fileRef = 70DCAC9B097AF7C0002F8733 /* primitive.cc */; };
B4FA258A0C5EB65E0086D4B5 /* cPlasticPhenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = B4FA25810C5EB6510086D4B5 /* cPlasticPhenotype.cc */; };
B4FA25A90C5EB7880086D4B5 /* cPhenPlastGenotype.cc in Sources */ = {isa = PBXBuildFile; fileRef = B4FA259E0C5EB7600086D4B5 /* cPhenPlastGenotype.cc */; };
+ B516AF840C91E2D400023D53 /* cDemeCellEvent.cc in Sources */ = {isa = PBXBuildFile; fileRef = B516AF790C91E24600023D53 /* cDemeCellEvent.cc */; };
DCD8AC1F0C8A7C30004CBE6F /* cAnalyzeGenotypeTreeStats.cc in Sources */ = {isa = PBXBuildFile; fileRef = DCA4BEC10C8A758800D81B58 /* cAnalyzeGenotypeTreeStats.cc */; };
/* End PBXBuildFile section */
@@ -716,6 +717,8 @@
B4FA25810C5EB6510086D4B5 /* cPlasticPhenotype.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cPlasticPhenotype.cc; sourceTree = "<group>"; };
B4FA25820C5EB6510086D4B5 /* cPlasticPhenotype.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cPlasticPhenotype.h; sourceTree = "<group>"; };
B4FA259E0C5EB7600086D4B5 /* cPhenPlastGenotype.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cPhenPlastGenotype.cc; sourceTree = "<group>"; };
+ B516AF790C91E24600023D53 /* cDemeCellEvent.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; name = cDemeCellEvent.cc; path = source/main/cDemeCellEvent.cc; sourceTree = SOURCE_ROOT; };
+ B516AF7A0C91E24600023D53 /* cDemeCellEvent.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; name = cDemeCellEvent.h; path = source/main/cDemeCellEvent.h; sourceTree = SOURCE_ROOT; };
DCA4BEC10C8A758800D81B58 /* cAnalyzeGenotypeTreeStats.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cAnalyzeGenotypeTreeStats.cc; sourceTree = "<group>"; };
DCA4BEC20C8A758800D81B58 /* cAnalyzeGenotypeTreeStats.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cAnalyzeGenotypeTreeStats.h; sourceTree = "<group>"; };
DCC30FCF0762539D008F7A48 /* Doxyfile */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = Doxyfile; sourceTree = "<group>"; };
@@ -736,7 +739,7 @@
DCC315CE076253A5008F7A48 /* environment.rotate */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.rotate; sourceTree = "<group>"; };
DCC315D0076253A5008F7A48 /* task_event_gen.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.cc; sourceTree = "<group>"; };
DCC315D1076253A5008F7A48 /* task_event_gen.old.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.old.cc; sourceTree = "<group>"; };
- DCC3164D07626CF3008F7A48 /* avida */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = avida; sourceTree = BUILT_PRODUCTS_DIR; };
+ DCC3164D07626CF3008F7A48 /* avida */ = {isa = PBXFileReference; includeInIndex = 0; lastKnownFileType = "compiled.mach-o.executable"; path = avida; sourceTree = BUILT_PRODUCTS_DIR; };
/* End PBXFileReference section */
/* Begin PBXFrameworksBuildPhase section */
@@ -1153,6 +1156,8 @@
70C1EFA308C39F2100F50912 /* cHardwareBase.cc */,
70C1EF9E08C39F0E00F50912 /* cHardwareBase.h */,
70C1EFA508C39F2100F50912 /* cHardwareCPU.cc */,
+ B516AF790C91E24600023D53 /* cDemeCellEvent.cc */,
+ B516AF7A0C91E24600023D53 /* cDemeCellEvent.h */,
70C1EFA008C39F0E00F50912 /* cHardwareCPU.h */,
423335880BC067E3000DF681 /* cHardwareGX.cc */,
423335890BC067E3000DF681 /* cHardwareGX.h */,
@@ -1721,6 +1726,7 @@
70436B6C0C36C98900A05ABA /* PlatformExpert.cc in Sources */,
B4FA258A0C5EB65E0086D4B5 /* cPlasticPhenotype.cc in Sources */,
B4FA25A90C5EB7880086D4B5 /* cPhenPlastGenotype.cc in Sources */,
+ B516AF840C91E2D400023D53 /* cDemeCellEvent.cc in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
Modified: stable/CMakeLists.txt
===================================================================
--- stable/CMakeLists.txt 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/CMakeLists.txt 2007-09-08 23:11:33 UTC (rev 2077)
@@ -187,6 +187,7 @@
${MAIN_DIR}/cAvidaConfig.cc
${MAIN_DIR}/cBirthChamber.cc
${MAIN_DIR}/cDeme.cc
+ ${MAIN_DIR}/cDemeCellEvent.cc
${MAIN_DIR}/cEnvironment.cc
${MAIN_DIR}/cEventList.cc
${MAIN_DIR}/cFitnessMatrix.cc
Modified: stable/documentation/analyze.html
===================================================================
--- stable/documentation/analyze.html 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/documentation/analyze.html 2007-09-08 23:11:33 UTC (rev 2077)
@@ -356,6 +356,14 @@
have been loaded in, or a RECALCULATE (or RECALC) must have been run to collect
it.
</dd>
+<dt><strong>
+ PRINT_PHENOTYPES [<span class="cmdargopt">file='phenotype.dat']
+ [<span class="cmdargopt">total_task_count]
+ [<span class="cmdargopt">total_task_performance_count]
+</strong></dt>
+<dd>
+ Prints phenotypes in the current batch as determined by task-signature. Default statistics for each phenotype are number of organisms, number of genotypes, average genome length, average gestation time, viability, and tasks performed. Using the total_task_count and/or total_task_performance_count flags will add that statistic to the output. (In the case of total_task_performance_count, this will be an average over the members of the phenotype.)
+</dd>
<dt><strong>DETAIL [<span class="cmdargopt">file='detail.dat'</span>] [<span class="cmdargopt">format ...</span>]</strong></dt>
<dd>
Print out all of the stats for each genotype, one per line. The
@@ -632,7 +640,11 @@
<tr>
<td><strong>task.n</strong> (# of times task number n is done)</td>
<td><strong>task.n:binary</strong> (is task n done, 0/1)</td>
+ <td><strong>total_task_count</strong> (# of different tasks done)</td>
</tr>
+<tr>
+ <td><strong>total_task_performance_count</strong> (total # of tasks done)</td>
+</tr>
</table>
</div>
Copied: stable/documentation/energy_model.html (from rev 2076, development/documentation/energy_model.html)
===================================================================
--- stable/documentation/energy_model.html (rev 0)
+++ stable/documentation/energy_model.html 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,131 @@
+<html>
+<head>
+ <title>Avida : Energy Model</title>
+ <link rel="stylesheet" type="text/css" href="main.css" />
+</head>
+<body>
+
+<div class="revision">
+Revised 2007-07-07 BEB
+</div>
+
+<p>
+<a href="index.html">Return to the Index</a> |
+<a href="config.html">The Configuration File</a>
+</p>
+<hr />
+
+<div align="center">
+<h1>Energy Model</h1>
+</div>
+
+<a name="Overview"><h2>Overview</h2></a>
+<p>
+The energy model provides an organism with a metabolic rate, which is proportional to its stored energy (shown below).
+
+An organism with a higher metabolic rate will pay more energy to execute instructions than one with a lower rate.
+
+An organism must pay both virtual CPU cycle and energy costs to execute instructions.
+
+As instructions are executed the organism's stored energy level is reduced.
+
+Energy can be taken up by the organism when it completes a task, among others.
+</p>
+
+<center>
+Metabolic Rate = Stored Energy / <a href="#NUM_INST_EXC_BEFORE_0_ENERGY">NUM_INST_EXC_BEFORE_0_ENERGY</a>
+</center>
+
+<a name="Settings"><h2>Settings</h2></a>
+<p>
+The settings below are defults from <code>avida.cfg</code>
+<pre>
+### ENERGY_GROUP ###
+# Energy Settings
+<a href="#ENERGY_ENABLED">ENERGY_ENABLED</a> 0 # Enable Energy Model. 0/1 (off/on)
+<a href="#ENERGY_GIVEN_ON_INJECT">ENERGY_GIVEN_ON_INJECT</a> 0 # Energy given to organism upon injection.
+<a href="#ENERGY_GIVEN_AT_BIRTH">ENERGY_GIVEN_AT_BIRTH</a> 0 # Energy given to offspring upon birth.
+<a href="#FRAC_PARENT_ENERGY_GIVEN_AT_BIRTH">FRAC_PARENT_ENERGY_GIVEN_AT_BIRTH</a> 0.5 # Fraction of perent's energy given to offspring.
+<a href="#FRAC_ENERGY_DECAY_AT_BIRTH">FRAC_ENERGY_DECAY_AT_BIRTH</a> 0.0 # Fraction of energy lost due to decay during reproduction.
+<a href="#NUM_INST_EXC_BEFORE_0_ENERGY">NUM_INST_EXC_BEFORE_0_ENERGY</a> 0 # Number of instructions executed before energy is exhausted.
+<a href="#ENERGY_CAP">ENERGY_CAP</a> -1 # Maximum amount of energy that can be stored in an organism.
+ # -1 means the cap is set to Max Int
+<a href="#APPLY_ENERGY_METHOD">APPLY_ENERGY_METHOD</a> 0 # When should rewarded energy be applied to current energy?
+ # 0 = on divide
+ # 1 = on completion of task
+ # 2 = on sleep
+<a href="#FRAC_ENERGY_TRANSFER">FRAC_ENERGY_TRANSFER</a> 0.0 # Fraction of replaced organism's energy take by new resident
+<a href="#LOG_SLEEP_TIMES">LOG_SLEEP_TIMES</a> 0 # Log sleep start and end times. 0/1 (off/on)
+ # WARNING: may use lots of memory.
+</pre>
+</p>
+
+<a name="Description of Settings"><h2>Description of Settings</h2></a>
+<strong><a name="ENERGY_ENABLED">ENERGY_ENABLED</a></strong>
+<p>
+Flag that disables/enables the us of the energy model.
+
+0 = off, 1 = on
+</p>
+
+<strong><a name="ENERGY_GIVEN_ON_INJECT">ENERGY_GIVEN_ON_INJECT</a></strong>
+<p>
+How much energy is given to an injected organism.
+
+This number should be large enough to sustain the population until it can gather its own energy through tasks, etc..
+</p>
+
+<strong><a name="ENERGY_GIVEN_AT_BIRTH">ENERGY_GIVEN_AT_BIRTH</a></strong>
+<p>
+How much energy is given to an organism when it is born.
+</p>
+
+<strong><a name="FRAC_PARENT_ENERGY_GIVEN_AT_BIRTH">FRAC_PARENT_ENERGY_GIVEN_AT_BIRTH</a></strong>
+<p>
+Fraction of the parent(s) energy which is taken from the parent and given to the offspring at birth.
+</p>
+
+<strong><a name="FRAC_ENERGY_DECAY_AT_BIRTH">FRAC_ENERGY_DECAY_AT_BIRTH</a></strong>
+<p>
+Fraction of energy that decays on birth.
+</p>
+
+<strong><a name="NUM_INST_EXC_BEFORE_0_ENERGY">NUM_INST_EXC_BEFORE_0_ENERGY</a></strong>
+<p>
+Number of instructions an organism can execute before it runs out of energy assuming no new energy.
+
+Note: if instructions have energy costs > 0 then this options needs to be altered accordingly.
+</p>
+
+<strong><a name="ENERGY_CAP">ENERGY_CAP</a></strong>
+<p>
+Maximum amount of energy that can be stored in an organism.
+</p>
+
+<strong><a name="APPLY_ENERGY_METHOD">APPLY_ENERGY_METHOD</a></strong>
+<p>
+Specifies when newly received energy is applied to the organism energy store and metabolic rate.
+
+Note: the <code>sleep</code> instruction can also be used as an eat instructions if needed.
+</p>
+
+<strong><a name="FRAC_ENERGY_TRANSFER">FRAC_ENERGY_TRANSFER</a></strong>
+<p>
+Fraction of a replaced organism's energy transfered to the replacing organism.
+</p>
+
+<strong><a name="LOG_SLEEP_TIMES">LOG_SLEEP_TIMES</a></strong>
+<p>
+Logs start and end times, in updates, of all executions of the <code>sleep</code> instruction.
+
+Note: can use a lot of memory.
+</p>
+
+<hr />
+<p>
+<a href="index.html">Return to the Index</a> |
+<a href="config.html">The Configuration File</a>
+</p>
+
+</body>
+</html>
Modified: stable/documentation/index.html
===================================================================
--- stable/documentation/index.html 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/documentation/index.html 2007-09-08 23:11:33 UTC (rev 2077)
@@ -31,6 +31,7 @@
<p>
<a href="config.html">Setting up the Avida Configuration File</a>
+<br /><a href="energy_model.html">Energy model configuration</a>
<br /><a href="inst_set.html">Setting up the Instruction Set</a>
<br /><a href="events.html">Guidelines to setting up the Events File</a>
<br /><a href="environment.html">Guidelines to setting up Environments</a>
Modified: stable/source/actions/EnvironmentActions.cc
===================================================================
--- stable/source/actions/EnvironmentActions.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/actions/EnvironmentActions.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -455,8 +455,40 @@
}
};
+class cActionDelayedDemeEvent : public cAction
+{
+private:
+ int m_x1, m_y1, m_x2, m_y2; // bounding box of event in deme
+ int m_delay; // deme age when event occurs
+ int m_duration; // length of event; subverted when deme is reset
+
+public:
+ cActionDelayedDemeEvent(cWorld* world, const cString& args) : cAction(world, args), m_x1(-1), m_y1(-1), m_x2(-1), m_y2(-1), m_delay(-1), m_duration(-1)
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_x1 = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_y1 = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_x2 = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_y2 = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_delay = largs.PopWord().AsInt();
+ if (largs.GetSize()) m_duration = largs.PopWord().AsInt();
+ }
+
+ static const cString GetDescription() { return "Arguments: <int x1> <int y1> <int x2> <int y2> <int delay> <int duraion>"; }
+
+ void Process(cAvidaContext& ctx)
+ {
+ cPopulation& pop = m_world->GetPopulation();
+ int numDemes = pop.GetNumDemes();
+ for(int i = 0; i < numDemes; i++) {
+ pop.GetDeme(i).SetCellEvent(m_x1, m_y1, m_x2, m_y2, m_delay, m_duration);
+ }
+ }
+};
+
void RegisterEnvironmentActions(cActionLibrary* action_lib)
{
+ action_lib->Register<cActionDelayedDemeEvent>("DelayedDemeEvent");
action_lib->Register<cActionInjectResource>("InjectResource");
action_lib->Register<cActionInjectScaledResource>("InjectScaledResource");
action_lib->Register<cActionOutflowScaledResource>("OutflowScaledResource");
Modified: stable/source/actions/PopulationActions.cc
===================================================================
--- stable/source/actions/PopulationActions.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/actions/PopulationActions.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -988,6 +988,7 @@
'all' - ...all non-empty demes in the population.
