[Avida-SVN] r3559 - in branches/biounit: . Avida.xcodeproj source/cpu source/drivers source/main source/targets/avida-viewer support/config/misc support/config/misc/Parasites tests/default_transsmt_100u
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Wed Dec 16 08:01:42 PST 2009
Author: brysonda
Date: 2009-12-16 11:01:42 -0500 (Wed, 16 Dec 2009)
New Revision: 3559
Added:
branches/biounit/support/config/misc/Parasites/
branches/biounit/support/config/misc/Parasites/avida.cfg
branches/biounit/support/config/misc/Parasites/default-smt.org
branches/biounit/support/config/misc/Parasites/dominant-org.org
branches/biounit/support/config/misc/Parasites/environment.cfg
branches/biounit/support/config/misc/Parasites/events.cfg
branches/biounit/support/config/misc/Parasites/instset-smt.cfg
branches/biounit/support/config/misc/Parasites/parasite-smt.org
Removed:
branches/biounit/support/config/misc/Parasites/avida.cfg
branches/biounit/support/config/misc/Parasites/default-smt.org
branches/biounit/support/config/misc/Parasites/dominant-org.org
branches/biounit/support/config/misc/Parasites/environment.cfg
branches/biounit/support/config/misc/Parasites/events.cfg
branches/biounit/support/config/misc/Parasites/instset-smt.cfg
branches/biounit/support/config/misc/Parasites/parasite-smt.org
Modified:
branches/biounit/
branches/biounit/Avida.xcodeproj/
branches/biounit/source/cpu/cHardwareTransSMT.cc
branches/biounit/source/drivers/cDefaultRunDriver.cc
branches/biounit/source/main/cAvidaConfig.h
branches/biounit/source/main/cOrganism.cc
branches/biounit/source/main/cPhenotype.cc
branches/biounit/source/main/cPhenotype.h
branches/biounit/source/main/cPopulation.cc
branches/biounit/source/main/cPopulationInterface.cc
branches/biounit/source/main/cPopulationInterface.h
branches/biounit/source/targets/avida-viewer/cSymbolUtil.cc
branches/biounit/tests/default_transsmt_100u/test_list
Log:
Merge r3507:3558 from branches/parasites into branches/biounit. Includes r3554:3558 from development.
Property changes on: branches/biounit
___________________________________________________________________
Name: svn:ignore
+ build
Property changes on: branches/biounit/Avida.xcodeproj
___________________________________________________________________
Name: svn:ignore
+ zamanlui.mode1v3
zamanlui.pbxuser
Modified: branches/biounit/source/cpu/cHardwareTransSMT.cc
===================================================================
--- branches/biounit/source/cpu/cHardwareTransSMT.cc 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/cpu/cHardwareTransSMT.cc 2009-12-16 16:01:42 UTC (rev 3559)
@@ -131,7 +131,7 @@
return new tInstLib<tMethod>(f_size, s_f_array, n_names, nop_mods, functions, def, null_inst);
}
-
+
cHardwareTransSMT::cHardwareTransSMT(cAvidaContext& ctx, cWorld* world, cOrganism* in_organism,
cInstSet* in_inst_set, int inst_set_id)
: cHardwareBase(world, in_organism, in_inst_set, inst_set_id), m_mem_array(1)
@@ -159,7 +159,7 @@
// Reset that single thread.
m_threads[0].Reset(this, 0);
m_cur_thread = 0;
-
+
// Reset all stacks (local and global)
for(int i = 0; i < NUM_STACKS; i++) {
Stack(i).Clear();
@@ -200,7 +200,7 @@
// Setup the hardware for the next instruction to be executed.
m_cur_thread++;
if (m_cur_thread >= m_threads.GetSize()) m_cur_thread = 0;
-
+
if (!ThreadIsRunning()) continue;
AdvanceIP() = true;
@@ -331,13 +331,13 @@
<< endl;
fp << " R-Head:(" << GetHead(nHardware::HEAD_READ).GetMemSpace() << ", "
- << GetHead(nHardware::HEAD_READ).GetPosition() << ") "
- << "W-Head:(" << GetHead(nHardware::HEAD_WRITE).GetMemSpace() << ", "
- << GetHead(nHardware::HEAD_WRITE).GetPosition() << ") "
- << "F-Head:(" << GetHead(nHardware::HEAD_FLOW).GetMemSpace() << ", "
- << GetHead(nHardware::HEAD_FLOW).GetPosition() << ") "
- << "RL:" << GetReadLabel().AsString() << " "
- << endl;
+ << GetHead(nHardware::HEAD_READ).GetPosition() << ") "
+ << "W-Head:(" << GetHead(nHardware::HEAD_WRITE).GetMemSpace() << ", "
+ << GetHead(nHardware::HEAD_WRITE).GetPosition() << ") "
+ << "F-Head:(" << GetHead(nHardware::HEAD_FLOW).GetMemSpace() << ", "
+ << GetHead(nHardware::HEAD_FLOW).GetPosition() << ") "
+ << "RL:" << GetReadLabel().AsString() << " "
+ << endl;
for (int i = 0; i < m_mem_array.GetSize(); i++) {
const cCPUMemory& mem = m_mem_array[i];
@@ -415,7 +415,7 @@
// memory. Return the first line _after_ the the found label. It is okay
// to find search label's match inside another label.
int cHardwareTransSMT::FindLabel_Forward(const cCodeLabel& search_label,
- const cGenome& search_genome, int pos)
+ const cGenome& search_genome, int pos)
{
assert (pos < search_genome.GetSize() && pos >= 0);
@@ -496,7 +496,7 @@
// memory. Return the first line _after_ the the found label. It is okay
// to find search label's match inside another label.