'full_deme' - ...demes that have been filled up.
'corners' - ...demes with upper left and lower right corners filled.
+ 'deme-age' - ...demes that are a certain age
*/
class cActionReplicateDemes : public cAction
Modified: stable/source/actions/PrintActions.cc
===================================================================
--- stable/source/actions/PrintActions.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/actions/PrintActions.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -2124,7 +2124,96 @@
}
};
+class cActionDumpEnergyGrid : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionDumpEnergyGrid(cWorld* world, const cString& args) : cAction(world, args), m_filename("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ }
+ static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ void Process(cAvidaContext& ctx)
+ {
+ cString filename(m_filename);
+ if (filename == "") filename.Set("grid_energy.%d.dat", m_world->GetStats().GetUpdate());
+ ofstream& fp = m_world->GetDataFileOFStream(filename);
+
+ for (int i = 0; i < m_world->GetPopulation().GetWorldY(); i++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldX(); j++) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(i * m_world->GetPopulation().GetWorldX() + j);
+ double cell_energy = (cell.IsOccupied()) ? cell.GetOrganism()->GetPhenotype().GetStoredEnergy() : 0.0;
+ fp << cell_energy << " ";
+ }
+ fp << endl;
+ }
+ m_world->GetDataFileManager().Remove(filename);
+ }
+};
+class cActionDumpExecutionRatioGrid : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionDumpExecutionRatioGrid(cWorld* world, const cString& args) : cAction(world, args), m_filename("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ }
+ static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ void Process(cAvidaContext& ctx)
+ {
+ cString filename(m_filename);
+ if (filename == "") filename.Set("grid_exe_ratio.%d.dat", m_world->GetStats().GetUpdate());
+ ofstream& fp = m_world->GetDataFileOFStream(filename);
+
+ for (int i = 0; i < m_world->GetPopulation().GetWorldY(); i++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldX(); j++) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(i * m_world->GetPopulation().GetWorldX() + j);
+ double cell_executionRatio = (cell.IsOccupied()) ? cell.GetOrganism()->GetPhenotype().GetEnergyUsageRatio() : 1.0;
+ fp << cell_executionRatio << " ";
+ }
+ fp << endl;
+ }
+ m_world->GetDataFileManager().Remove(filename);
+ }
+};
+
+class cActionDumpCellDataGrid : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionDumpCellDataGrid(cWorld* world, const cString& args) : cAction(world, args), m_filename("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ }
+ static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ void Process(cAvidaContext& ctx)
+ {
+ cString filename(m_filename);
+ if (filename == "") filename.Set("grid_cell_data.%d.dat", m_world->GetStats().GetUpdate());
+ ofstream& fp = m_world->GetDataFileOFStream(filename);
+
+ for (int i = 0; i < m_world->GetPopulation().GetWorldY(); i++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldX(); j++) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(i * m_world->GetPopulation().GetWorldX() + j);
+ double cell_data = cell.GetCellData();
+ fp << cell_data << " ";
+ }
+ fp << endl;
+ }
+ m_world->GetDataFileManager().Remove(filename);
+ }
+};
+
class cActionDumpFitnessGrid : public cAction
{
private:
@@ -2248,6 +2337,35 @@
}
};
+class cActionDumpSleepGrid : public cAction
+{
+private:
+ cString m_filename;
+
+public:
+ cActionDumpSleepGrid(cWorld* world, const cString& args) : cAction(world, args), m_filename("")
+ {
+ cString largs(args);
+ if (largs.GetSize()) m_filename = largs.PopWord();
+ }
+ static const cString GetDescription() { return "Arguments: [string fname='']"; }
+ void Process(cAvidaContext& ctx)
+ {
+ cString filename(m_filename);
+ if (filename == "") filename.Set("grid_sleep.%d.dat", m_world->GetStats().GetUpdate());
+ ofstream& fp = m_world->GetDataFileOFStream(filename);
+
+ for (int i = 0; i < m_world->GetPopulation().GetWorldY(); i++) {
+ for (int j = 0; j < m_world->GetPopulation().GetWorldX(); j++) {
+ cPopulationCell& cell = m_world->GetPopulation().GetCell(i * m_world->GetPopulation().GetWorldX() + j);
+ double cell_energy = (cell.IsOccupied()) ? cell.GetOrganism()->IsSleeping() : 0.0;
+ fp << cell_energy << " ";
+ }
+ fp << endl;
+ }
+ m_world->GetDataFileManager().Remove(filename);
+ }
+};
class cActionDumpTaskGrid : public cAction
{
@@ -2563,6 +2681,10 @@
action_lib->Register<cActionDumpTaskGrid>("DumpTaskGrid");
action_lib->Register<cActionDumpDonorGrid>("DumpDonorGrid");
action_lib->Register<cActionDumpReceiverGrid>("DumpReceiverGrid");
+ action_lib->Register<cActionDumpEnergyGrid>("DumpEnergyGrid");
+ action_lib->Register<cActionDumpExecutionRatioGrid>("DumpExecutionRatioGrid");
+ action_lib->Register<cActionDumpCellDataGrid>("DumpCellDataGrid");
+ action_lib->Register<cActionDumpSleepGrid>("DumpSleepGrid");
// Print Settings
action_lib->Register<cActionSetVerbose>("SetVerbose");
Modified: stable/source/analyze/cAnalyze.cc
===================================================================
--- stable/source/analyze/cAnalyze.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/analyze/cAnalyze.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -2554,7 +2554,16 @@
// Load in the variables...
cString filename("phenotype.dat");
if (cur_string.GetSize() != 0) filename = cur_string.PopWord();
-
+
+ cString flag("");
+ bool print_ttc = false;
+ bool print_ttpc = false;
+ while (cur_string.GetSize() != 0) {
+ flag = cur_string.PopWord();
+ if (flag == "total_task_count") print_ttc = true;
+ else if (flag == "total_task_performance_count") print_ttpc = true;
+ }
+
// Make sure we have at least one genotype...
if (batch[cur_batch].List().GetSize() == 0) return;
@@ -2565,11 +2574,15 @@
tArray<int> genotype_counts(num_phenotypes);
tArray<double> total_length(num_phenotypes);
tArray<double> total_gest(num_phenotypes);
+ tArray<int> total_task_count(num_phenotypes);
+ tArray<int> total_task_performance_count(num_phenotypes);
phenotype_counts.SetAll(0);
genotype_counts.SetAll(0);
total_length.SetAll(0.0);
total_gest.SetAll(0.0);
+ total_task_count.SetAll(0);
+ total_task_performance_count.SetAll(0);
// Loop through all of the genotypes in this batch...
tListIterator<cAnalyzeGenotype> batch_it(batch[cur_batch].List());
@@ -2584,6 +2597,10 @@
genotype_counts[phen_id]++;
total_length[phen_id] += genotype->GetNumCPUs() * genotype->GetLength();
total_gest[phen_id] += genotype->GetNumCPUs() * genotype->GetGestTime();
+ for (int i = 0; i < num_tasks; i++) {
+ total_task_count[phen_id] += ((genotype->GetTaskCount(i) > 0) ? 1 : 0);
+ total_task_performance_count[phen_id] += genotype->GetTaskCount(i);
+ }
}
// Print out the results...
@@ -2594,9 +2611,22 @@
<< "# 2: Number of genotypes of this phenotye" << endl
<< "# 3: Average Genome Length" << endl
<< "# 4: Average Gestation Time" << endl
- << "# 5: Viability of Phenotype" << endl
- << "# 6+: Tasks performed in this phenotype" << endl
- << endl;
+ << "# 5: Viability of Phenotype" << endl;
+ if (print_ttc && print_ttpc) {
+ fp << "# 6: Total # of different tasks performed by this phenotype" << endl
+ << "# 7: Average # of tasks performed by this phenotype" << endl
+ << "# 8+: Tasks performed in this phenotype" << endl;
+ }
+ else if (print_ttc) {
+ fp << "# 6: Total # of different tasks performed by this phenotype" << endl
+ << "# 7+: Tasks performed in this phenotype" << endl;
+ }
+ else if (print_ttpc) {
+ fp << "# 6: Total # of tasks performed by this phenotype" << endl
+ << "# 7+: Tasks performed in this phenotype" << endl;
+ }
+ else { fp << "# 6+: Tasks performed in this phenotype" << endl; }
+ fp << endl;
// @CAO Lets do this inefficiently for the moment, but print out the
// phenotypes in order.
@@ -2619,6 +2649,10 @@
<< total_length[max_position] / phenotype_counts[max_position] << " "
<< total_gest[max_position] / phenotype_counts[max_position] << " "
<< (max_position & 1) << " ";
+ if (print_ttc) { fp << total_task_count[max_position] / genotype_counts[max_position] << " "; }
+ if (print_ttpc) {
+ fp << total_task_performance_count[max_position] / genotype_counts[max_position] << " ";
+ }
for (int i = 1; i <= num_tasks; i++) {
if ((max_position >> i) & 1 > 0) fp << "1 ";
else fp << "0 ";
@@ -8263,6 +8297,10 @@
ADD_GDATA(cString, "link.tasksites", "Phenotype Map", GetMapLink, SetNULL, 0, 0, 0);
ADD_GDATA(cString, "html.sequence", "Genome Sequence", GetHTMLSequence, SetNULL, 0, "(N/A)", "");
+ // coarse-grained task stats
+ ADD_GDATA(int, "total_task_count","# Different Tasks", GetTotalTaskCount, SetNULL, 1, 0, 0);
+ ADD_GDATA(int, "total_task_performance_count", "Total Tasks Performed", GetTotalTaskPerformanceCount, SetNULL, 1, 0, 0);
+
const cEnvironment& environment = m_world->GetEnvironment();
for (int i = 0; i < environment.GetNumTasks(); i++) {
cString t_name, t_desc;
Modified: stable/source/analyze/cAnalyzeGenotype.h
===================================================================
--- stable/source/analyze/cAnalyzeGenotype.h 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/analyze/cAnalyzeGenotype.h 2007-09-08 23:11:33 UTC (rev 2077)
@@ -376,6 +376,31 @@
const tArray<int> & GetTaskCounts() const {
return task_counts;
}
+
+ double GetTaskQuality(int task_id) const {
+ if (task_id >= task_counts.GetSize()) return 0;
+ return task_qualities[task_id];
+ }
+ const tArray<double> & GetTaskQualities() const {
+ return task_qualities;
+ }
+
+ // number of different tasks performed
+ int GetTotalTaskCount() const {
+ int total_task_count = 0;
+ for(int i = 0; i < task_counts.GetSize(); i++)
+ { if (task_counts[i] > 0) total_task_count++; }
+ return total_task_count;
+ }
+
+ // total number of tasks performed, including multiple performances
+ int GetTotalTaskPerformanceCount() const {
+ int total_task_performance_count = 0;
+ for(int i = 0; i < task_counts.GetSize(); i++)
+ { total_task_performance_count += task_counts[i]; }
+ return total_task_performance_count;
+ }
+
int GetEnvInput(int input_id) const{
if (input_id >= m_env_inputs.GetSize()) return 0;
return m_env_inputs[input_id];
@@ -384,14 +409,6 @@
return m_env_inputs;
}
- double GetTaskQuality(int task_id) const {
- if (task_id >= task_counts.GetSize()) return 0;
- return task_qualities[task_id];
- }
- const tArray<double> & GetTaskQualities() const {
- return task_qualities;
- }
-
// Comparisons... Compares a genotype to the "previous" one, which is
// passed in, in one specified phenotype.
// Return values are:
Modified: stable/source/cpu/cHardwareBase.cc
===================================================================
--- stable/source/cpu/cHardwareBase.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/cpu/cHardwareBase.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -817,8 +817,11 @@
}
bool cHardwareBase::Inst_DoubleEnergyUsage(cAvidaContext& ctx) {
- organism->GetPhenotype().DoubleEnergyUsage();
- return true;
+ double energy_req = inst_energy_cost[IP().GetNextInst().GetOp()]
+ * cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio() * 2.0, m_world)
+ / 100.0; //compensate by factor of 100
+
+ return organism->GetPhenotype().DoubleEnergyUsage(energy_req);
}
bool cHardwareBase::Inst_HalfEnergyUsage(cAvidaContext& ctx) {
@@ -826,7 +829,6 @@
return true;
}
-
// This method will test to see if all costs have been paid associated
// with executing an instruction and only return true when that instruction
// should proceed.
@@ -840,6 +842,7 @@
double energy_req = inst_energy_cost[cur_inst.GetOp()] * (organism->GetPhenotype().GetMerit().GetDouble() / 100.0); //compensate by factor of 100
if (energy_req > 0.0) {
+ int cellID = organism->GetCellID();
if (organism->GetPhenotype().GetStoredEnergy() >= energy_req) {
inst_energy_cost[cur_inst.GetOp()] = 0;
// subtract energy used from current org energy.