int cHardwareTransSMT::FindLabel_Backward(const cCodeLabel & search_label,
- const cGenome & search_genome, int pos)
+ const cGenome & search_genome, int pos)
{
assert (pos < search_genome.GetSize());
@@ -648,8 +648,11 @@
bool cHardwareTransSMT::InjectHost(const cCodeLabel& in_label, const cGenome& inject_code)
{
// Inject fails if the memory space is already in use or thread exists
- if (MemorySpaceExists(in_label) || FindThreadLabel(in_label) != -1) return false;
-
+ if (MemorySpaceExists(in_label) || FindThreadLabel(in_label) != -1)
+ {
+ return false;
+ }
+
// Otherwise create the memory space and copy in the genome
int mem_space_used = FindMemorySpaceLabel(in_label, -1);
assert(mem_space_used != -1);
@@ -657,7 +660,7 @@
// Create a thread for this parasite
if (!ThreadCreate(in_label, mem_space_used)) return false; // Partially failed injection, could not create thread
-
+
return true;
}
@@ -716,7 +719,7 @@
// Add new thread entry
m_threads.Resize(thread_id + 1);
m_thread_lbls.Add(hash_key, thread_id);
-
+
// Setup this thread into the current selected memory space (Flow Head)
m_threads[thread_id].Reset(this, mem_space);
@@ -726,7 +729,7 @@
bool cHardwareTransSMT::ThreadKill(const int thread_id)
{
if (thread_id < 1 || thread_id >= m_threads.GetSize()) return false;
-
+
// Increment thread, if killing current thread
if (m_cur_thread == thread_id) ThreadNext();
@@ -840,59 +843,50 @@
m_organism->GetPhenotype().SetDivType(mut_multiplier);
// Divide Mutations (per site)
- if(m_organism->GetDivMutProb() > 0){
- int num_mut = ctx.GetRandom().GetRandBinomial(injected_code.GetSize(),
- m_organism->GetInjectMutProb() / mut_multiplier);
- // If we have lines to mutate...
- if( num_mut > 0 ){
- for (int i = 0; i < num_mut; i++) {
- int site = ctx.GetRandom().GetUInt(injected_code.GetSize());
- injected_code[site] = m_inst_set->GetRandomInst(ctx);
- }
+ int num_mut = ctx.GetRandom().GetRandBinomial(injected_code.GetSize(),
+ m_organism->GetInjectMutProb() / mut_multiplier);
+ // If we have lines to mutate...
+ if( num_mut > 0 ){
+ for (int i = 0; i < num_mut; i++) {
+ int site = ctx.GetRandom().GetUInt(injected_code.GetSize());
+ injected_code[site] = m_inst_set->GetRandomInst(ctx);
}
}
-
// Insert Mutations (per site)
- if(m_organism->GetDivInsProb() > 0){
- int num_mut = ctx.GetRandom().GetRandBinomial(injected_code.GetSize(),
- m_organism->GetInjectInsProb());
- // If would make creature to big, insert up to MAX_CREATURE_SIZE
- if( num_mut + injected_code.GetSize() > MAX_CREATURE_SIZE ){
- num_mut = MAX_CREATURE_SIZE - injected_code.GetSize();
+ num_mut = ctx.GetRandom().GetRandBinomial(injected_code.GetSize(),
+ m_organism->GetInjectInsProb());
+ // If would make creature to big, insert up to MAX_CREATURE_SIZE
+ if( num_mut + injected_code.GetSize() > MAX_CREATURE_SIZE )
+ num_mut = MAX_CREATURE_SIZE - injected_code.GetSize();
+ // If we have lines to insert...
+ if( num_mut > 0 ){
+ // Build a list of the sites where mutations occured
+ static int mut_sites[MAX_CREATURE_SIZE];
+ for (int i = 0; i < num_mut; i++) {
+ mut_sites[i] = ctx.GetRandom().GetUInt(injected_code.GetSize() + 1);
}
- // If we have lines to insert...
- if( num_mut > 0 ){
- // Build a list of the sites where mutations occured
- static int mut_sites[MAX_CREATURE_SIZE];
- for (int i = 0; i < num_mut; i++) {
- mut_sites[i] = ctx.GetRandom().GetUInt(injected_code.GetSize() + 1);
- }
- // Sort the list
- qsort( (void*)mut_sites, num_mut, sizeof(int), &IntCompareFunction );
- // Actually do the mutations (in reverse sort order)
- for(int i = num_mut-1; i >= 0; i--) {
- injected_code.Insert(mut_sites[i], m_inst_set->GetRandomInst(ctx));
- }
+ // Sort the list
+ qsort( (void*)mut_sites, num_mut, sizeof(int), &IntCompareFunction );
+ // Actually do the mutations (in reverse sort order)
+ for(int i = num_mut-1; i >= 0; i--) {
+ injected_code.Insert(mut_sites[i], m_inst_set->GetRandomInst(ctx));
}
}
-
// Delete Mutations (per site)
- if( m_organism->GetDivDelProb() > 0 ){
- int num_mut = ctx.GetRandom().GetRandBinomial(injected_code.GetSize(),
- m_organism->GetInjectDelProb());
- // If would make creature too small, delete down to MIN_CREATURE_SIZE
- if (injected_code.GetSize() - num_mut < MIN_CREATURE_SIZE) {
- num_mut = injected_code.GetSize() - MIN_CREATURE_SIZE;
- }
-
- // If we have lines to delete...
- for (int i = 0; i < num_mut; i++) {
- int site = ctx.GetRandom().GetUInt(injected_code.GetSize());
- injected_code.Remove(site);
- }
+ num_mut = ctx.GetRandom().GetRandBinomial(injected_code.GetSize(),
+ m_organism->GetInjectDelProb());
+ // If would make creature too small, delete down to MIN_CREATURE_SIZE
+ if (injected_code.GetSize() - num_mut < MIN_CREATURE_SIZE) {
+ num_mut = injected_code.GetSize() - MIN_CREATURE_SIZE;
}
+
+ // If we have lines to delete...
+ for (int i = 0; i < num_mut; i++) {
+ int site = ctx.GetRandom().GetUInt(injected_code.GetSize());
+ injected_code.Remove(site);
+ }
// Mutations in the parent's genome
if (m_organism->GetParentMutProb() > 0) {
@@ -906,6 +900,7 @@
}
+
bool cHardwareTransSMT::Divide_Main(cAvidaContext& ctx, double mut_multiplier)
{
const int mem_space_used = GetHead(nHardware::HEAD_WRITE).GetMemSpace();
@@ -913,7 +908,7 @@
// Make sure the memory space we're using exists
if (m_mem_array.GetSize() <= mem_space_used) return false;
-
+
// Make sure this divide will produce a viable offspring.
m_cur_child = mem_space_used; // save current child memory space for use by dependent functions (e.g. calcCopiedSize())
if (!Divide_CheckViable(ctx, m_mem_array[0].GetSize(), write_head_pos)) return false;
@@ -954,13 +949,13 @@
case DIVIDE_METHOD_SPLIT:
Reset(ctx); // This will wipe out all parasites on a divide.
break;
-
+
case DIVIDE_METHOD_BIRTH:
// Reset only the calling thread's state
for(int x = 0; x < nHardware::NUM_HEADS; x++) GetHead(x).Reset(this, 0);
for(int x = 0; x < NUM_LOCAL_STACKS; x++) Stack(x).Clear();
break;
-
+
case DIVIDE_METHOD_OFFSPRING:
default:
break;
@@ -1125,11 +1120,15 @@
// Mutations only occur on the read, for the moment.
int read_inst = 0;
+
if (m_organism->TestCopyMut(ctx)) {
read_inst = m_inst_set->GetRandomInst(ctx).GetOp();
} else {
read_inst = GetHead(head_id).GetInst().GetOp();
}
+
+
+ read_inst = GetHead(head_id).GetInst().GetOp();
Stack(dst).Push(read_inst);
ReadInst(read_inst);
@@ -1142,7 +1141,7 @@
{
const int head_id = FindModifiedHead(nHardware::HEAD_WRITE);
const int src = FindModifiedStack(STACK_AX);
-
+
cHeadCPU & active_head = GetHead(head_id);
int mem_space_used = active_head.GetMemSpace();
@@ -1451,7 +1450,7 @@
bool cHardwareTransSMT::Inst_CallFlow(cAvidaContext& ctx)
{
const int dst = FindModifiedStack(STACK_AX);
-
+
const int location = IP().GetPosition() & 0xFFFF;
const int mem_space = IP().GetMemSpace() << 8;
const int ra = location | mem_space;
Modified: branches/biounit/source/drivers/cDefaultRunDriver.cc
===================================================================
--- branches/biounit/source/drivers/cDefaultRunDriver.cc 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/drivers/cDefaultRunDriver.cc 2009-12-16 16:01:42 UTC (rev 3559)
@@ -46,7 +46,7 @@
cDefaultRunDriver::cDefaultRunDriver(cWorld* world) : m_world(world), m_done(false),
- m_fastforward(false),m_last_generation(0), m_generation_same_update_count(0)
+m_fastforward(false),m_last_generation(0), m_generation_same_update_count(0)
{
cDriverManager::Register(this);
world->SetDriver(this);
@@ -110,7 +110,7 @@
// Process the update.
const int UD_size = ave_time_slice * population.GetNumOrganisms();
const double step_size = 1.0 / (double) UD_size;
-
+
for (int i = 0; i < UD_size; i++) {
if (population.GetNumOrganisms() == 0) {
m_done = true;
@@ -122,21 +122,21 @@
// end of update stats...
population.ProcessPostUpdate(ctx);
-
+
// No viewer; print out status for this update....
if (m_world->GetVerbosity() > VERBOSE_SILENT) {
cout.setf(ios::left);
cout.setf(ios::showpoint);
cout << "UD: " << setw(6) << stats.GetUpdate() << " "
- << "Gen: " << setw(9) << setprecision(7) << stats.SumGeneration().Average() << " "
- << "Fit: " << setw(9) << setprecision(7) << stats.GetAveFitness() << " "
+ << "Gen: " << setw(9) << setprecision(7) << stats.SumGeneration().Average() << " "
+ << "Fit: " << setw(9) << setprecision(7) << stats.GetAveFitness() << " "
// << "Energy: " << setw(9) << setprecision(7) << stats.GetAveEnergy() << " "
-// << "Merit: " << setw(9) << setprecision(7) << stats.GetAveMerit() << " "
- << "Orgs: " << setw(6) << population.GetNumOrganisms() << " ";
-// << "Spec: " << setw(6) << setprecision(4) << stats.GetAveSpeculative() << " "
-// << "SWst: " << setw(6) << setprecision(4) << (((double)stats.GetSpeculativeWaste() / (double)UD_size) * 100.0) << "%"
-// << "Thrd: " << setw(6) << stats.GetNumThreads() << " "
-// << "Para: " << stats.GetNumParasites()
+ << "Merit: " << setw(9) << setprecision(7) << stats.GetAveMerit() << " "
+ << "Orgs: " << setw(6) << population.GetNumOrganisms() << " "
+ // << "Spec: " << setw(6) << setprecision(4) << stats.GetAveSpeculative() << " "
+ // << "SWst: " << setw(6) << setprecision(4) << (((double)stats.GetSpeculativeWaste() / (double)UD_size) * 100.0) << "%"
+ << "Thrd: " << setw(6) << stats.GetNumThreads() << " "
+ << "Para: " << stats.GetNumParasites() << " GenEntr: " << stats.GetEntropy() << " ";
if (m_world->GetPopulation().GetNumDemes() > 1) cout << "Demes: " << setw(4) << stats.GetNumOccupiedDemes() << " ";
cout << endl;
}
@@ -153,7 +153,7 @@
// Keep track of changes in generation for fast-forward purposes
UpdateFastForward(stats.GetGeneration(),stats.GetNumCreatures());
-
+
// Exit conditons...
if (population.GetNumOrganisms() == 0) m_done = true;
}
@@ -184,11 +184,11 @@
{
if (bool(m_population_fastforward_threshold))
{
- if (population >= m_population_fastforward_threshold) m_fastforward = true;
- else m_fastforward = false;
+ if (population >= m_population_fastforward_threshold) m_fastforward = true;
+ else m_fastforward = false;
}
if (!m_generation_update_fastforward_threshold) return;
-
+
if (inGeneration == m_last_generation)
{
m_generation_same_update_count++;
Modified: branches/biounit/source/main/cAvidaConfig.h
===================================================================
--- branches/biounit/source/main/cAvidaConfig.h 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/main/cAvidaConfig.h 2009-12-16 16:01:42 UTC (rev 3559)
@@ -150,8 +150,7 @@
bool use_overide;
public:
- cBaseConfigEntry(const cString& _name, const cString& _type,
- const cString& _def, const cString& _desc);
+ cBaseConfigEntry(const cString& _name, const cString& _type, const cString& _def, const cString& _desc);
virtual ~cBaseConfigEntry() { ; }
virtual void LoadString(const cString& str_value) = 0;
@@ -175,7 +174,7 @@
tList<cBaseConfigEntry> entry_list;
public:
cBaseConfigGroup(const cString& _name, const cString& _desc)
- : group_name(_name), description(_desc) { global_group_list.PushRear(this); }
+ : group_name(_name), description(_desc) { global_group_list.PushRear(this); }
~cBaseConfigGroup() { ; }
const cString& GetName() const { return group_name; }
@@ -195,7 +194,7 @@
cString m_description;
tList<cBaseConfigFormatEntry> m_entry_list;
cStringList m_value;
-
+
public:
cBaseConfigCustomFormat(const cString& _name, const cString& _desc)
: m_format_name(_name), m_description(_desc) { global_format_list.PushRear(this); }
@@ -207,11 +206,11 @@
const tList<cBaseConfigFormatEntry>& GetEntryList() const { return m_entry_list; }
void AddEntry(cBaseConfigFormatEntry* _entry) { m_entry_list.PushRear(_entry); }
-
+
const cStringList& Get() const { return m_value; }
void Add(const cString& value) { m_value.PushRear(value); }
};
-
+
// The cConfigFormatEntry class is a bass class for all configuration entries.