@@ -847,7 +850,6 @@
// tracking sleeping organisms
cString instName = m_world->GetHardwareManager().GetInstSet().GetName(cur_inst);
- int cellID = organism->GetCellID();
if( instName == cString("sleep") || instName == cString("sleep1") || instName == cString("sleep2") ||
instName == cString("sleep3") || instName == cString("sleep4")) {
cPopulation& pop = m_world->GetPopulation();
@@ -857,7 +859,8 @@
pop.GetCell(cellID).GetOrganism()->SetSleeping(true);
m_world->GetStats().incNumAsleep(pop.GetCell(cellID).GetDemeID());
}
- } else { // not enough energy
+ } else {
+ organism->GetPhenotype().SetToDie();
return false;
}
}
Modified: stable/source/cpu/cHardwareCPU.cc
===================================================================
--- stable/source/cpu/cHardwareCPU.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/cpu/cHardwareCPU.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -50,6 +50,7 @@
#include <climits>
#include <fstream>
+#include <cmath>
using namespace std;
@@ -202,7 +203,9 @@
tInstLibEntry<tMethod>("sense", &cHardwareCPU::Inst_SenseLog2), // If you add more sense instructions
tInstLibEntry<tMethod>("sense-unit", &cHardwareCPU::Inst_SenseUnit), // and want to keep stats, also add
tInstLibEntry<tMethod>("sense-m100", &cHardwareCPU::Inst_SenseMult100), // the names to cStats::cStats() @JEB
-
+ // Data collection
+ tInstLibEntry<tMethod>("collect-cell-data", &cHardwareCPU::Inst_CollectCellData),
+
tInstLibEntry<tMethod>("donate-rnd", &cHardwareCPU::Inst_DonateRandom),
tInstLibEntry<tMethod>("donate-kin", &cHardwareCPU::Inst_DonateKin),
tInstLibEntry<tMethod>("donate-edt", &cHardwareCPU::Inst_DonateEditDist),
@@ -220,11 +223,12 @@
tInstLibEntry<tMethod>("rotate-r", &cHardwareCPU::Inst_RotateR),
tInstLibEntry<tMethod>("rotate-left-one", &cHardwareCPU::Inst_RotateLeftOne),
tInstLibEntry<tMethod>("rotate-right-one", &cHardwareCPU::Inst_RotateRightOne),
-
tInstLibEntry<tMethod>("rotate-label", &cHardwareCPU::Inst_RotateLabel),
tInstLibEntry<tMethod>("set-cmut", &cHardwareCPU::Inst_SetCopyMut),
tInstLibEntry<tMethod>("mod-cmut", &cHardwareCPU::Inst_ModCopyMut),
+ tInstLibEntry<tMethod>("get-cell-xy", &cHardwareCPU::Inst_GetCellPosition),
+ tInstLibEntry<tMethod>("dist-from-diag", &cHardwareCPU::Inst_GetDistanceFromDiagonal),
// @WRE additions for movement
tInstLibEntry<tMethod>("tumble", &cHardwareCPU::Inst_Tumble),
tInstLibEntry<tMethod>("move", &cHardwareCPU::Inst_Move),
@@ -355,6 +359,8 @@
// Promoter Model
tInstLibEntry<tMethod>("promoter", &cHardwareCPU::Inst_Promoter),
tInstLibEntry<tMethod>("terminate", &cHardwareCPU::Inst_Terminate),
+ tInstLibEntry<tMethod>("promoter", &cHardwareCPU::Inst_Promoter),
+ tInstLibEntry<tMethod>("terminate", &cHardwareCPU::Inst_Terminate),
tInstLibEntry<tMethod>("regulate", &cHardwareCPU::Inst_Regulate),
tInstLibEntry<tMethod>("numberate", &cHardwareCPU::Inst_Numberate),
@@ -365,7 +371,7 @@
// Messaging
tInstLibEntry<tMethod>("send-msg", &cHardwareCPU::Inst_SendMessage),
tInstLibEntry<tMethod>("retrieve-msg", &cHardwareCPU::Inst_RetrieveMessage),
-
+
// Placebo instructions
tInstLibEntry<tMethod>("skip", &cHardwareCPU::Inst_Skip),
@@ -3088,6 +3094,13 @@
// Note that we are converting <double> resources to <int> register values
}
+bool cHardwareCPU::Inst_CollectCellData(cAvidaContext& ctx) {
+ int cellID = organism->GetCellID();
+ const int out_reg = FindModifiedRegister(REG_BX);
+ GetRegister(out_reg) = m_world->GetPopulation().GetCell(cellID).GetCellData();
+ return true;
+}
+
void cHardwareCPU::DoDonate(cOrganism* to_org)
{
assert(to_org != NULL);
@@ -3119,12 +3132,12 @@
//update energy store and merit of donor
organism->GetPhenotype().ReduceEnergy(energy_given);
- double senderMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy(), m_world) * organism->GetPhenotype().GetExecutionRatio();
+ double senderMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio(), m_world);
organism->UpdateMerit(senderMerit);
// update energy store and merit of donee
to_org->GetPhenotype().ReduceEnergy(-1.0*energy_given);
- double receiverMerit = cMerit::EnergyToMerit(to_org->GetPhenotype().GetStoredEnergy(), m_world) * to_org->GetPhenotype().GetExecutionRatio();
+ double receiverMerit = cMerit::EnergyToMerit(to_org->GetPhenotype().GetStoredEnergy() * to_org->GetPhenotype().GetEnergyUsageRatio(), m_world);
to_org->UpdateMerit(receiverMerit);
}
@@ -4224,17 +4237,17 @@
bool cHardwareCPU::Inst_Sleep(cAvidaContext& ctx) {
cPopulation& pop = m_world->GetPopulation();
+ int cellID = organism->GetCellID();
if(m_world->GetConfig().LOG_SLEEP_TIMES.Get() == 1) {
- pop.AddEndSleep(organism->GetCellID(), m_world->GetStats().GetUpdate());
+ pop.AddEndSleep(cellID, m_world->GetStats().GetUpdate());
}
- int cellID = organism->GetCellID();
organism->SetSleeping(false); //this instruction get executed at the end of a sleep cycle
m_world->GetStats().decNumAsleep(pop.GetCell(cellID).GetDemeID());
if(m_world->GetConfig().APPLY_ENERGY_METHOD.Get() == 2) {
organism->GetPhenotype().RefreshEnergy();
organism->GetPhenotype().ApplyToEnergyStore();
- double newMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy(), m_world) * organism->GetPhenotype().GetExecutionRatio();
- pop.UpdateMerit(organism->GetCellID(), newMerit);
+ double newMerit = cMerit::EnergyToMerit(organism->GetPhenotype().GetStoredEnergy() * organism->GetPhenotype().GetEnergyUsageRatio(), m_world);
+ pop.UpdateMerit(cellID, newMerit);
}
return true;
}
@@ -4245,13 +4258,40 @@
return true;
}
+bool cHardwareCPU::Inst_GetCellPosition(cAvidaContext& ctx) {
+ int absolute_cell_ID = organism->GetCellID();
+ int deme_id = organism->GetOrgInterface().GetDemeID();
+ std::pair<int, int> pos = m_world->GetPopulation().GetDeme(deme_id).GetCellPosition(absolute_cell_ID);
+ const int xreg = FindModifiedRegister(REG_BX);
+ const int yreg = FindNextRegister(xreg);
+ GetRegister(xreg) = pos.first;
+ GetRegister(yreg) = pos.second;
+ return true;
+}
+bool cHardwareCPU::Inst_GetDistanceFromDiagonal(cAvidaContext& ctx) {
+ int absolute_cell_ID = organism->GetOrgInterface().GetCellID();
+ int deme_id = organism->GetOrgInterface().GetDemeID();
+ std::pair<int, int> pos = m_world->GetPopulation().GetDeme(deme_id).GetCellPosition(absolute_cell_ID);
+ const int reg = FindModifiedRegister(REG_BX);
+
+ if(pos.first > pos.second) {
+ GetRegister(reg) = (int)ceil((pos.first - pos.second)/2.0);
+ } else {
+ GetRegister(reg) = (int)floor((pos.first - pos.second)/2.0);
+ }
+// std::cerr<<"x = "<<pos.first<<" y = "<<pos.second<<" ans = "<<GetRegister(reg)<<std::endl;
+ return true;
+}
+
//// Promoter Model ////
bool cHardwareCPU::Inst_Promoter(cAvidaContext& ctx)
{
// Promoters don't do anything themselves
return true;
+// std::cerr<<"x = "<<pos.first<<" y = "<<pos.second<<" ans = "<<GetRegister(reg)<<std::endl;
+ return true;
}
// Move the instruction ptr to the next active promoter
@@ -4435,7 +4475,6 @@
return code;
}
-
/*! Send a message to the organism that is currently faced by this cell,
where the label field of sent message is from register ?BX?, and the data field
is from register ~?BX?.
Modified: stable/source/cpu/cHardwareCPU.h
===================================================================
--- stable/source/cpu/cHardwareCPU.h 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/cpu/cHardwareCPU.h 2007-09-08 23:11:33 UTC (rev 2077)
@@ -441,6 +441,7 @@
bool Inst_SenseUnit(cAvidaContext& ctx);
bool Inst_SenseMult100(cAvidaContext& ctx);
bool DoSense(cAvidaContext& ctx, int conversion_method, double base);
+ bool Inst_CollectCellData(cAvidaContext& ctx);
void DoDonate(cOrganism * to_org);
void DoEnergyDonate(cOrganism* to_org);
@@ -470,6 +471,8 @@
bool Inst_RotateLabel(cAvidaContext& ctx);
bool Inst_SetCopyMut(cAvidaContext& ctx);
bool Inst_ModCopyMut(cAvidaContext& ctx);
+ bool Inst_GetCellPosition(cAvidaContext& ctx);
+ bool Inst_GetDistanceFromDiagonal(cAvidaContext& ctx);
// @WRE additions for movement
bool Inst_Tumble(cAvidaContext& ctx);
bool Inst_Move(cAvidaContext& ctx);
Modified: stable/source/main/avida.cc
===================================================================
--- stable/source/main/avida.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/avida.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -137,7 +137,7 @@
bool flag_interactive = false;
bool flag_load = false; cString val_load;
bool flag_review = false;
- bool flag_verbosity = false; int val_verbosity;
+ bool flag_verbosity = false; int val_verbosity = 0;
bool flag_seed = false; int val_seed = 0;
// Then scan through and process the rest of the args.
Modified: stable/source/main/cAvidaConfig.h
===================================================================
--- stable/source/main/cAvidaConfig.h 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cAvidaConfig.h 2007-09-08 23:11:33 UTC (rev 2077)
@@ -298,7 +298,7 @@
CONFIG_ADD_VAR(DEMES_HAVE_MERIT, int, 0, "Whether demes have merit; 0=no");
CONFIG_ADD_VAR(GERMLINE_COPY_MUT, double, 0.0075, "Prob. of copy mutations occuring during\ngermline replication.");
CONFIG_ADD_VAR(GERMLINE_REPLACES_SOURCE, int, 0, "Whether the source germline is updated\non replication; 0=no.");
- CONFIG_ADD_VAR(GERMLINE_RANDOM_PLACEMENT, int, 0, "Whether the seed for a germline is placed\n randomly within the deme; 0=no.");
+ CONFIG_ADD_VAR(GERMLINE_RANDOM_PLACEMENT, int, 0, "Defines how the seed for a germline is placed\n within the deme;\n0 = organisms is placed in center of deme, no orientation\n1 = organisms is placed in center of deme and oriented\n2 = organism is randomly placed in deme, no orientation");
CONFIG_ADD_VAR(MAX_DEME_AGE, int, 500, "The maximum age of a deme (in updates) to be\nused for age-based replication (default=500).");
CONFIG_ADD_GROUP(REPRODUCTION_GROUP, "Birth and Death");
Modified: stable/source/main/cDeme.cc
===================================================================
--- stable/source/main/cDeme.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cDeme.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -22,15 +22,17 @@
*/
#include "cDeme.h"
+#include "cPopulation.h"
#include "cPopulationCell.h"
#include "cResource.h"
+#include "cWorld.h"
-
-void cDeme::Setup(const tArray<int> & in_cells, int in_width)
+void cDeme::Setup(const tArray<int> & in_cells, int in_width, cWorld* world)
{
cell_ids = in_cells;
birth_count = 0;
org_count = 0;
+ m_world = world;
// If width is negative, set it to the full number of cells.
width = in_width;
@@ -60,11 +62,36 @@
return std::make_pair(cellid % GetWidth(), cellid / GetWidth());
}
+void cDeme::ProcessUpdate() {
+ for(int i = 0; i < cell_events.GetSize(); i++) {
+ cDemeCellEvent& event = cell_events[i];
+ if(event.GetDelay() == _age) {
+ event.ActivateEvent(m_world); //start event
+ int eventCell = event.GetNextEventCellID();
+ while(eventCell != -1) {
+ // place event ID in cells' data
+ m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(event.GetEventID());
+ eventCell = event.GetNextEventCellID();
+ }
+ } else if(event.GetDelay()+event.GetDuration() == _age) {
+ int eventCell = event.GetNextEventCellID();
+ while(eventCell != -1) {
+ if(event.GetEventID() == m_world->GetPopulation().GetCell(GetCellID(eventCell)).GetCellData()) { // eventID == CellData
+ //set cell data to 0
+ m_world->GetPopulation().GetCell(GetCellID(eventCell)).SetCellData(0);
+ eventCell = event.GetNextEventCellID();
+ }
+ }
+ event.DeactivateEvent(); //event over
+ }
+ }
+ ++_age;
+}
void cDeme::Reset()
{
birth_count = 0;
- _age = 0;
+ _age = 0;
//clear cell energy
deme_resource_count.ReinitializeResources();
@@ -141,3 +168,8 @@
}
deme_resource_count.ModifyCell(cell_resources, relative_cell_id);
}
+
+void cDeme::SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration) {
+ cDemeCellEvent demeEvent = cDemeCellEvent(x1, y1, x2, y2, delay, duration, width);
+ cell_events.Push(demeEvent);
+}
Modified: stable/source/main/cDeme.h
===================================================================
--- stable/source/main/cDeme.h 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cDeme.h 2007-09-08 23:11:33 UTC (rev 2077)
@@ -24,12 +24,14 @@
#ifndef cDeme_h
#define cDeme_h
+#include "cDemeCellEvent.h"
#include "cGermline.h"
#include "tArray.h"
#include "cResourceCount.h"
#include "cStringList.h"
class cResource;
+class cWorld;
/*! Demes are groups of cells in the population that are somehow bound together
as a unit. The deme object is used from within cPopulation to manage these
@@ -38,6 +40,7 @@
class cDeme
{
private:
+ cWorld* m_world;
tArray<int> cell_ids;
int width; //!< Width of this deme.
int birth_count; //!< Number of organisms that have been born into this deme since reset.
@@ -51,11 +54,13 @@
cResourceCount deme_resource_count; //!< Resources available to the deme
tArray<int> energy_res_ids; //!< IDs of energy resources
+ tArray<cDemeCellEvent> cell_events;
+
public:
cDeme() : width(0), birth_count(0), org_count(0), _age(0), deme_resource_count(0) { ; }
~cDeme() { ; }
- void Setup(const tArray<int>& in_cells, int in_width = -1);
+ void Setup(const tArray<int>& in_cells, int in_width = -1, cWorld* world = NULL);
int GetSize() const { return cell_ids.GetSize(); }
int GetCellID(int pos) const { return cell_ids[pos]; }
@@ -85,7 +90,7 @@
// -= Update support =-
//! Called once, at the end of every update.