// It is used to manage the various types of entries in a dynamic fashion.
class cBaseConfigFormatEntry {
@@ -247,8 +246,8 @@
static tList<cBaseConfigCustomFormat> global_format_list;
tList<cBaseConfigGroup> m_group_list;
tList<cBaseConfigCustomFormat> m_format_list;
-
-
+
+
public:
cAvidaConfig()
{
@@ -257,7 +256,7 @@
global_list_mutex.Unlock();
}
~cAvidaConfig() { ; }
-
+
#ifdef OVERRIDE_CONFIG
#include "config_overrides.h"
#else
@@ -339,7 +338,7 @@
CONFIG_ADD_VAR(DEMES_PREFER_EMPTY, int, 0, "Give empty demes preference as targets of deme replication?");
CONFIG_ADD_VAR(DEMES_PROTECTION_POINTS, int, 0, "The number of points a deme receives for each suicide.");
CONFIG_ADD_VAR(POINT_DECAY_PERCENT, int, 0, "The percentage of points decayed each time cActionDecayPoints is called.");
-
+
CONFIG_ADD_GROUP(REPRODUCTION_GROUP, "Birth and Death");
CONFIG_ADD_VAR(BIRTH_METHOD, int, 0, "Which organism should be replaced on birth?\n0 = Random organism in neighborhood\n1 = Oldest in neighborhood\n2 = Largest Age/Merit in neighborhood\n3 = None (use only empty cells in neighborhood)\n4 = Random from population (Mass Action)\n5 = Oldest in entire population\n6 = Random within deme\n7 = Organism faced by parent\n8 = Next grid cell (id+1)\n9 = Largest energy used in entire population\n10 = Largest energy used in neighborhood\n11 = Local neighborhood dispersal");
CONFIG_ADD_VAR(PREFER_EMPTY, int, 1, "Give empty cells preference in offsping placement?");
@@ -355,6 +354,11 @@
CONFIG_ADD_VAR(GENERATION_INC_METHOD, int, 1, "0 = Only the generation of the child is\n increased on divide.\n1 = Both the generation of the mother and child are\n increased on divide (good with DIVIDE_METHOD 1).");
CONFIG_ADD_VAR(RESET_INPUTS_ON_DIVIDE, int, 0, "Reset environment inputs of parent upon successful divide.");
CONFIG_ADD_VAR(REPRO_METHOD, int, 1, "Replace existing organism: 1=yes");
+
+
+ CONFIG_ADD_VAR(INJECT_PROB_FROM_TASKS, int, 1, "Inject occurs based on probability from performing tasks");
+ CONFIG_ADD_VAR(INJECT_STERILIZES_HOST, int, 0, "Infection causes host steralization");
+ CONFIG_ADD_VAR(INJECT_PROB_SIGMOID, int, 1, "Inject Probs follow a psuedo-sigmoid path - only works if task probs are turned on");
CONFIG_ADD_GROUP(RECOMBINATION_GROUP, "Sexual Recombination and Modularity");
CONFIG_ADD_VAR(RECOMBINATION_PROB, double, 1.0, "probability of recombination in div-sex");
@@ -366,7 +370,7 @@
CONFIG_ADD_VAR(SAME_LENGTH_SEX, int, 0, "0 = recombine with any genome\n1 = only recombine w/ same length");
CONFIG_ADD_VAR(ALLOW_MATE_SELECTION, bool, 0, "Allow organisms to select mates (requires instruction set support)");
CONFIG_ADD_VAR(LEGACY_GRID_LOCAL_SELECTION, bool, 0, "Enable legacy grid local mate selection (ignores population structure)");
-
+
CONFIG_ADD_GROUP(DIVIDE_GROUP, "Divide Restrictions");
CONFIG_ADD_VAR(CHILD_SIZE_RANGE, double, 2.0, "Maximal differential between child and parent sizes.\n(Checked BEFORE mutations applied on divide.)");
CONFIG_ADD_VAR(MIN_COPIED_LINES, double, 0.5, "Code fraction which must be copied before divide.");
@@ -387,13 +391,13 @@
CONFIG_ADD_GROUP(MUTATION_GROUP, "Mutations");
CONFIG_ADD_VAR(POINT_MUT_PROB, double, 0.0, "Mutation rate (per-location per update)");
-
+
CONFIG_ADD_VAR(COPY_MUT_PROB, double, 0.0075, "Mutation rate (per copy)");
CONFIG_ADD_VAR(COPY_INS_PROB, double, 0.0, "Insertion rate (per copy)");
CONFIG_ADD_VAR(COPY_DEL_PROB, double, 0.0, "Deletion rate (per copy)");
CONFIG_ADD_VAR(COPY_UNIFORM_PROB, double, 0.0, "Uniform mutation probability (per copy)\n- Randomly applies any of the three classes of mutations (ins, del, point).");
CONFIG_ADD_VAR(COPY_SLIP_PROB, double, 0.0, "Slip rate (per copy)");
-
+
CONFIG_ADD_VAR(DIV_MUT_PROB, double, 0.0, "Mutation rate (per site, applied on divide)");
CONFIG_ADD_VAR(DIV_INS_PROB, double, 0.0, "Insertion rate (per site, applied on divide)");
CONFIG_ADD_VAR(DIV_DEL_PROB, double, 0.0, "Deletion rate (per site, applied on divide)");
@@ -409,9 +413,9 @@
CONFIG_ADD_VAR(DIVIDE_POISSON_INS_MEAN, double, 0.0, "Insertion rate (Poisson distributed, per divide)");
CONFIG_ADD_VAR(DIVIDE_POISSON_DEL_MEAN, double, 0.0, "Deletion rate (Poisson distributed, per divide)");
CONFIG_ADD_VAR(DIVIDE_POISSON_SLIP_MEAN, double, 0.0, "Slip rate (Poisson distributed, per divide)");
-
+
CONFIG_ADD_VAR(DIVIDE_UNIFORM_PROB, double, 0.0, "Uniform mutation probability (per divide)\n- Randomly applies any of the three classes of mutations (ins, del, point).");
-
+
CONFIG_ADD_VAR(DEATH_PROB, double, 0.0, "Death rate (parent organism, per divide)");
CONFIG_ADD_VAR(INJECT_INS_PROB, double, 0.0, "Insertion rate (per site, applied on inject)");
@@ -426,7 +430,7 @@
CONFIG_ADD_VAR(META_STD_DEV, double, 0.0, "Standard deviation of meta mutation size.");
CONFIG_ADD_VAR(MUT_RATE_SOURCE, int, 1, "1 = Mutation rates determined by environment.\n2 = Mutation rates inherited from parent.");
CONFIG_ADD_VAR(MIGRATION_RATE, double, 0.0, "Uniform probability of offspring migrating to a new deme.");
-
+
CONFIG_ADD_GROUP(REVERSION_GROUP, "Mutation Reversion\nThese slow down avida a lot, and should be set to 0.0 normally.");
CONFIG_ADD_VAR(REVERT_FATAL, double, 0.0, "Should any mutations be reverted on birth?");
CONFIG_ADD_VAR(REVERT_DETRIMENTAL, double, 0.0, " 0.0 to 1.0; Probability of reversion.");
@@ -474,7 +478,7 @@
CONFIG_ADD_VAR(FASTFORWARD_UPDATES, int, 0, "Fast-forward if the average generation has not changed in this many updates. (0 = off)");
CONFIG_ADD_VAR(FASTFORWARD_NUM_ORGS, int, 0, "Fast-forward if population is equal to this");
CONFIG_ADD_VAR(GENOTYPE_PHENPLAST_CALC, int, 100, "Number of times to test a genotype's\nplasticity during runtime.");
-
+
CONFIG_ADD_GROUP(GENEOLOGY_GROUP, "Geneology");
CONFIG_ADD_VAR(TRACK_MAIN_LINEAGE, int, 1, "Keep all ancestors of the active population?\n0=no, 1=yes, 2=yes,w/sexual population");
CONFIG_ADD_VAR(THRESHOLD, int, 3, "Number of organisms in a genotype needed for it\n to be considered viable.");
@@ -507,7 +511,7 @@
CONFIG_ADD_VAR(MESSAGE_SEND_BUFFER_SIZE, bool, 1, "Size of message send buffer (stores messages that were sent)\nTASKS NOT CHECKED ON 0!\n-1=inf, default=1.");
CONFIG_ADD_VAR(MESSAGE_RECV_BUFFER_SIZE, bool, 8, "Size of message receive buffer (stores messages that are received); -1=inf, default=8.");
CONFIG_ADD_VAR(MESSAGE_RECV_BUFFER_BEHAVIOR, bool, 0, "Behavior of message receive buffer; 0=drop oldest (default), 1=drop incoming");
-
+
CONFIG_ADD_GROUP(BUY_SELL_GROUP, "Buying and Selling Parameters");
CONFIG_ADD_VAR(SAVE_RECEIVED, bool, 0, "Enable storage of all inputs bought from other orgs");
CONFIG_ADD_VAR(BUY_PRICE, int, 0, "price offered by organisms attempting to buy");
@@ -561,7 +565,7 @@
CONFIG_ADD_GROUP(SECOND_PASS_GROUP, "Tracking metrics known after the running experiment previously");
CONFIG_ADD_VAR(TRACK_CCLADES, int, 0, "Enable tracking of coalescence clades");
CONFIG_ADD_VAR(TRACK_CCLADES_IDS, cString, "coalescence.ids", "File storing coalescence IDs");
-
+
CONFIG_ADD_GROUP(GX_GROUP, "Gene Expression CPU Settings");
CONFIG_ADD_VAR(MAX_PROGRAMIDS, int, 16, "Maximum number of programids an organism can create.");
CONFIG_ADD_VAR(MAX_PROGRAMID_AGE, int, 2000, "Max number of CPU cycles a programid executes before it is removed.");
@@ -570,7 +574,7 @@
CONFIG_ADD_VAR(IMPLICIT_TURNOVER_RATE, double, 0.0, "Number of programids recycled per CPU cycle. 0 = OFF");
CONFIG_ADD_VAR(IMPLICIT_MAX_PROGRAMID_LENGTH, int, 0, "Creation of an executable programid terminates after this many instructions. 0 = disabled");
// CONFIG_ADD_VAR(CLEAR_ON_OUTPUT, int, 0, "Reset input buffer every time output called?"); @JEB Not fully implemented
-
+
CONFIG_ADD_GROUP(PROMOTER_GROUP, "Promoters");
CONFIG_ADD_VAR(PROMOTERS_ENABLED, int, 0, "Use the promoter/terminator execution scheme.\nCertain instructions must also be included.");
CONFIG_ADD_VAR(PROMOTER_INST_MAX, int, 0, "Maximum number of instructions to execute before terminating. 0 = off");
@@ -585,7 +589,7 @@
CONFIG_ADD_VAR(INST_CODE_LENGTH, int, 3, "Instruction binary code length (number of bits)");
CONFIG_ADD_VAR(INST_CODE_DEFAULT_TYPE, int, 0, "Default value of instruction binary code value.\n0 = All zeros\n1 = Based off the instruction number");
CONFIG_ADD_VAR(CONSTITUTIVE_REGULATION, int, 0, "Sense a new regulation value before each CPU cycle?");
-
+
CONFIG_ADD_GROUP(COLORS_GROUP, "Output colors for when data files are printed in HTML mode.\nThere are two sets of these; the first are for lineages,\nand the second are for mutation tests.");
CONFIG_ADD_VAR(COLOR_DIFF, cString, "CCCCFF", "Color to flag stat that has changed since parent.");
CONFIG_ADD_VAR(COLOR_SAME, cString, "FFFFFF", "Color to flag stat that has NOT changed since parent.");
@@ -593,12 +597,12 @@
CONFIG_ADD_VAR(COLOR_NEG1, cString, "FFCCCC", "Color to flag stat that is minorly worse than parent.");
CONFIG_ADD_VAR(COLOR_POS1, cString, "CCFFCC", "Color to flag stat that is minorly better than parent.");
CONFIG_ADD_VAR(COLOR_POS2, cString, "00FF00", "Color to flag stat that is significantly better than parent.");
-
+
CONFIG_ADD_VAR(COLOR_MUT_POS, cString, "00FF00", "Color to flag stat that has changed since parent.");
CONFIG_ADD_VAR(COLOR_MUT_NEUT, cString, "FFFFFF", "Color to flag stat that has changed since parent.");
CONFIG_ADD_VAR(COLOR_MUT_NEG, cString, "FFFF00", "Color to flag stat that has changed since parent.");
CONFIG_ADD_VAR(COLOR_MUT_LETHAL, cString, "FF0000", "Color to flag stat that has changed since parent.");
-
+
// @WRE: Additions for approaching various features of biological organisms
CONFIG_ADD_GROUP(BIOMIMETIC_GROUP, "Biomimetic Features Settings");
CONFIG_ADD_VAR(BIOMIMETIC_REFRACTORY_PERIOD, double, 0.0, "Number of updates affected by refractory period");
@@ -607,7 +611,7 @@
CONFIG_ADD_VAR(BIOMIMETIC_MOVEMENT_FACTOR, double, 1.0, "Scale merit bonus due to movement (m<1.0 applies a cost)");
CONFIG_ADD_VAR(BIOMIMETIC_EVAL_ON_MOVEMENT, int, 0, "Force task evaluation on each movement step");
CONFIG_ADD_VAR(BIOMIMETIC_K, int, 0, "Carrying capacity in number of organisms");
-
+
// BDC: Additions for pheromones