- void ProcessUpdate() { ++_age; }
+ void ProcessUpdate();
/*! Returns the age of this deme, updates. Age is defined as the number of
updates since the last time Reset() was called. */
int GetAge() const { return _age; }
@@ -100,6 +105,8 @@
void UpdateDemeRes() { deme_resource_count.GetResources(); }
void Update(double time_step) { deme_resource_count.Update(time_step); }
int GetRelativeCellID(int absolute_cell_id) { return absolute_cell_id % GetSize(); } //!< assumes all demes are the same size
+
+ void SetCellEvent(int x1, int y1, int x2, int y2, int delay, int duration);
};
#endif
Copied: stable/source/main/cDemeCellEvent.cc (from rev 2076, development/source/main/cDemeCellEvent.cc)
===================================================================
--- stable/source/main/cDemeCellEvent.cc (rev 0)
+++ stable/source/main/cDemeCellEvent.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,41 @@
+#include "cDemeCellEvent.h"
+#include "cWorld.h"
+
+cDemeCellEvent::cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int width) :
+ m_delay(delay)
+ , m_duration(duration)
+ , m_iter(0)
+ , m_active(false)
+{
+ assert(x1 <= x2);
+ assert(y1 <= y2);
+ assert(y1 < width && y2 < width);
+ assert(delay >= 0);
+ assert(duration >= 0);
+ m_event_cells.ResizeClear((x2-x1+1) * (y2-y1+1));
+
+ int i = 0;
+ for(int j = y1; j <= y2; j++) {
+ for(int k = x1; k <= x2; k++) {
+ m_event_cells[i] = j*width+k;
+ i++;
+ }
+ }
+}
+
+int cDemeCellEvent::GetNextEventCellID() {
+ if(m_active && m_iter < m_event_cells.GetSize()) {
+ return m_event_cells[m_iter++];
+ }
+ m_iter = 0;
+ return -1;
+}
+
+void cDemeCellEvent::ActivateEvent(cWorld* m_world) {
+ m_eventID = m_world->GetRandom().GetInt(0x7FFFFFFF);
+ m_active = true;
+}
+
+void cDemeCellEvent::DeactivateEvent() {
+ m_active = false;
+}
Copied: stable/source/main/cDemeCellEvent.h (from rev 2076, development/source/main/cDemeCellEvent.h)
===================================================================
--- stable/source/main/cDemeCellEvent.h (rev 0)
+++ stable/source/main/cDemeCellEvent.h 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,24 @@
+#ifndef cDemeCellEvent_h
+#define cDemeCellEvent_h
+
+#include "tArray.h"
+class cWorld;
+
+class cDemeCellEvent {
+private:
+ tArray<int> m_event_cells;
+ int m_delay, m_duration, m_eventID, m_iter;
+ bool m_active;
+
+public:
+ cDemeCellEvent() { cDemeCellEvent(-1, -1, -1, -1, 0, 0, 0); }
+ cDemeCellEvent(int x1, int y1, int x2, int y2, int delay, int duration, int width);
+ int GetNextEventCellID();
+ int GetDelay() { return m_delay; }
+ int GetDuration() { return m_duration; }
+ int GetEventID() { return m_eventID; }
+
+ void ActivateEvent(cWorld* m_world);
+ void DeactivateEvent();
+};
+#endif
Modified: stable/source/main/cOrganism.cc
===================================================================
--- stable/source/main/cOrganism.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cOrganism.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -253,7 +253,7 @@
if(m_world->GetConfig().ENERGY_ENABLED.Get() && m_world->GetConfig().APPLY_ENERGY_METHOD.Get() == 1 && task_completed) {
m_phenotype.RefreshEnergy();
m_phenotype.ApplyToEnergyStore();
- double newMerit = cMerit::EnergyToMerit(GetPhenotype().GetStoredEnergy(), m_world) * GetPhenotype().GetExecutionRatio();
+ double newMerit = cMerit::EnergyToMerit(GetPhenotype().GetStoredEnergy() * GetPhenotype().GetEnergyUsageRatio(), m_world);
if(newMerit != -1) {
m_interface->UpdateMerit(newMerit);
}
Modified: stable/source/main/cPhenotype.cc
===================================================================
--- stable/source/main/cPhenotype.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cPhenotype.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1346,6 +1346,19 @@
energy_store = max(0.0, min(value, (double) m_world->GetConfig().ENERGY_CAP.Get()));
}
+bool cPhenotype::DoubleEnergyUsage(double energy_req) {
+ if(GetStoredEnergy() < energy_req) {
+ return false;
+ }
+ executionRatio *= 2.0;
+ return true;
+}
+
+void cPhenotype::HalfEnergyUsage() {
+ executionRatio *= 0.5;
+}
+
+
/**
Credit organism with energy reward, but only update energy store if APPLY_ENERGY_METHOD = "on task completion" (1)
*/
@@ -1393,13 +1406,9 @@
ReduceEnergy(child_energy - 2*energy_given_at_birth); // 2*energy_given_at_birth: 1 in child_energy & 1 for parent
//TODO: add energy_given_at_birth to Stored_energy
- cMerit parentMerit = cMerit(cMerit::EnergyToMerit(GetStoredEnergy(), m_world) * GetExecutionRatio());
+ cMerit parentMerit = cMerit(cMerit::EnergyToMerit(GetStoredEnergy() * GetEnergyUsageRatio(), m_world));
SetMerit(parentMerit);
-/* if(m_world->GetConfig().ENERGY_VERBOSE.Get()) {
- cerr<<"child merit: "<<merit_array[0]<<endl<<"child energy: "<< child_energy <<endl
- <<"parent merit: "<<GetMerit()<<endl<<"parent energy: "<< GetStoredEnergy() <<endl;
- }*/
return child_energy;
}
Modified: stable/source/main/cPhenotype.h
===================================================================
--- stable/source/main/cPhenotype.h 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cPhenotype.h 2007-09-08 23:11:33 UTC (rev 2077)
@@ -272,7 +272,7 @@
///////////////////// Accessors -- Retrieving ////////////////////
const cMerit & GetMerit() const { assert(initialized == true); return merit; }
- double GetExecutionRatio() const { assert(initialized == true); return executionRatio; }
+ double GetEnergyUsageRatio() const { assert(initialized == true); return executionRatio; }
int GetGenomeLength() const { assert(initialized == true); return genome_length; }
int GetCopiedSize() const { assert(initialized == true); return copied_size; }
int GetExecutedSize() const { assert(initialized == true); return executed_size; }
@@ -451,8 +451,8 @@
bool& ChildFertile() { assert(initialized == true); return child_fertile; }
bool& IsMultiThread() { assert(initialized == true); return is_multi_thread; }
- void DoubleEnergyUsage() { executionRatio *= 2.0; }
- void HalfEnergyUsage() { executionRatio *= 0.5; }
+ bool DoubleEnergyUsage(double inst_energy_cost);
+ void HalfEnergyUsage();
void RefreshEnergy();
void ApplyToEnergyStore();
double ExtractParentEnergy();
Modified: stable/source/main/cPopulation.cc
===================================================================
--- stable/source/main/cPopulation.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cPopulation.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -119,7 +119,6 @@
// Allocate the cells, resources, and market.
cell_array.ResizeClear(num_cells);
-// resource_count.ResizeSpatialGrids(world_x, world_y);
market.Resize(MARKET_SIZE);
// Setup the cells. Do things that are not dependent upon topology here.
@@ -145,7 +144,7 @@
deme_cells[offset] = cell_id;
cell_array[cell_id].SetDemeID(deme_id);
}
- deme_array[deme_id].Setup(deme_cells, deme_size_x);
+ deme_array[deme_id].Setup(deme_cells, deme_size_x, m_world);
}
// Setup the topology.
@@ -195,11 +194,7 @@
for(int i = 0; i < GetNumDemes(); i++) {
cResourceCount tmp_deme_res_count(num_deme_res);
GetDeme(i).SetDemeResourceCount(tmp_deme_res_count);
- //TODO: make sure grid is the right grid/size
- //GetDeme(i).GetDemeResourceCount().ResizeSpatialGrids(world_x, world_y);
-
GetDeme(i).ResizeSpatialGrids(deme_size_x, deme_size_y);
-// GetDeme(i).GetDemeResourceCount().
}
for (int i = 0; i < resource_lib.GetSize(); i++) {
@@ -1058,6 +1053,7 @@
0: 'all' - ...all non-empty demes in the population.
1: 'full_deme' - ...demes that have been filled up.
2: 'corners' - ...demes with upper left and lower right corners filled.
+3: 'deme-age' - ...demes who have reached their maximum age
*/
void cPopulation::ReplicateDemes(int rep_trigger)
@@ -1163,18 +1159,33 @@
source_deme.Reset();
target_deme.Reset();
- // Lineage label is wrong here; fix.
- if(m_world->GetConfig().GERMLINE_RANDOM_PLACEMENT.Get()) {
- InjectGenome(source_deme.GetCellID(m_world->GetRandom().GetInt(0, source_deme.GetSize()-1)),
- source_germline.GetLatest(), 0);
- InjectGenome(target_deme.GetCellID(m_world->GetRandom().GetInt(0, target_deme.GetSize()-1)),
- target_germline.GetLatest(), 0);
+ int source_deme_inject_cell;
+ int target_deme_inject_cell;
+
+ if(m_world->GetConfig().GERMLINE_RANDOM_PLACEMENT.Get() == 2) {
+ // organism is randomly placed in deme
+ source_deme_inject_cell = source_deme.GetCellID(m_world->GetRandom().GetInt(0, source_deme.GetSize()-1));
+ target_deme_inject_cell = target_deme.GetCellID(m_world->GetRandom().GetInt(0, target_deme.GetSize()-1));
} else {
- InjectGenome(source_deme.GetCellID(source_deme.GetSize()/2), source_germline.GetLatest(), 0);
- InjectGenome(target_deme.GetCellID(target_deme.GetSize()/2), target_germline.GetLatest(), 0);
+ // organisms is placed in center of deme
+ source_deme_inject_cell = source_deme.GetCellID(source_deme.GetSize()/2);
+ target_deme_inject_cell = target_deme.GetCellID(target_deme.GetSize()/2);
}
+ // Lineage label is wrong here; fix.
+ InjectGenome(source_deme_inject_cell, source_germline.GetLatest(), 0); // source deme
+ InjectGenome(target_deme_inject_cell, target_germline.GetLatest(), 0); // target deme
- // Note: not rotating the clones.
+ if(m_world->GetConfig().GERMLINE_RANDOM_PLACEMENT.Get() == 1) {
+ // Rotate both injected cells to face northwest.
+ int offset = source_deme.GetCellID(0);
+ cell_array[source_deme_inject_cell].Rotate(cell_array[GridNeighbor(source_deme_inject_cell-offset,
+ source_deme.GetWidth(),
+ source_deme.GetHeight(), -1, -1)+offset]);
+ offset = target_deme.GetCellID(0);
+ cell_array[target_deme_inject_cell].Rotate(cell_array[GridNeighbor(target_deme_inject_cell-offset,
+ target_deme.GetWidth(),
+ target_deme.GetHeight(), -1, -1)+offset]);
+ }
} else {
// Not using germline; choose a random organism from this deme.
int cell1_id = -1;
@@ -1187,7 +1198,7 @@
cGenome seed_genome = seed_org->GetGenome();
int seed_lineage = seed_org->GetLineageLabel();
- // Kill all the organisms in the source deme. Orgs. in dest. deme are already killed
+ // Kill all the organisms in the source deme. Orgs. in target deme have already been killed
for (int i=0; i<source_deme.GetSize(); i++) {
KillOrganism(cell_array[source_deme.GetCellID(i)]);
}
@@ -1195,9 +1206,23 @@
source_deme.Reset();
target_deme.Reset();
- InjectGenome(source_deme.GetCellID(source_deme.GetSize()/2), seed_genome, seed_lineage); // source deme
- InjectGenome(target_deme.GetCellID(target_deme.GetSize()/2), seed_genome, seed_lineage); // destination deme
+ int source_deme_inject_cell = source_deme.GetCellID(source_deme.GetSize()/2);
+ int target_deme_inject_cell = target_deme.GetCellID(target_deme.GetSize()/2);
+ InjectGenome(source_deme_inject_cell, seed_genome, seed_lineage); // source deme
+ InjectGenome(target_deme_inject_cell, seed_genome, seed_lineage); // target deme
+
+ // Rotate both injected cells to face northwest.
+ int offset = source_deme.GetCellID(0);
+ cell_array[source_deme_inject_cell].Rotate(cell_array[GridNeighbor(source_deme_inject_cell-offset,
+ source_deme.GetWidth(),
+ source_deme.GetHeight(), -1, -1)+offset]);
+ offset = target_deme.GetCellID(0);
+ cell_array[target_deme_inject_cell].Rotate(cell_array[GridNeighbor(target_deme_inject_cell-offset,
+ target_deme.GetWidth(),
+ target_deme.GetHeight(), -1, -1)+offset]);
+
+
} else {
cOrganism* seed = cell_array[cell1_id].GetOrganism();
@@ -1224,8 +1249,7 @@
cell_array[cell3_id].Rotate(cell_array[GridNeighbor(cell3_id-offset,
source_deme.GetWidth(),
source_deme.GetHeight(), -1, -1)+offset]);
-
-
+
// This is in the wrong place. Reset should be done after the demes are cleared and before the org. is injected.
source_deme.Reset();
target_deme.Reset();
Modified: stable/source/main/cPopulationCell.cc
===================================================================
--- stable/source/main/cPopulationCell.cc 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cPopulationCell.cc 2007-09-08 23:11:33 UTC (rev 2077)
@@ -45,6 +45,7 @@
, m_cell_id(in_cell.m_cell_id)
, m_deme_id(in_cell.m_deme_id)
, m_organism_count(in_cell.m_organism_count)
+ , m_cell_data(in_cell.m_cell_data)
{
// Copy the mutation rates into a new structure
m_mut_rates = new cMutationRates(*in_cell.m_mut_rates);
@@ -64,6 +65,7 @@
m_cell_id = in_cell.m_cell_id;
m_deme_id = in_cell.m_deme_id;
m_organism_count = in_cell.m_organism_count;
+ m_cell_data = in_cell.m_cell_data;
// Copy the mutation rates, constructing the structure as necessary
if (m_mut_rates == NULL)
@@ -84,6 +86,7 @@
m_x = x;
m_y = y;
m_deme_id = -1;
+ m_cell_data = 0;
if (m_mut_rates == NULL)
m_mut_rates = new cMutationRates(in_rates);
@@ -179,7 +182,7 @@
if(uptake_energy != 0.0) {
// update energy and merit
m_organism->GetPhenotype().ReduceEnergy(-1.0 * uptake_energy);
- m_organism->GetPhenotype().SetMerit(cMerit(cMerit::EnergyToMerit(m_organism->GetPhenotype().GetStoredEnergy(), m_world) * m_organism->GetPhenotype().GetExecutionRatio()));
+ m_organism->GetPhenotype().SetMerit(cMerit(cMerit::EnergyToMerit(m_organism->GetPhenotype().GetStoredEnergy() * m_organism->GetPhenotype().GetEnergyUsageRatio(), m_world)));
}
}
}
Modified: stable/source/main/cPopulationCell.h
===================================================================
--- stable/source/main/cPopulationCell.h 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/source/main/cPopulationCell.h 2007-09-08 23:11:33 UTC (rev 2077)
@@ -59,6 +59,7 @@
int m_cell_id; // Unique id for position of cell in population.
int m_deme_id; // ID of the deme that this cell is part of.
int m_organism_count; // Total number of orgs to ever inhabit this cell.
+ int m_cell_data; // "data" that is local to the cell and can be retrieaved by the org.
// location in population
int m_x; //!< The x-coordinate of the position of this cell in the environment.
@@ -98,6 +99,8 @@
inline int GetID() const { return m_cell_id; }
inline int GetDemeID() const { return m_deme_id; }
inline int GetOrganismCount() const { return m_organism_count; }
+ inline int GetCellData() const { return m_cell_data; }
+ void SetCellData(const int data) { m_cell_data = data; }
inline bool IsOccupied() const { return m_organism != NULL; }
Copied: stable/tests/energy_deme_level_res/expected (from rev 2076, development/tests/energy_deme_level_res/expected)
Copied: stable/tests/energy_deme_level_res/expected/data (from rev 2076, development/tests/energy_deme_level_res/expected/data)
Deleted: stable/tests/energy_deme_level_res/expected/data/average.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/average.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/average.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,30 +0,0 @@
-# Avida Average Data
-# Fri Sep 7 16:09:20 2007
-# 1: Update
-# 2: Merit
-# 3: Gestation Time
-# 4: Fitness
-# 5: Repro Rate?