CONFIG_ADD_GROUP(PHEROMONE_GROUP, "Pheromone Settings");
CONFIG_ADD_VAR(PHEROMONE_ENABLED, bool, 0, "Enable pheromone usage. 0/1 (off/on)");
@@ -631,7 +635,7 @@
// -------- Consensus config options --------
CONFIG_ADD_GROUP(CONSENSUS_GROUP, "Consensus settings");
CONFIG_ADD_VAR(CONSENSUS_HOLD_TIME, int, 1, "Number of updates that consensus must be held for.");
-
+
CONFIG_ADD_CUSTOM_FORMAT(INST_SET_NEW, "Instruction Set Definition");
CONFIG_ADD_FORMAT_VAR(INST, "Instruction entry in the instruction set");
@@ -664,14 +668,14 @@
// -------- Horizontal Gene Transfer (HGT) config options --------
CONFIG_ADD_GROUP(HGT_GROUP, "Horizontal gene transfer settings");
CONFIG_ADD_VAR(ENABLE_HGT, int, 0, "Whether HGT is enabled; 0=false (default),\n 1=true.");
- CONFIG_ADD_VAR(HGT_FRAGMENT_SELECTION, int, 0, "Method used to select fragments for HGT mutation (0=random [default]\n1=trimmed selection).");
+ CONFIG_ADD_VAR(HGT_FRAGMENT_SELECTION, int, 0, "Method used to select fragments for HGT mutation (0=random [default]\n1=trimmed selection\n2=random placement).");
CONFIG_ADD_VAR(HGT_FRAGMENT_SIZE_MEAN, double, 10, "Mean size of fragments (drawn from a normal\ndist., default=10).");
CONFIG_ADD_VAR(HGT_FRAGMENT_SIZE_VARIANCE, double, 2, "Variance of fragments (drawn from a normal\ndist., default=2).");
CONFIG_ADD_VAR(HGT_MAX_FRAGMENTS_PER_CELL, int, 100, "Max. allowed number of fragments\nper cell (default=100).");
CONFIG_ADD_VAR(HGT_DIFFUSION_METHOD, int, 0, "Method to use for diffusion of genome\nfragments (0=none [default]).");
CONFIG_ADD_VAR(HGT_MUTATION_P, double, 0.0, "Probability that an HGT mutation will occur on divide (default=0.0).");
CONFIG_ADD_VAR(HGT_INSERTION_MUT_P, double, 0.5, "Probability that an HGT mutation will result in an insertion (default=0.5); replacement if false.");
-
+
CONFIG_ADD_GROUP(INST_RES_GROUP, "Resource-Dependent Instructions Settings");
CONFIG_ADD_VAR(INST_RES, cString, "", "Resource upon which the execution of certain instruction depends");
CONFIG_ADD_VAR(INST_RES_FLOOR, double, 0.0, "Assumed lower level of resource in environment. Used for probability dist.");
Modified: branches/biounit/source/main/cOrganism.cc
===================================================================
--- branches/biounit/source/main/cOrganism.cc 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/main/cOrganism.cc 2009-12-16 16:01:42 UTC (rev 3559)
@@ -423,6 +423,9 @@
bool task_completed = m_phenotype.TestOutput(ctx, taskctx, globalAndDeme_resource_count,
m_phenotype.GetCurRBinsAvail(), globalAndDeme_res_change,
insts_triggered);
+
+ if(task_completed)
+ cout << "task done" << endl;
// Handle merit increases that take the organism above it's current population merit
if (m_world->GetConfig().MERIT_INC_APPLY_IMMEDIATE.Get()) {
Modified: branches/biounit/source/main/cPhenotype.cc
===================================================================
--- branches/biounit/source/main/cPhenotype.cc 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/main/cPhenotype.cc 2009-12-16 16:01:42 UTC (rev 3559)
@@ -41,34 +41,34 @@
cPhenotype::cPhenotype(cWorld* world, int parent_generation)
- : m_world(world)
- , initialized(false)
- , cur_task_count(m_world->GetEnvironment().GetNumTasks())
- , cur_internal_task_count(m_world->GetEnvironment().GetNumTasks())
- , eff_task_count(m_world->GetEnvironment().GetNumTasks())
- , cur_task_quality(m_world->GetEnvironment().GetNumTasks())
- , cur_task_value(m_world->GetEnvironment().GetNumTasks())
- , cur_internal_task_quality(m_world->GetEnvironment().GetNumTasks())
- , cur_rbins_total(m_world->GetEnvironment().GetResourceLib().GetSize())
- , cur_rbins_avail(m_world->GetEnvironment().GetResourceLib().GetSize())
- , cur_collect_spec_counts(m_world->GetNumResourceSpecs())
- , cur_reaction_count(m_world->GetEnvironment().GetReactionLib().GetSize())
- , cur_reaction_add_reward(m_world->GetEnvironment().GetReactionLib().GetSize())
- , cur_sense_count(m_world->GetStats().GetSenseSize())
- , sensed_resources(m_world->GetEnvironment().GetResourceLib().GetSize())
- , cur_task_time(m_world->GetEnvironment().GetNumTasks()) // Added for tracking time; WRE 03-18-07
- , m_reaction_result(NULL)
- , last_task_count(m_world->GetEnvironment().GetNumTasks())
- , last_internal_task_count(m_world->GetEnvironment().GetNumTasks())
- , last_task_quality(m_world->GetEnvironment().GetNumTasks())
- , last_task_value(m_world->GetEnvironment().GetNumTasks())
- , last_internal_task_quality(m_world->GetEnvironment().GetNumTasks())
- , last_rbins_total(m_world->GetEnvironment().GetResourceLib().GetSize())
- , last_rbins_avail(m_world->GetEnvironment().GetResourceLib().GetSize())
- , last_collect_spec_counts()
- , last_reaction_count(m_world->GetEnvironment().GetReactionLib().GetSize())
- , last_reaction_add_reward(m_world->GetEnvironment().GetReactionLib().GetSize())
- , last_sense_count(m_world->GetStats().GetSenseSize())
+: m_world(world)
+, initialized(false)
+, cur_task_count(m_world->GetEnvironment().GetNumTasks())
+, cur_internal_task_count(m_world->GetEnvironment().GetNumTasks())