-# 6: Size
-# 7: Copied Size
-# 8: Executed Size
-# 9: Abundance
-# 10: Proportion of organisms that gave birth in this update
-# 11: Proportion of Breed True Organisms
-# 12: Genotype Depth
-# 13: Generation
-# 14: Neutral Metric
-# 15: Lineage Label
-# 16: True Replication Rate (based on births/update, time-averaged)
-
-0 10.000000 146.000000 0.000000 0.000000 42.000000 42.000000 39.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
-10 3.09738 146 0.267123 0 41.75 42 39 2 0.25 0.25 0.25 2 -3.21718 0 0
-20 1.81026 146 0.267123 0 42 42 39 2.75 0.272727 0.272727 0.272727 3.63636 -2.57527 0 0
-30 1.44961 144.087 0.25792 0 42 41.087 37.3478 3.28571 0.173913 0.130435 0.304348 5.04348 -2.95184 0 0
-40 1.21065 145.521 0.264239 0 42.0625 41.5625 38.5 4.36364 0.0625 0.0625 0.270833 7 -3.61784 0 0
-50 1.14769 146.649 0.261818 0 42.1596 41.6277 38.4149 2.41026 0.0744681 0.0319149 0.648936 9.06383 -2.59815 0 0
-60 1.10636 145.67 0.261279 0 42.02 41.65 38.16 2.94118 0.16 0.11 0.65 11.22 -2.0348 0 0
-70 3.76973 144.333 0.265592 0 41.1667 41.1667 38.3333 1.5 0.333333 0.166667 0.666667 1.66667 -1.24153 -1 0
-80 2.23904 143.769 0.26538 0 41.1538 41.1538 38.1538 2.6 0 0 0.615385 2.84615 -1.55024 -1 0
-90 1.35539 144.705 0.263789 0 41.2045 41.1591 38.1591 2.75 0 0 0.886364 4.88636 -0.868435 -1 0
-100 1.01945 144.394 0.259282 0 41.2477 40.789 37.4954 2.27083 0.0550459 0.0275229 1.13761 6.88073 -0.773531 -1 0
Copied: stable/tests/energy_deme_level_res/expected/data/average.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/average.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/average.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/average.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,30 @@
+# Avida Average Data
+# Fri Sep 7 16:09:20 2007
+# 1: Update
+# 2: Merit
+# 3: Gestation Time
+# 4: Fitness
+# 5: Repro Rate?
+# 6: Size
+# 7: Copied Size
+# 8: Executed Size
+# 9: Abundance
+# 10: Proportion of organisms that gave birth in this update
+# 11: Proportion of Breed True Organisms
+# 12: Genotype Depth
+# 13: Generation
+# 14: Neutral Metric
+# 15: Lineage Label
+# 16: True Replication Rate (based on births/update, time-averaged)
+
+0 10.000000 146.000000 0.000000 0.000000 42.000000 42.000000 39.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000
+10 3.09738 146 0.267123 0 41.75 42 39 2 0.25 0.25 0.25 2 -3.21718 0 0
+20 1.81026 146 0.267123 0 42 42 39 2.75 0.272727 0.272727 0.272727 3.63636 -2.57527 0 0
+30 1.44961 144.087 0.25792 0 42 41.087 37.3478 3.28571 0.173913 0.130435 0.304348 5.04348 -2.95184 0 0
+40 1.21065 145.521 0.264239 0 42.0625 41.5625 38.5 4.36364 0.0625 0.0625 0.270833 7 -3.61784 0 0
+50 1.14769 146.649 0.261818 0 42.1596 41.6277 38.4149 2.41026 0.0744681 0.0319149 0.648936 9.06383 -2.59815 0 0
+60 1.10636 145.67 0.261279 0 42.02 41.65 38.16 2.94118 0.16 0.11 0.65 11.22 -2.0348 0 0
+70 3.76973 144.333 0.265592 0 41.1667 41.1667 38.3333 1.5 0.333333 0.166667 0.666667 1.66667 -1.24153 -1 0
+80 2.23904 143.769 0.26538 0 41.1538 41.1538 38.1538 2.6 0 0 0.615385 2.84615 -1.55024 -1 0
+90 1.35539 144.705 0.263789 0 41.2045 41.1591 38.1591 2.75 0 0 0.886364 4.88636 -0.868435 -1 0
+100 1.01945 144.394 0.259282 0 41.2477 40.789 37.4954 2.27083 0.0550459 0.0275229 1.13761 6.88073 -0.773531 -1 0
Deleted: stable/tests/energy_deme_level_res/expected/data/count.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/count.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/count.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,30 +0,0 @@
-# Avida count data
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: number of insts executed this update
-# 3: number of organisms
-# 4: number of different genotypes
-# 5: number of different threshold genotypes
-# 6: number of different species
-# 7: number of different threshold species
-# 8: number of different lineages
-# 9: number of births in this update
-# 10: number of deaths in this update
-# 11: number of breed true
-# 12: number of breed true organisms?
-# 13: number of no-birth organisms
-# 14: number of single-threaded organisms
-# 15: number of multi-threaded organisms
-# 16: number of modified organisms
-
-0 30 1 1 1 0 0 0 1 0 1 1 1 1 0 0
-10 90 4 2 1 0 0 0 1 0 1 3 2 4 0 0
-20 240 11 4 1 0 0 0 3 0 3 8 7 11 0 0
-30 570 23 7 1 0 0 0 4 0 3 17 12 23 0 0
-40 1350 48 11 1 0 0 0 3 0 3 39 26 48 0 0
-50 2730 94 39 6 0 0 0 7 4 3 62 51 94 0 0
-60 3000 100 34 6 0 0 0 16 16 11 71 60 100 0 0
-70 120 6 4 1 0 0 0 2 0 1 3 3 6 0 0
-80 390 13 5 2 0 0 0 0 0 0 9 7 13 0 0
-90 1320 44 16 4 0 0 0 0 0 0 29 25 44 0 0
-100 3120 109 48 6 0 0 0 6 1 3 67 62 109 0 0
Copied: stable/tests/energy_deme_level_res/expected/data/count.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/count.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/count.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/count.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,30 @@
+# Avida count data
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: number of insts executed this update
+# 3: number of organisms
+# 4: number of different genotypes
+# 5: number of different threshold genotypes
+# 6: number of different species
+# 7: number of different threshold species
+# 8: number of different lineages
+# 9: number of births in this update
+# 10: number of deaths in this update
+# 11: number of breed true
+# 12: number of breed true organisms?
+# 13: number of no-birth organisms
+# 14: number of single-threaded organisms
+# 15: number of multi-threaded organisms
+# 16: number of modified organisms
+
+0 30 1 1 1 0 0 0 1 0 1 1 1 1 0 0
+10 90 4 2 1 0 0 0 1 0 1 3 2 4 0 0
+20 240 11 4 1 0 0 0 3 0 3 8 7 11 0 0
+30 570 23 7 1 0 0 0 4 0 3 17 12 23 0 0
+40 1350 48 11 1 0 0 0 3 0 3 39 26 48 0 0
+50 2730 94 39 6 0 0 0 7 4 3 62 51 94 0 0
+60 3000 100 34 6 0 0 0 16 16 11 71 60 100 0 0
+70 120 6 4 1 0 0 0 2 0 1 3 3 6 0 0
+80 390 13 5 2 0 0 0 0 0 0 9 7 13 0 0
+90 1320 44 16 4 0 0 0 0 0 0 29 25 44 0 0
+100 3120 109 48 6 0 0 0 6 1 3 67 62 109 0 0
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,144 +0,0 @@
-deme_0000000_energy_0000000 = [ ...
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-
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-deme_0000000_energy_0000010 = [ ...
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-
-deme_0000000_energy_0000020 = [ ...
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-
-deme_0000000_energy_0000030 = [ ...
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-13506 13408.1 19614.3 0 0 0 0 12521.8 13470.7 0
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-deme_0000000_energy_0000040 = [ ...
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-];
-
-deme_0000000_energy_0000050 = [ ...
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-deme_0000000_energy_0000060 = [ ...
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-deme_0000000_energy_0000070 = [ ...
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-deme_0000000_energy_0000080 = [ ...
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-deme_0000000_energy_0000090 = [ ...
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-deme_0000000_energy_0000100 = [ ...
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-];
-
Copied: stable/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_0000000_spacial_energy.m 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,144 @@
+deme_0000000_energy_0000000 = [ ...
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+];
+
+
+deme_0000000_energy_0000010 = [ ...
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+];
+
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+deme_0000000_energy_0000060 = [ ...
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+];
+
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,144 +0,0 @@
-deme_0000001_energy_0000000 = [ ...
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-deme_0000001_energy_0000010 = [ ...
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-deme_0000001_energy_0000020 = [ ...
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 12592.4 0
-12621.7 43959.9 12621.7 0 0 0 0 0 12595 12621.7
-12630.6 12587.3 12565.7 0 0 0 0 0 12644.6 12616.6
-12615.3 12578.4 12586.1 0 0 0 0 0 0 12621.7
-0 0 12573.3 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_energy_0000100 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 10919.2 0
-11044.2 0 0 0 0 0 0 11033.9 10924.7 11000.4
-11078.5 11064.3 0 11109.7 10351.3 0 0 0 11046.1 11365.2
-11040.9 11038.3 11093 10363.8 0 0 0 11126.5 11039.4 11069.6
-11088.5 11019.4 11046.1 11065.1 11081.9 0 0 11409.5 11124.3 11052.8
-11072.9 11090.8 11021.6 11022.7 0 0 0 0 11089.7 11086.3
-11011.6 11085.2 11040.6 11049.5 11062.9 0 0 10603.7 11116.5 11065.1
-11050.6 11019.4 11070.7 0 0 0 0 11119.8 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
Copied: stable/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_0000001_spacial_energy.m 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,144 @@
+deme_0000001_energy_0000000 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+
+deme_0000001_energy_0000010 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000020 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000030 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000040 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000050 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000060 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000070 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 51811.7 0 0 0 0 0 0 0 0
+51785.5 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000080 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 48902.1 0 0 0 0 0 0 0 19665.6
+19667.6 19663.6 19653.6 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000090 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 12592.4 0
+12621.7 43959.9 12621.7 0 0 0 0 0 12595 12621.7
+12630.6 12587.3 12565.7 0 0 0 0 0 12644.6 12616.6
+12615.3 12578.4 12586.1 0 0 0 0 0 0 12621.7
+0 0 12573.3 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_energy_0000100 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 10919.2 0
+11044.2 0 0 0 0 0 0 11033.9 10924.7 11000.4
+11078.5 11064.3 0 11109.7 10351.3 0 0 0 11046.1 11365.2
+11040.9 11038.3 11093 10363.8 0 0 0 11126.5 11039.4 11069.6
+11088.5 11019.4 11046.1 11065.1 11081.9 0 0 11409.5 11124.3 11052.8
+11072.9 11090.8 11021.6 11022.7 0 0 0 0 11089.7 11086.3
+11011.6 11085.2 11040.6 11049.5 11062.9 0 0 10603.7 11116.5 11065.1
+11050.6 11019.4 11070.7 0 0 0 0 11119.8 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_donor.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_donor.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_donor.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,17 +0,0 @@
-# Num orgs doing doing a donate for each deme in population
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0
-# 3: Deme 1
-
-0 0.000000 0.000000
-10 0 0
-20 0 0
-30 0 0
-40 0 0
-50 0 0
-60 0 0
-70 0 0
-80 0 0
-90 0 0
-100 0 0
Copied: stable/tests/energy_deme_level_res/expected/data/deme_donor.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_donor.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_donor.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_donor.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,17 @@
+# Num orgs doing doing a donate for each deme in population
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0
+# 3: Deme 1
+
+0 0.000000 0.000000
+10 0 0
+20 0 0
+30 0 0
+40 0 0
+50 0 0
+60 0 0
+70 0 0
+80 0 0
+90 0 0
+100 0 0
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_fitness.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_fitness.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_fitness.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,17 +0,0 @@
-# Average fitnesses for each deme in the population
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0
-# 3: Deme 1
-
-0 0.000000 0.000000
-10 0.267123 0
-20 0.267123 0
-30 0.25792 0
-40 0.264239 0
-50 0.261818 0
-60 0.261279 0
-70 0.26552 0.265734
-80 0.265158 0.265734
-90 0.262677 0.265734
-100 0.255996 0.264135
Copied: stable/tests/energy_deme_level_res/expected/data/deme_fitness.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_fitness.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_fitness.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_fitness.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,17 @@
+# Average fitnesses for each deme in the population
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0
+# 3: Deme 1
+
+0 0.000000 0.000000
+10 0.267123 0
+20 0.267123 0
+30 0.25792 0
+40 0.264239 0
+50 0.261818 0
+60 0.261279 0
+70 0.26552 0.265734
+80 0.265158 0.265734
+90 0.262677 0.265734
+100 0.255996 0.264135
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_gest_time.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_gest_time.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_gest_time.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,17 +0,0 @@
-# Average gestation time for each deme in population
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0
-# 3: Deme 1
-
-0 146.000000 0.000000
-10 146 0
-20 146 0
-30 144.087 0
-40 145.521 0
-50 146.649 0
-60 145.67 0
-70 145 143
-80 144.25 143
-90 145.679 143
-100 144.492 144.25
Copied: stable/tests/energy_deme_level_res/expected/data/deme_gest_time.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_gest_time.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_gest_time.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_gest_time.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,17 @@
+# Average gestation time for each deme in population
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0
+# 3: Deme 1
+
+0 146.000000 0.000000
+10 146 0
+20 146 0
+30 144.087 0
+40 145.521 0
+50 146.649 0
+60 145.67 0
+70 145 143
+80 144.25 143
+90 145.679 143
+100 144.492 144.25
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,48 +0,0 @@
-# Number of times each instruction is exectued in deme 0