+, eff_task_count(m_world->GetEnvironment().GetNumTasks())
+, cur_task_quality(m_world->GetEnvironment().GetNumTasks())
+, cur_task_value(m_world->GetEnvironment().GetNumTasks())
+, cur_internal_task_quality(m_world->GetEnvironment().GetNumTasks())
+, cur_rbins_total(m_world->GetEnvironment().GetResourceLib().GetSize())
+, cur_rbins_avail(m_world->GetEnvironment().GetResourceLib().GetSize())
+, cur_collect_spec_counts(m_world->GetNumResourceSpecs())
+, cur_reaction_count(m_world->GetEnvironment().GetReactionLib().GetSize())
+, cur_reaction_add_reward(m_world->GetEnvironment().GetReactionLib().GetSize())
+, cur_sense_count(m_world->GetStats().GetSenseSize())
+, sensed_resources(m_world->GetEnvironment().GetResourceLib().GetSize())
+, cur_task_time(m_world->GetEnvironment().GetNumTasks()) // Added for tracking time; WRE 03-18-07
+, m_reaction_result(NULL)
+, last_task_count(m_world->GetEnvironment().GetNumTasks())
+, last_internal_task_count(m_world->GetEnvironment().GetNumTasks())
+, last_task_quality(m_world->GetEnvironment().GetNumTasks())
+, last_task_value(m_world->GetEnvironment().GetNumTasks())
+, last_internal_task_quality(m_world->GetEnvironment().GetNumTasks())
+, last_rbins_total(m_world->GetEnvironment().GetResourceLib().GetSize())
+, last_rbins_avail(m_world->GetEnvironment().GetResourceLib().GetSize())
+, last_collect_spec_counts()
+, last_reaction_count(m_world->GetEnvironment().GetReactionLib().GetSize())
+, last_reaction_add_reward(m_world->GetEnvironment().GetReactionLib().GetSize())
+, last_sense_count(m_world->GetStats().GetSenseSize())
, generation(0)
{
if (parent_generation >= 0) {
@@ -112,7 +112,7 @@
copied_size = in_phen.copied_size;
executed_size = in_phen.executed_size;
gestation_time = in_phen.gestation_time;
-
+
gestation_start = in_phen.gestation_start;
fitness = in_phen.fitness;
div_type = in_phen.div_type;
@@ -138,7 +138,7 @@
sensed_resources = in_phen.sensed_resources;
cur_task_time = in_phen.cur_task_time;
cur_child_germline_propensity = in_phen.cur_child_germline_propensity;
-
+
// Dynamically allocated m_task_states requires special handling
tList<cTaskState*> hash_values;
tList<void*> hash_keys;
@@ -174,7 +174,7 @@
total_energy_donated = in_phen.total_energy_donated;
total_energy_received = in_phen.total_energy_received;
total_energy_applied = in_phen.total_energy_applied;
-
+
// 4. Records from this organisms life...
num_divides = in_phen.num_divides;
generation = in_phen.generation;
@@ -250,7 +250,7 @@
total_energy_donated = in_phen.total_energy_donated;
total_energy_received = in_phen.total_energy_received;
total_energy_applied = in_phen.total_energy_applied;
-
+
// 6. Child information...
copy_true = in_phen.copy_true;
divide_sex = in_phen.divide_sex;
@@ -259,10 +259,10 @@
child_fertile = in_phen.child_fertile;
last_child_fertile = in_phen.last_child_fertile;
child_copied_size = in_phen.child_copied_size;
-
+
// 7. Permanent information...
permanent_germline_propensity = in_phen.permanent_germline_propensity;
-
+
return *this;
}
@@ -311,7 +311,7 @@
executionRatio = 1.0;
else
executionRatio = parent_phenotype.executionRatio;
-
+
energy_store = min(energy_store, m_world->GetConfig().ENERGY_CAP.Get());
energy_tobe_applied = 0.0;
energy_testament = 0.0;
@@ -325,12 +325,12 @@
cpu_cycles_used = 0;
fitness = parent_phenotype.fitness;
div_type = parent_phenotype.div_type;
-
+
assert(genome_length > 0);
assert(copied_size > 0);
assert(gestation_time >= 0); //@JEB 0 valid for some fitness methods
assert(div_type > 0);
-
+
// Initialize current values, as neeeded.
cur_bonus = m_world->GetConfig().DEFAULT_BONUS.Get();
cur_energy_bonus = 0.0;
@@ -346,7 +346,7 @@
// parent's resources have already been halved in DivideReset;
// offspring gets that value too.
for (int i = 0; i < cur_rbins_avail.GetSize(); i++)
- cur_rbins_avail[i] = parent_phenotype.cur_rbins_avail[i];
+ cur_rbins_avail[i] = parent_phenotype.cur_rbins_avail[i];
cur_collect_spec_counts.SetAll(0);
cur_reaction_count.SetAll(0);
cur_reaction_add_reward.SetAll(0);
@@ -354,14 +354,14 @@
cur_sense_count.SetAll(0);
cur_task_time.SetAll(0.0); // Added for time tracking; WRE 03-18-07
for (int j = 0; j < sensed_resources.GetSize(); j++)
- sensed_resources[j] = parent_phenotype.sensed_resources[j];
+ sensed_resources[j] = parent_phenotype.sensed_resources[j];
cur_trial_fitnesses.Resize(0);
cur_trial_bonuses.Resize(0);
cur_trial_times_used.Resize(0);
trial_time_used = 0;
trial_cpu_cycles_used = 0;
cur_child_germline_propensity = m_world->GetConfig().DEMES_DEFAULT_GERMLINE_PROPENSITY.Get();
-
+
// Copy last values from parent
last_merit_base = parent_phenotype.last_merit_base;
last_bonus = parent_phenotype.last_bonus;
@@ -382,7 +382,7 @@
last_sense_count = parent_phenotype.last_sense_count;
last_fitness = CalcFitness(last_merit_base, last_bonus, gestation_time, last_cpu_cycles_used);
last_child_germline_propensity = parent_phenotype.last_child_germline_propensity; // chance of child being a germline cell; @JEB
-
+
// Setup other miscellaneous values...