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Inst 0
-# 3: Inst 1
-# 4: Inst 2
-# 5: Inst 3
-# 6: Inst 4
-# 7: Inst 5
-# 8: Inst 6
-# 9: Inst 7
-# 10: Inst 8
-# 11: Inst 9
-# 12: Inst 10
-# 13: Inst 11
-# 14: Inst 12
-# 15: Inst 13
-# 16: Inst 14
-# 17: Inst 15
-# 18: Inst 16
-# 19: Inst 17
-# 20: Inst 18
-# 21: Inst 19
-# 22: Inst 20
-# 23: Inst 21
-# 24: Inst 22
-# 25: Inst 23
-# 26: Inst 24
-# 27: Inst 25
-# 28: Inst 26
-# 29: Inst 27
-# 30: Inst 28
-# 31: Inst 29
-# 32: Inst 30
-# 33: Inst 31
-# 34: Inst 32
-
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 56 4 4 168 8 168 0 0 168 0 0 0 0 0 0 0 0
-20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 154 11 11 462 22 462 0 0 462 0 0 0 0 0 0 0 0
-30 42 0 0 0 42 2 0 0 0 0 0 0 0 0 0 46 320 23 23 924 46 924 0 0 882 0 0 0 0 0 0 0 0
-40 21 0 2 0 21 1 0 0 0 0 0 0 0 0 0 93 666 48 48 1995 96 1995 0 0 1975 0 0 4 0 0 0 0 0
-50 63 0 5 0 23 1 0 0 0 0 0 4 0 3 44 181 1308 94 94 3894 190 3893 0 88 3835 0 0 2 0 0 0 0 0
-60 82 0 52 1 1 2 0 0 0 0 0 0 0 5 42 195 1387 100 100 4123 200 4123 2 3 4046 0 0 0 0 2 0 0 0
-70 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 8 52 4 4 166 8 166 0 0 166 0 0 0 0 0 0 0 0
-80 0 4 8 0 0 0 0 0 0 0 0 0 0 0 0 16 104 8 8 330 16 330 0 0 330 0 0 0 0 0 0 0 0
-90 0 14 32 0 0 0 0 0 2 0 0 0 0 0 0 58 356 28 28 1155 56 1155 0 0 1155 0 0 0 0 4 0 0 0
-100 42 32 75 0 0 0 2 0 6 46 0 0 0 0 0 131 820 65 65 2599 130 2599 0 0 2557 0 0 0 3 10 2 0 0
Copied: stable/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_instruction-0.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,48 @@
+# Number of times each instruction is exectued in deme 0
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Inst 0
+# 3: Inst 1
+# 4: Inst 2
+# 5: Inst 3
+# 6: Inst 4
+# 7: Inst 5
+# 8: Inst 6
+# 9: Inst 7
+# 10: Inst 8
+# 11: Inst 9
+# 12: Inst 10
+# 13: Inst 11
+# 14: Inst 12
+# 15: Inst 13
+# 16: Inst 14
+# 17: Inst 15
+# 18: Inst 16
+# 19: Inst 17
+# 20: Inst 18
+# 21: Inst 19
+# 22: Inst 20
+# 23: Inst 21
+# 24: Inst 22
+# 25: Inst 23
+# 26: Inst 24
+# 27: Inst 25
+# 28: Inst 26
+# 29: Inst 27
+# 30: Inst 28
+# 31: Inst 29
+# 32: Inst 30
+# 33: Inst 31
+# 34: Inst 32
+
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 56 4 4 168 8 168 0 0 168 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 154 11 11 462 22 462 0 0 462 0 0 0 0 0 0 0 0
+30 42 0 0 0 42 2 0 0 0 0 0 0 0 0 0 46 320 23 23 924 46 924 0 0 882 0 0 0 0 0 0 0 0
+40 21 0 2 0 21 1 0 0 0 0 0 0 0 0 0 93 666 48 48 1995 96 1995 0 0 1975 0 0 4 0 0 0 0 0
+50 63 0 5 0 23 1 0 0 0 0 0 4 0 3 44 181 1308 94 94 3894 190 3893 0 88 3835 0 0 2 0 0 0 0 0
+60 82 0 52 1 1 2 0 0 0 0 0 0 0 5 42 195 1387 100 100 4123 200 4123 2 3 4046 0 0 0 0 2 0 0 0
+70 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 8 52 4 4 166 8 166 0 0 166 0 0 0 0 0 0 0 0
+80 0 4 8 0 0 0 0 0 0 0 0 0 0 0 0 16 104 8 8 330 16 330 0 0 330 0 0 0 0 0 0 0 0
+90 0 14 32 0 0 0 0 0 2 0 0 0 0 0 0 58 356 28 28 1155 56 1155 0 0 1155 0 0 0 0 4 0 0 0
+100 42 32 75 0 0 0 2 0 6 46 0 0 0 0 0 131 820 65 65 2599 130 2599 0 0 2557 0 0 0 3 10 2 0 0
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,48 +0,0 @@
-# Number of times each instruction is exectued in deme 1
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Inst 0
-# 3: Inst 1
-# 4: Inst 2
-# 5: Inst 3
-# 6: Inst 4
-# 7: Inst 5
-# 8: Inst 6
-# 9: Inst 7
-# 10: Inst 8
-# 11: Inst 9
-# 12: Inst 10
-# 13: Inst 11
-# 14: Inst 12
-# 15: Inst 13
-# 16: Inst 14
-# 17: Inst 15
-# 18: Inst 16
-# 19: Inst 17
-# 20: Inst 18
-# 21: Inst 19
-# 22: Inst 20
-# 23: Inst 21
-# 24: Inst 22
-# 25: Inst 23
-# 26: Inst 24
-# 27: Inst 25
-# 28: Inst 26
-# 29: Inst 27
-# 30: Inst 28
-# 31: Inst 29
-# 32: Inst 30
-# 33: Inst 31
-# 34: Inst 32
-
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-70 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 4 26 2 2 82 4 82 0 0 82 0 0 0 0 0 0 0 0
-80 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 10 65 5 5 205 10 205 0 0 205 0 0 0 0 0 0 0 0
-90 0 0 16 0 0 0 0 0 0 0 0 0 0 0 0 32 208 16 16 656 32 656 0 0 656 0 0 0 0 0 0 0 0
-100 0 0 46 0 0 0 0 2 0 0 0 1 0 0 0 88 570 44 44 1807 88 1807 0 0 1807 3 0 0 0 0 2 0 0
Copied: stable/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_instruction-1.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,48 @@
+# Number of times each instruction is exectued in deme 1
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Inst 0
+# 3: Inst 1
+# 4: Inst 2
+# 5: Inst 3
+# 6: Inst 4
+# 7: Inst 5
+# 8: Inst 6
+# 9: Inst 7
+# 10: Inst 8
+# 11: Inst 9
+# 12: Inst 10
+# 13: Inst 11
+# 14: Inst 12
+# 15: Inst 13
+# 16: Inst 14
+# 17: Inst 15
+# 18: Inst 16
+# 19: Inst 17
+# 20: Inst 18
+# 21: Inst 19
+# 22: Inst 20
+# 23: Inst 21
+# 24: Inst 22
+# 25: Inst 23
+# 26: Inst 24
+# 27: Inst 25
+# 28: Inst 26
+# 29: Inst 27
+# 30: Inst 28
+# 31: Inst 29
+# 32: Inst 30
+# 33: Inst 31
+# 34: Inst 32
+
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+70 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 4 26 2 2 82 4 82 0 0 82 0 0 0 0 0 0 0 0
+80 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 10 65 5 5 205 10 205 0 0 205 0 0 0 0 0 0 0 0
+90 0 0 16 0 0 0 0 0 0 0 0 0 0 0 0 32 208 16 16 656 32 656 0 0 656 0 0 0 0 0 0 0 0
+100 0 0 46 0 0 0 0 2 0 0 0 1 0 0 0 88 570 44 44 1807 88 1807 0 0 1807 3 0 0 0 0 2 0 0
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,17 +0,0 @@
-# Average life fitnesses for each deme in the population
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0
-# 3: Deme 1
-
-0 0.000000 0.000000
-10 0.267123 0
-20 0.267123 0
-30 0.25792 0
-40 0.264239 0
-50 0.261818 0
-60 0.261279 0
-70 0.26552 0.265734
-80 0.265158 0.265734
-90 0.262677 0.265734
-100 0.255996 0.264135
Copied: stable/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_lifetime_fitness.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,17 @@
+# Average life fitnesses for each deme in the population
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0
+# 3: Deme 1
+
+0 0.000000 0.000000
+10 0.267123 0
+20 0.267123 0
+30 0.25792 0
+40 0.264239 0
+50 0.261818 0
+60 0.261279 0
+70 0.26552 0.265734
+80 0.265158 0.265734
+90 0.262677 0.265734
+100 0.255996 0.264135
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_merit.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_merit.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_merit.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,17 +0,0 @@
-# Average merits for each deme in population
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0
-# 3: Deme 1
-
-0 10.000000 0.000000
-10 3.09738 0
-20 1.81026 0
-30 1.44961 0
-40 1.21065 0
-50 1.14769 0
-60 1.10636 0
-70 3.02856 5.25207
-80 1.98782 2.641
-90 1.2605 1.52144
-100 0.956297 1.11275
Copied: stable/tests/energy_deme_level_res/expected/data/deme_merit.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_merit.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_merit.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_merit.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,17 @@
+# Average merits for each deme in population
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0
+# 3: Deme 1
+
+0 10.000000 0.000000
+10 3.09738 0
+20 1.81026 0
+30 1.44961 0
+40 1.21065 0
+50 1.14769 0
+60 1.10636 0
+70 3.02856 5.25207
+80 1.98782 2.641
+90 1.2605 1.52144
+100 0.956297 1.11275
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,18 +0,0 @@
-# Average mutation rates for organisms in each deme
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0
-# 3: Deme 1
-# 4: Average deme mutation rate averaged across Demes.
-
-0 0.007500 0.000000 0.003750
-10 0.0075 0 0.00375
-20 0.0075 0 0.00375
-30 0.0075 0 0.00375
-40 0.0075 0 0.00375
-50 0.0075 0 0.00375
-60 0.0075 0 0.00375
-70 0.0075 0.0075 0.0075
-80 0.0075 0.0075 0.0075
-90 0.0075 0.0075 0.0075
-100 0.0075 0.0075 0.0075
Copied: stable/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_mut_rates.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,18 @@
+# Average mutation rates for organisms in each deme
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0
+# 3: Deme 1
+# 4: Average deme mutation rate averaged across Demes.
+
+0 0.007500 0.000000 0.003750
+10 0.0075 0 0.00375
+20 0.0075 0 0.00375
+30 0.0075 0 0.00375
+40 0.0075 0 0.00375
+50 0.0075 0 0.00375
+60 0.0075 0 0.00375
+70 0.0075 0.0075 0.0075
+80 0.0075 0.0075 0.0075
+90 0.0075 0.0075 0.0075
+100 0.0075 0.0075 0.0075
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_receiver.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_receiver.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_receiver.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,17 +0,0 @@
-# Num orgs doing receiving a donate for each deme in population
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0
-# 3: Deme 1
-
-0 0.000000 0.000000
-10 0 0
-20 0 0
-30 0 0
-40 0 0
-50 0 0
-60 0 0
-70 0 0
-80 0 0
-90 0 0
-100 0 0
Copied: stable/tests/energy_deme_level_res/expected/data/deme_receiver.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_receiver.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_receiver.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_receiver.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,17 @@
+# Num orgs doing receiving a donate for each deme in population
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0
+# 3: Deme 1
+
+0 0.000000 0.000000
+10 0 0
+20 0 0
+30 0 0
+40 0 0
+50 0 0
+60 0 0
+70 0 0
+80 0 0
+90 0 0
+100 0 0
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_resources.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_resources.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_resources.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,19 +0,0 @@
-# Avida deme resource data
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0 Resource deme_ResA
-# 3: Deme 0 Resource deme_ResB
-# 4: Deme 1 Resource deme_ResA
-# 5: Deme 1 Resource deme_ResB
-
-0 2.000000 1000.000000 1.000000 1000.000000
-10 7.5 11931.4 1 11931.4
-20 17.5 20912.2 1 20912.2
-30 42 30904.2 1 30904.2
-40 109 40901.5 1 40901.5
-50 265.5 50900.5 1 50900.5
-60 464.5 60900.2 1 60900.2
-70 4 10934.9 4 10934.9
-80 16 20912.2 10 20912.2
-90 58.5 30904.2 33 30904.2
-100 139.5 40901.5 106 40901.5
Copied: stable/tests/energy_deme_level_res/expected/data/deme_resources.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_resources.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_resources.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_resources.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,19 @@
+# Avida deme resource data
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0 Resource deme_ResA
+# 3: Deme 0 Resource deme_ResB
+# 4: Deme 1 Resource deme_ResA
+# 5: Deme 1 Resource deme_ResB
+
+0 2.000000 1000.000000 1.000000 1000.000000
+10 7.5 11931.4 1 11931.4
+20 17.5 20912.2 1 20912.2
+30 42 30904.2 1 30904.2
+40 109 40901.5 1 40901.5
+50 265.5 50900.5 1 50900.5
+60 464.5 60900.2 1 60900.2
+70 4 10934.9 4 10934.9
+80 16 20912.2 10 20912.2
+90 58.5 30904.2 33 30904.2
+100 139.5 40901.5 106 40901.5
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,287 +0,0 @@
-deme_0000000_deme_ResB_0000000 = [ ...
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-
-deme_0000001_deme_ResB_0000000 = [ ...
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000010 = [ ...
-10 10 10 10 10 10 10 10 10 10
-1110 1110 1110 1110 1110 1110 1110 1110 1110 1110
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000010 = [ ...
-10 10 10 10 10 10 10 10 10 10
-1110 1110 1110 1110 1110 1110 1110 1110 1110 1110
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000020 = [ ...
-10 10 10 10 10 10 10 10 10 10
-2010 2010 2010 2010 2010 2010 2010 2010 2010 2010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000020 = [ ...
-10 10 10 10 10 10 10 10 10 10
-2010 2010 2010 2010 2010 2010 2010 2010 2010 2010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000030 = [ ...
-10 10 10 10 10 10 10 10 10 10
-3010 3010 3010 3010 3010 3010 3010 3010 3010 3010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000030 = [ ...
-10 10 10 10 10 10 10 10 10 10
-3010 3010 3010 3010 3010 3010 3010 3010 3010 3010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000040 = [ ...
-10 10 10 10 10 10 10 10 10 10
-4010 4010 4010 4010 4010 4010 4010 4010 4010 4010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000040 = [ ...
-10 10 10 10 10 10 10 10 10 10
-4010 4010 4010 4010 4010 4010 4010 4010 4010 4010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000050 = [ ...
-10 10 10 10 10 10 10 10 10 10
-5010 5010 5010 5010 5010 5010 5010 5010 5010 5010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000050 = [ ...
-10 10 10 10 10 10 10 10 10 10
-5010 5010 5010 5010 5010 5010 5010 5010 5010 5010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378 0.0515378
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000060 = [ ...
-10 10 10 10 10 10 10 10 10 10
-6010 6010 6010 6010 6010 6010 6010 6010 6010 6010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000060 = [ ...
-10 10 10 10 10 10 10 10 10 10
-6010 6010 6010 6010 6010 6010 6010 6010 6010 6010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701 0.0179701
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000070 = [ ...
-10 10 10 10 10 10 10 10 10 10
-1010 1010 1010 1010 1010 1010 1010 1010 1010 1010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-3.48678 3.48678 3.48678 3.48678 3.48678 3.48678 3.48678 3.48678 3.48678 3.48678
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000070 = [ ...
-10 10 10 10 10 10 10 10 10 10
-1010 1010 1010 1010 1010 1010 1010 1010 1010 1010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-3.48678 3.48678 3.48678 3.48678 3.48678 3.48678 3.48678 3.48678 3.48678 3.48678
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000080 = [ ...
-10 10 10 10 10 10 10 10 10 10
-2010 2010 2010 2010 2010 2010 2010 2010 2010 2010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000080 = [ ...
-10 10 10 10 10 10 10 10 10 10
-2010 2010 2010 2010 2010 2010 2010 2010 2010 2010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577 1.21577
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000090 = [ ...
-10 10 10 10 10 10 10 10 10 10
-3010 3010 3010 3010 3010 3010 3010 3010 3010 3010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000090 = [ ...
-10 10 10 10 10 10 10 10 10 10
-3010 3010 3010 3010 3010 3010 3010 3010 3010 3010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912 0.423912
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000000_deme_ResB_0000100 = [ ...
-10 10 10 10 10 10 10 10 10 10
-4010 4010 4010 4010 4010 4010 4010 4010 4010 4010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
-deme_0000001_deme_ResB_0000100 = [ ...
-10 10 10 10 10 10 10 10 10 10
-4010 4010 4010 4010 4010 4010 4010 4010 4010 4010
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809 0.147809
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-10 10 10 10 10 10 10 10 10 10
-];
-
Copied: stable/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_spacial_resource_deme_ResB.m 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,287 @@
+deme_0000000_deme_ResB_0000000 = [ ...
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+];
+
+
+deme_0000001_deme_ResB_0000000 = [ ...
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+];
+
+deme_0000000_deme_ResB_0000010 = [ ...
+10 10 10 10 10 10 10 10 10 10
+1110 1110 1110 1110 1110 1110 1110 1110 1110 1110
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+];
+
+deme_0000001_deme_ResB_0000010 = [ ...
+10 10 10 10 10 10 10 10 10 10
+1110 1110 1110 1110 1110 1110 1110 1110 1110 1110
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
+3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811 3.13811
+10 10 10 10 10 10 10 10 10 10
+10 10 10 10 10 10 10 10 10 10
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+deme_0000000_deme_ResB_0000020 = [ ...
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+deme_0000001_deme_ResB_0000020 = [ ...
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+deme_0000000_deme_ResB_0000030 = [ ...
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+deme_0000001_deme_ResB_0000030 = [ ...
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+deme_0000000_deme_ResB_0000040 = [ ...
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+deme_0000001_deme_ResB_0000040 = [ ...
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+deme_0000000_deme_ResB_0000050 = [ ...
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+deme_0000001_deme_ResB_0000050 = [ ...
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+];
+
+deme_0000000_deme_ResB_0000060 = [ ...
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+];
+
+deme_0000001_deme_ResB_0000060 = [ ...
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+];
+
+deme_0000000_deme_ResB_0000070 = [ ...
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+];
+
+deme_0000001_deme_ResB_0000070 = [ ...
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+];
+
+deme_0000000_deme_ResB_0000080 = [ ...
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+];
+
+deme_0000001_deme_ResB_0000080 = [ ...
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+];
+
+deme_0000000_deme_ResB_0000090 = [ ...
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+];
+
+deme_0000001_deme_ResB_0000090 = [ ...
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+];
+
+deme_0000000_deme_ResB_0000100 = [ ...
+10 10 10 10 10 10 10 10 10 10
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+];
+
+deme_0000001_deme_ResB_0000100 = [ ...
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+10 10 10 10 10 10 10 10 10 10
+];
+
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,287 +0,0 @@
-deme_0000000_sleep_0000000 = [ ...
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-
-deme_0000001_sleep_0000000 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000010 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000010 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000020 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000020 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000030 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000030 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000040 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000040 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000050 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000050 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000060 = [ ...
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000060 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000070 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000070 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
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-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000080 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000080 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000090 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000090 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000000_sleep_0000100 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 1 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
-deme_0000001_sleep_0000100 = [ ...
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-0 0 0 0 0 0 0 0 0 0
-];
-
Copied: stable/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_spacial_sleep.m 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,287 @@
+deme_0000000_sleep_0000000 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
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+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+
+deme_0000001_sleep_0000000 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000010 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
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+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000010 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000020 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000020 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
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+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000030 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000030 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000040 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000040 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000050 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000050 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000060 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000060 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000070 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000070 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000080 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000080 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000090 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000090 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000000_sleep_0000100 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 1 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
+deme_0000001_sleep_0000100 = [ ...
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0
+];
+
Deleted: stable/tests/energy_deme_level_res/expected/data/deme_task.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/deme_task.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/deme_task.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,19 +0,0 @@
-# Num orgs doing each task for each deme in population
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: Deme 0, Task 0
-# 3: Deme 0, Task 1
-# 4: Deme 1, Task 0
-# 5: Deme 1, Task 1
-
-0 0 0 0 0
-10 4 4 0 0
-20 11 11 0 0
-30 23 23 0 0
-40 48 48 0 0
-50 94 92 0 0
-60 100 97 0 0
-70 4 4 2 2
-80 8 8 5 5
-90 28 28 16 16
-100 65 65 44 44
Copied: stable/tests/energy_deme_level_res/expected/data/deme_task.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/deme_task.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/deme_task.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/deme_task.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,19 @@
+# Num orgs doing each task for each deme in population
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: Deme 0, Task 0
+# 3: Deme 0, Task 1
+# 4: Deme 1, Task 0
+# 5: Deme 1, Task 1
+
+0 0 0 0 0
+10 4 4 0 0
+20 11 11 0 0
+30 23 23 0 0
+40 48 48 0 0
+50 94 92 0 0
+60 100 97 0 0
+70 4 4 2 2
+80 8 8 5 5
+90 28 28 16 16
+100 65 65 44 44
Deleted: stable/tests/energy_deme_level_res/expected/data/dominant.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/dominant.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/dominant.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,30 +0,0 @@
-# Avida Dominant Data
-# Fri Sep 7 16:09:20 2007
-# 1: Update
-# 2: Average Merit of the Dominant Genotype
-# 3: Average Gestation Time of the Dominant Genotype
-# 4: Average Fitness of the Dominant Genotype
-# 5: Repro Rate?
-# 6: Size of Dominant Genotype
-# 7: Copied Size of Dominant Genotype
-# 8: Executed Size of Dominant Genotype
-# 9: Abundance of Dominant Genotype
-# 10: Number of Births
-# 11: Number of Dominant Breed True?
-# 12: Dominant Gene Depth
-# 13: Dominant Breed In
-# 14: Max Fitness?
-# 15: Genotype ID of Dominant Genotype
-# 16: Name of the Dominant Genotype
-
-0 0.000000 0.000000 0.000000 0.000000 42 0.000000 0.000000 1 0 0 0 0 0.000000 1 042-aaaaa
-10 3.83097 146 0.267123 0.00684932 42 42 39 3 1 1 0 0 0.267123 1 042-aaaaa
-20 2.40352 146 0.267123 0.00684932 42 42 39 8 3 3 0 0 0.267123 1 042-aaaaa
-30 1.84153 146 0.267123 0.00684932 42 42 39 17 3 3 0 0 0.267123 1 042-aaaaa
-40 1.46002 146 0.267123 0.00684932 42 42 39 36 3 3 0 0 0.267123 1 042-aaaaa
-50 1.3038 146 0.267123 0.00684932 42 42 39 42 4 2 0 0 0.272727 1 042-aaaaa
-60 1.24913 146 0.267123 0.00684932 42 42 39 45 11 7 0 0 0.267123 1 042-aaaaa
-70 4.51107 143 0.265734 0.00699301 41 41 38 2 1 0 0 0 0.265734 85 041-aaaaa
-80 3.21814 143 0.265734 0.00699301 41 41 38 5 0 0 0 0 0.265734 85 041-aaaaa
-90 1.94358 143 0.265734 0.00699301 41 41 38 15 0 0 0 0 0.265734 85 041-aaaaa
-100 1.43684 143 0.265734 0.00699301 41 41 38 31 1 0 0 0 0.265734 85 041-aaaaa
Copied: stable/tests/energy_deme_level_res/expected/data/dominant.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/dominant.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/dominant.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/dominant.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,30 @@
+# Avida Dominant Data
+# Fri Sep 7 16:09:20 2007
+# 1: Update
+# 2: Average Merit of the Dominant Genotype
+# 3: Average Gestation Time of the Dominant Genotype
+# 4: Average Fitness of the Dominant Genotype
+# 5: Repro Rate?
+# 6: Size of Dominant Genotype
+# 7: Copied Size of Dominant Genotype
+# 8: Executed Size of Dominant Genotype
+# 9: Abundance of Dominant Genotype
+# 10: Number of Births
+# 11: Number of Dominant Breed True?
+# 12: Dominant Gene Depth
+# 13: Dominant Breed In
+# 14: Max Fitness?
+# 15: Genotype ID of Dominant Genotype
+# 16: Name of the Dominant Genotype
+
+0 0.000000 0.000000 0.000000 0.000000 42 0.000000 0.000000 1 0 0 0 0 0.000000 1 042-aaaaa
+10 3.83097 146 0.267123 0.00684932 42 42 39 3 1 1 0 0 0.267123 1 042-aaaaa
+20 2.40352 146 0.267123 0.00684932 42 42 39 8 3 3 0 0 0.267123 1 042-aaaaa
+30 1.84153 146 0.267123 0.00684932 42 42 39 17 3 3 0 0 0.267123 1 042-aaaaa
+40 1.46002 146 0.267123 0.00684932 42 42 39 36 3 3 0 0 0.267123 1 042-aaaaa
+50 1.3038 146 0.267123 0.00684932 42 42 39 42 4 2 0 0 0.272727 1 042-aaaaa
+60 1.24913 146 0.267123 0.00684932 42 42 39 45 11 7 0 0 0.267123 1 042-aaaaa
+70 4.51107 143 0.265734 0.00699301 41 41 38 2 1 0 0 0 0.265734 85 041-aaaaa
+80 3.21814 143 0.265734 0.00699301 41 41 38 5 0 0 0 0 0.265734 85 041-aaaaa
+90 1.94358 143 0.265734 0.00699301 41 41 38 15 0 0 0 0 0.265734 85 041-aaaaa
+100 1.43684 143 0.265734 0.00699301 41 41 38 31 1 0 0 0 0.265734 85 041-aaaaa
Deleted: stable/tests/energy_deme_level_res/expected/data/instruction.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/instruction.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/instruction.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,48 +0,0 @@
-# Avida instruction execution data
-# Fri Sep 7 16:09:20 2007
-# 1: Update
-# 2: nop-A
-# 3: nop-B
-# 4: nop-C
-# 5: if-n-equ
-# 6: if-less
-# 7: pop
-# 8: push
-# 9: swap-stk
-# 10: swap
-# 11: shift-r
-# 12: shift-l
-# 13: inc
-# 14: dec
-# 15: add
-# 16: sub
-# 17: nand
-# 18: IO
-# 19: h-alloc
-# 20: h-divide
-# 21: h-copy
-# 22: h-search
-# 23: mov-head
-# 24: jmp-head
-# 25: get-head
-# 26: if-label
-# 27: set-flow
-# 28: sense-m100
-# 29: if-equ-0
-# 30: time
-# 31: sleep1
-# 32: sleep2
-# 33: sleep3
-# 34: sleep4
-
-0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 56 4 4 168 8 168 0 0 168 0 0 0 0 0 0 0 0
-20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 154 11 11 462 22 462 0 0 462 0 0 0 0 0 0 0 0
-30 42 0 0 0 42 2 0 0 0 0 0 0 0 0 0 46 320 23 23 924 46 924 0 0 882 0 0 0 0 0 0 0 0
-40 21 0 2 0 21 1 0 0 0 0 0 0 0 0 0 93 666 48 48 1995 96 1995 0 0 1975 0 0 4 0 0 0 0 0
-50 63 0 5 0 23 1 0 0 0 0 0 4 0 3 44 181 1308 94 94 3894 190 3893 0 88 3835 0 0 2 0 0 0 0 0
-60 82 0 52 1 1 2 0 0 0 0 0 0 0 5 42 195 1387 100 100 4123 200 4123 2 3 4046 0 0 0 0 2 0 0 0
-70 0 2 6 0 0 0 0 0 0 0 0 0 0 0 0 12 78 6 6 248 12 248 0 0 248 0 0 0 0 0 0 0 0
-80 0 4 13 0 0 0 0 0 0 0 0 0 0 0 0 26 169 13 13 535 26 535 0 0 535 0 0 0 0 0 0 0 0
-90 0 14 48 0 0 0 0 0 2 0 0 0 0 0 0 90 564 44 44 1811 88 1811 0 0 1811 0 0 0 0 4 0 0 0
-100 42 32 121 0 0 0 2 2 6 46 0 1 0 0 0 219 1390 109 109 4406 218 4406 0 0 4364 3 0 0 3 10 4 0 0
Copied: stable/tests/energy_deme_level_res/expected/data/instruction.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/instruction.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/instruction.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/instruction.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,48 @@
+# Avida instruction execution data
+# Fri Sep 7 16:09:20 2007
+# 1: Update
+# 2: nop-A
+# 3: nop-B
+# 4: nop-C
+# 5: if-n-equ
+# 6: if-less
+# 7: pop
+# 8: push
+# 9: swap-stk
+# 10: swap
+# 11: shift-r
+# 12: shift-l
+# 13: inc
+# 14: dec
+# 15: add
+# 16: sub
+# 17: nand
+# 18: IO
+# 19: h-alloc
+# 20: h-divide
+# 21: h-copy
+# 22: h-search
+# 23: mov-head
+# 24: jmp-head
+# 25: get-head
+# 26: if-label
+# 27: set-flow
+# 28: sense-m100
+# 29: if-equ-0
+# 30: time
+# 31: sleep1
+# 32: sleep2
+# 33: sleep3
+# 34: sleep4
+
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 56 4 4 168 8 168 0 0 168 0 0 0 0 0 0 0 0
+20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 154 11 11 462 22 462 0 0 462 0 0 0 0 0 0 0 0
+30 42 0 0 0 42 2 0 0 0 0 0 0 0 0 0 46 320 23 23 924 46 924 0 0 882 0 0 0 0 0 0 0 0
+40 21 0 2 0 21 1 0 0 0 0 0 0 0 0 0 93 666 48 48 1995 96 1995 0 0 1975 0 0 4 0 0 0 0 0
+50 63 0 5 0 23 1 0 0 0 0 0 4 0 3 44 181 1308 94 94 3894 190 3893 0 88 3835 0 0 2 0 0 0 0 0
+60 82 0 52 1 1 2 0 0 0 0 0 0 0 5 42 195 1387 100 100 4123 200 4123 2 3 4046 0 0 0 0 2 0 0 0
+70 0 2 6 0 0 0 0 0 0 0 0 0 0 0 0 12 78 6 6 248 12 248 0 0 248 0 0 0 0 0 0 0 0
+80 0 4 13 0 0 0 0 0 0 0 0 0 0 0 0 26 169 13 13 535 26 535 0 0 535 0 0 0 0 0 0 0 0
+90 0 14 48 0 0 0 0 0 2 0 0 0 0 0 0 90 564 44 44 1811 88 1811 0 0 1811 0 0 0 0 4 0 0 0
+100 42 32 121 0 0 0 2 2 6 46 0 1 0 0 0 219 1390 109 109 4406 218 4406 0 0 4364 3 0 0 3 10 4 0 0
Deleted: stable/tests/energy_deme_level_res/expected/data/instruction_histogram.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/instruction_histogram.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/instruction_histogram.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,46 +0,0 @@
-# 1: Update
-# 2: nop-A
-# 3: nop-B
-# 4: nop-C
-# 5: if-n-equ
-# 6: if-less
-# 7: pop
-# 8: push
-# 9: swap-stk
-# 10: swap
-# 11: shift-r
-# 12: shift-l
-# 13: inc
-# 14: dec
-# 15: add
-# 16: sub
-# 17: nand
-# 18: IO
-# 19: h-alloc
-# 20: h-divide
-# 21: h-copy
-# 22: h-search
-# 23: mov-head
-# 24: jmp-head
-# 25: get-head
-# 26: if-label
-# 27: set-flow
-# 28: sense-m100
-# 29: if-equ-0
-# 30: time
-# 31: sleep1
-# 32: sleep2
-# 33: sleep3
-# 34: sleep4
-
-0 84 1 15 0 0 0 0 0 0 0 0 0 0 0 0 2 14 2 1 1 3 2 0 0 1 0 0 0 0 0 0 0 0
-10 340 3 56 0 0 0 0 0 0 0 0 0 0 0 0 8 56 7 4 4 11 8 0 0 4 0 0 0 0 0 0 0 0
-20 966 10 147 0 0 0 0 0 0 0 0 0 0 0 0 18 126 29 11 14 32 20 0 0 12 0 1 0 0 0 0 0 0
-30 1449 22 449 0 1 2 0 0 0 0 0 0 0 0 0 58 428 50 24 30 68 55 0 0 26 0 1 3 0 0 0 1 0
-40 3026 48 1107 0 1 2 1 0 0 2 0 3 0 2 0 136 1089 97 51 61 146 135 0 1 57 0 0 8 0 0 0 0 0
-50 6163 94 1923 0 3 3 2 0 0 1 1 7 0 6 5 232 1876 202 100 107 296 254 0 6 105 0 2 3 4 2 2 7 0
-60 6379 100 1954 3 1 3 2 1 1 2 0 0 1 7 2 253 1933 176 109 116 286 256 2 7 118 0 0 1 1 5 2 2 1
-70 474 8 84 0 0 0 0 0 0 0 0 0 0 0 0 12 78 23 7 6 29 13 0 0 7 0 0 0 0 0 0 0 0
-80 732 21 322 0 0 0 0 0 1 0 0 0 0 0 0 42 297 41 15 17 57 39 0 0 18 0 0 1 0 2 0 0 0
-90 2863 69 942 1 0 0 0 1 4 2 0 0 0 0 1 110 831 104 43 48 151 123 0 0 47 2 0 2 8 4 1 0 0
-100 6680 154 2108 5 3 1 6 3 8 10 1 4 0 1 2 246 1880 202 111 116 310 281 4 2 116 7 1 6 11 11 5 0 1
Copied: stable/tests/energy_deme_level_res/expected/data/instruction_histogram.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/instruction_histogram.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/instruction_histogram.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/instruction_histogram.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,46 @@
+# 1: Update
+# 2: nop-A
+# 3: nop-B
+# 4: nop-C
+# 5: if-n-equ
+# 6: if-less
+# 7: pop
+# 8: push
+# 9: swap-stk
+# 10: swap
+# 11: shift-r
+# 12: shift-l
+# 13: inc
+# 14: dec
+# 15: add
+# 16: sub
+# 17: nand
+# 18: IO
+# 19: h-alloc
+# 20: h-divide
+# 21: h-copy
+# 22: h-search
+# 23: mov-head
+# 24: jmp-head
+# 25: get-head
+# 26: if-label
+# 27: set-flow
+# 28: sense-m100
+# 29: if-equ-0
+# 30: time
+# 31: sleep1
+# 32: sleep2
+# 33: sleep3
+# 34: sleep4
+
+0 84 1 15 0 0 0 0 0 0 0 0 0 0 0 0 2 14 2 1 1 3 2 0 0 1 0 0 0 0 0 0 0 0
+10 340 3 56 0 0 0 0 0 0 0 0 0 0 0 0 8 56 7 4 4 11 8 0 0 4 0 0 0 0 0 0 0 0
+20 966 10 147 0 0 0 0 0 0 0 0 0 0 0 0 18 126 29 11 14 32 20 0 0 12 0 1 0 0 0 0 0 0
+30 1449 22 449 0 1 2 0 0 0 0 0 0 0 0 0 58 428 50 24 30 68 55 0 0 26 0 1 3 0 0 0 1 0
+40 3026 48 1107 0 1 2 1 0 0 2 0 3 0 2 0 136 1089 97 51 61 146 135 0 1 57 0 0 8 0 0 0 0 0
+50 6163 94 1923 0 3 3 2 0 0 1 1 7 0 6 5 232 1876 202 100 107 296 254 0 6 105 0 2 3 4 2 2 7 0
+60 6379 100 1954 3 1 3 2 1 1 2 0 0 1 7 2 253 1933 176 109 116 286 256 2 7 118 0 0 1 1 5 2 2 1
+70 474 8 84 0 0 0 0 0 0 0 0 0 0 0 0 12 78 23 7 6 29 13 0 0 7 0 0 0 0 0 0 0 0
+80 732 21 322 0 0 0 0 0 1 0 0 0 0 0 0 42 297 41 15 17 57 39 0 0 18 0 0 1 0 2 0 0 0
+90 2863 69 942 1 0 0 0 1 4 2 0 0 0 0 1 110 831 104 43 48 151 123 0 0 47 2 0 2 8 4 1 0 0
+100 6680 154 2108 5 3 1 6 3 8 10 1 4 0 1 2 246 1880 202 111 116 310 281 4 2 116 7 1 6 11 11 5 0 1
Deleted: stable/tests/energy_deme_level_res/expected/data/resource.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/resource.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/resource.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,18 +0,0 @@
-# Avida resource data
-# Fri Sep 7 16:09:20 2007
-# First column gives the current update, all further columns give the quantity
-# of the particular resource at that update.
-# 1: Update
-# 2: global
-
-0 11.000000
-10 71
-20 193
-30 383
-40 1107
-50 2811
-60 4908
-70 4964
-80 5123
-90 5700
-100 7091
Copied: stable/tests/energy_deme_level_res/expected/data/resource.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/resource.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/resource.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/resource.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,18 @@
+# Avida resource data
+# Fri Sep 7 16:09:20 2007
+# First column gives the current update, all further columns give the quantity
+# of the particular resource at that update.
+# 1: Update
+# 2: global
+
+0 11.000000
+10 71
+20 193
+30 383
+40 1107
+50 2811
+60 4908
+70 4964
+80 5123
+90 5700
+100 7091
Deleted: stable/tests/energy_deme_level_res/expected/data/sleep.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/sleep.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/sleep.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,17 +0,0 @@
-# Number of organisms sleeping
-
-# total number of organisms sleeping
-# 1: update
-# 2: DemeID 0
-# 3: DemeID 1
-
-10 0 0
-20 0 0
-30 0 0
-40 0 0
-50 0 0
-60 0 0
-70 0 0
-80 0 0
-90 0 0
-100 1 0
Copied: stable/tests/energy_deme_level_res/expected/data/sleep.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/sleep.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/sleep.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/sleep.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,17 @@
+# Number of organisms sleeping
+
+# total number of organisms sleeping
+# 1: update
+# 2: DemeID 0
+# 3: DemeID 1
+
+10 0 0
+20 0 0
+30 0 0
+40 0 0
+50 0 0
+60 0 0
+70 0 0
+80 0 0
+90 0 0
+100 1 0
Deleted: stable/tests/energy_deme_level_res/expected/data/stats.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/stats.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/stats.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,26 +0,0 @@
-# Generic Statistics Data
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: average inferiority (energy)
-# 3: ave probability of any mutations in genome
-# 4: probability of any mutations in dom genome
-# 5: log(average fidelity)
-# 6: log(dominant fidelity)
-# 7: change in number of genotypes
-# 8: genotypic entropy
-# 9: species entropy
-# 10: depth of most reacent coalescence
-# 11: Total number of resamplings this generation
-# 12: Total number of organisms that failed to resample this generation
-
-0 0.000000 0.335790 0.335790 0.409157 0.409157 1 0.000000 0.000000 0 0 0
-10 0 0.334577 0.33579 0.407332 0.409157 0 0.562335 0 0 0 0
-20 0 0.33579 0.33579 0.409157 0.409157 0 0.885574 0 0 0 0
-30 0.0350592 0.33579 0.33579 0.409157 0.409157 1 1.04138 0 0 0 0
-40 0.0108545 0.336093 0.33579 0.409613 0.409157 0 1.1258 0 0 0 0
-50 0.0200609 0.336563 0.33579 0.410322 0.409157 4 2.61504 0 0 0 0
-60 0.0221213 0.335887 0.33579 0.409303 0.409157 -3 2.49965 0 0 0 0
-70 0.000537201 0.331738 0.330924 0.403075 0.401858 1 1.32966 0 0 0 0
-80 0.00133527 0.331675 0.330924 0.402981 0.401858 0 1.41274 0 0 0 0
-90 0.00734858 0.331922 0.330924 0.403351 0.401858 0 2.17912 0 0 0 0
-100 0.0245821 0.332133 0.330924 0.403666 0.401858 3 3.04144 0 0 0 0
Copied: stable/tests/energy_deme_level_res/expected/data/stats.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/stats.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/stats.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/stats.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,26 @@
+# Generic Statistics Data
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: average inferiority (energy)
+# 3: ave probability of any mutations in genome
+# 4: probability of any mutations in dom genome
+# 5: log(average fidelity)
+# 6: log(dominant fidelity)
+# 7: change in number of genotypes
+# 8: genotypic entropy
+# 9: species entropy
+# 10: depth of most reacent coalescence
+# 11: Total number of resamplings this generation
+# 12: Total number of organisms that failed to resample this generation
+
+0 0.000000 0.335790 0.335790 0.409157 0.409157 1 0.000000 0.000000 0 0 0
+10 0 0.334577 0.33579 0.407332 0.409157 0 0.562335 0 0 0 0
+20 0 0.33579 0.33579 0.409157 0.409157 0 0.885574 0 0 0 0
+30 0.0350592 0.33579 0.33579 0.409157 0.409157 1 1.04138 0 0 0 0
+40 0.0108545 0.336093 0.33579 0.409613 0.409157 0 1.1258 0 0 0 0
+50 0.0200609 0.336563 0.33579 0.410322 0.409157 4 2.61504 0 0 0 0
+60 0.0221213 0.335887 0.33579 0.409303 0.409157 -3 2.49965 0 0 0 0
+70 0.000537201 0.331738 0.330924 0.403075 0.401858 1 1.32966 0 0 0 0
+80 0.00133527 0.331675 0.330924 0.402981 0.401858 0 1.41274 0 0 0 0
+90 0.00734858 0.331922 0.330924 0.403351 0.401858 0 2.17912 0 0 0 0
+100 0.0245821 0.332133 0.330924 0.403666 0.401858 3 3.04144 0 0 0 0
Deleted: stable/tests/energy_deme_level_res/expected/data/tasks.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/tasks.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/tasks.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,19 +0,0 @@
-# Avida tasks data
-# Fri Sep 7 16:09:20 2007
-# First column gives the current update, next columns give the number
-# of organisms that have the particular task as a component of their merit
-# 1: Update
-# 2: Echo
-# 3: Nand
-
-0 0 0
-10 4 4
-20 11 11
-30 23 23
-40 48 48
-50 94 92
-60 100 97
-70 6 6
-80 13 13
-90 44 44
-100 109 109
Copied: stable/tests/energy_deme_level_res/expected/data/tasks.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/tasks.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/tasks.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/tasks.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,19 @@
+# Avida tasks data
+# Fri Sep 7 16:09:20 2007
+# First column gives the current update, next columns give the number
+# of organisms that have the particular task as a component of their merit
+# 1: Update
+# 2: Echo
+# 3: Nand
+
+0 0 0
+10 4 4
+20 11 11
+30 23 23
+40 48 48
+50 94 92
+60 100 97
+70 6 6
+80 13 13
+90 44 44
+100 109 109
Deleted: stable/tests/energy_deme_level_res/expected/data/tasks_exe.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/tasks_exe.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/tasks_exe.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,18 +0,0 @@
-# Avida tasks execution data
-# Fri Sep 7 16:09:20 2007
-# First column gives the current update, all further columns give the number
-# of times the particular task has been executed this update.
-# 1: Update
-# 2: Echo
-# 3: Nand
-
-10 40 8
-20 110 22
-30 228 44
-40 475 92
-50 924 172
-60 986 188
-70 54 12
-80 117 26
-90 386 88
-100 953 209
Copied: stable/tests/energy_deme_level_res/expected/data/tasks_exe.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/tasks_exe.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/tasks_exe.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/tasks_exe.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,18 @@
+# Avida tasks execution data
+# Fri Sep 7 16:09:20 2007
+# First column gives the current update, all further columns give the number
+# of times the particular task has been executed this update.
+# 1: Update
+# 2: Echo
+# 3: Nand
+
+10 40 8
+20 110 22
+30 228 44
+40 475 92
+50 924 172
+60 986 188
+70 54 12
+80 117 26
+90 386 88
+100 953 209
Deleted: stable/tests/energy_deme_level_res/expected/data/time.dat
===================================================================
--- development/tests/energy_deme_level_res/expected/data/time.dat 2007-09-08 19:00:15 UTC (rev 2076)
+++ stable/tests/energy_deme_level_res/expected/data/time.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -1,18 +0,0 @@
-# Avida time data
-# Fri Sep 7 16:09:20 2007
-# 1: update
-# 2: avida time
-# 3: average generation
-# 4: num_executed?
-
-0 0.000000 0.000000 30
-10 1.60476 2 90
-20 5.59914 3.63636 240
-30 11.5839 5.04348 570
-40 19.2077 7 1350
-50 27.907 9.06383 2730
-60 36.7739 11.22 3000
-70 38.9856 1.66667 120
-80 42.5677 2.84615 390
-90 48.8138 4.88636 1320
-100 57.1728 6.88073 3120
Copied: stable/tests/energy_deme_level_res/expected/data/time.dat (from rev 2076, development/tests/energy_deme_level_res/expected/data/time.dat)
===================================================================
--- stable/tests/energy_deme_level_res/expected/data/time.dat (rev 0)
+++ stable/tests/energy_deme_level_res/expected/data/time.dat 2007-09-08 23:11:33 UTC (rev 2077)
@@ -0,0 +1,18 @@
+# Avida time data
+# Fri Sep 7 16:09:20 2007
+# 1: update
+# 2: avida time
+# 3: average generation
+# 4: num_executed?
+
+0 0.000000 0.000000 30
+10 1.60476 2 90
+20 5.59914 3.63636 240
+30 11.5839 5.04348 570
+40 19.2077 7 1350
+50 27.907 9.06383 2730
+60 36.7739 11.22 3000
+70 38.9856 1.66667 120
+80 42.5677 2.84615 390
+90 48.8138 4.88636 1320
+100 57.1728 6.88073 3120
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