num_divides = 0;
generation = parent_phenotype.generation;
@@ -451,7 +451,7 @@
parent_cross_num = parent_phenotype.cross_num;
to_die = false;
to_delete = false;
-
+
is_energy_requestor = false;
is_energy_donor = false;
is_energy_receiver = false;
@@ -460,7 +460,7 @@
total_energy_donated = 0.0;
total_energy_received = 0.0;
total_energy_applied = 0.0;
-
+
// Setup child info...
copy_true = false;
divide_sex = false;
@@ -469,10 +469,10 @@
last_child_fertile = is_fertile;
child_fertile = true;
child_copied_size = 0;
-
+
// permanently set germline propensity of org (since DivideReset is called first, it is now in the "last" slot...)
permanent_germline_propensity = parent_phenotype.last_child_germline_propensity;
-
+
initialized = true;
}
@@ -502,7 +502,7 @@
gestation_start = 0;
fitness = 0;
div_type = 1;
-
+
// Initialize current values, as neeeded.
cur_bonus = m_world->GetConfig().DEFAULT_BONUS.Get();
cur_energy_bonus = 0.0;
@@ -529,7 +529,7 @@
trial_time_used = 0;
trial_cpu_cycles_used = 0;
cur_child_germline_propensity = m_world->GetConfig().DEMES_DEFAULT_GERMLINE_PROPENSITY.Get();
-
+
// New organism has no parent and so cannot use its last values; initialize as needed
last_merit_base = genome_length;
last_bonus = 1;
@@ -549,7 +549,7 @@
last_inst_count.SetAll(0);
last_sense_count.SetAll(0);
last_child_germline_propensity = m_world->GetConfig().DEMES_DEFAULT_GERMLINE_PROPENSITY.Get();
-
+
// Setup other miscellaneous values...
num_divides = 0;
generation = 0;
@@ -561,7 +561,7 @@
life_fitness = 0;
exec_time_born = 0;
birth_update = m_world->GetStats().GetUpdate();
-
+
num_thresh_gb_donations = 0;
num_thresh_gb_donations_last = 0;
num_quanta_thresh_gb_donations = 0;
@@ -626,7 +626,7 @@
total_energy_donated = 0.0;
total_energy_received = 0.0;
total_energy_applied = 0.0;
-
+
// Setup child info...
copy_true = false;
divide_sex = false;
@@ -635,9 +635,9 @@
child_fertile = true;
last_child_fertile = true;
child_copied_size = 0;
-
+
permanent_germline_propensity = m_world->GetConfig().DEMES_DEFAULT_GERMLINE_PROPENSITY.Get();
-
+
initialized = true;
}
@@ -645,12 +645,12 @@
/**
* This function is run whenever an organism executes a successful divide.
**/
-
- void cPhenotype::DivideReset(const cGenome & _genome)
+
+void cPhenotype::DivideReset(const cGenome & _genome)
{
assert(time_used >= 0);
assert(initialized == true);
-
+
// Update these values as needed...
int cur_merit_base = CalcSizeMerit();
@@ -673,12 +673,12 @@
gestation_time = time_used - gestation_start;
gestation_start = time_used;
fitness = CalcFitness( cur_merit_base, cur_bonus, gestation_time, cpu_cycles_used);
-
+
// Lock in cur values as last values.
last_merit_base = cur_merit_base;
last_bonus = cur_bonus;
last_cpu_cycles_used = cpu_cycles_used;
-//TODO? last_energy = cur_energy_bonus;
+ //TODO? last_energy = cur_energy_bonus;
last_num_errors = cur_num_errors;
last_num_donates = cur_num_donates;
last_task_count = cur_task_count;
@@ -694,7 +694,7 @@
last_inst_count = cur_inst_count;
last_sense_count = cur_sense_count;
last_child_germline_propensity = cur_child_germline_propensity;
-
+
// Reset cur values.
cur_bonus = m_world->GetConfig().DEFAULT_BONUS.Get();
cpu_cycles_used = 0;
@@ -717,7 +717,7 @@
cur_sense_count.SetAll(0);
cur_task_time.SetAll(0.0);
cur_child_germline_propensity = m_world->GetConfig().DEMES_DEFAULT_GERMLINE_PROPENSITY.Get();
-
+
// Setup other miscellaneous values...
num_divides++;
(void) generation;
@@ -728,7 +728,7 @@
life_fitness = fitness;
exec_time_born += gestation_time; //@MRR Treating organism as sibling
birth_update = m_world->GetStats().GetUpdate();
-
+
num_thresh_gb_donations_last = num_thresh_gb_donations;
num_thresh_gb_donations = 0;
num_quanta_thresh_gb_donations_last = num_quanta_thresh_gb_donations;
@@ -782,7 +782,7 @@
(void) parent_true;
(void) parent_sex;
(void) parent_cross_num;
-
+
// Reset child info...
(void) copy_true;
(void) divide_sex;
@@ -791,16 +791,16 @@
last_child_fertile = child_fertile;
child_fertile = true;
(void) child_copied_size;;
-
+
// A few final changes if the parent was supposed to be be considered
// a second child on the divide.
- if (m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) {
+ if ((m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) || (m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_BIRTH)) {
gestation_start = 0;
cpu_cycles_used = 0;
time_used = 0;
neutral_metric += m_world->GetRandom().GetRandNormal();
}
-
+
if (m_world->GetConfig().GENERATION_INC_METHOD.Get() == GENERATION_INC_BOTH) generation++;
// Reset Task States
@@ -820,7 +820,7 @@
{
assert(time_used > 0);
assert(initialized == true);
-
+
// Update these values as needed...
int cur_merit_base = CalcSizeMerit();
const int merit_default_bonus = m_world->GetConfig().MERIT_DEFAULT_BONUS.Get();
@@ -828,7 +828,7 @@
cur_bonus = merit_default_bonus;
}
merit = cur_merit_base * cur_bonus;
-
+
genome_length = _genome.GetSize();
(void) copied_size; // Unchanged
(void) executed_size; // Unchanged
@@ -836,7 +836,7 @@
gestation_start = time_used;
fitness = CalcFitness(cur_merit_base, cur_bonus, gestation_time, cpu_cycles_used);
(void) div_type; // Unchanged
-
+
// Lock in cur values as last values.
last_merit_base = cur_merit_base;
last_bonus = cur_bonus;
@@ -884,7 +884,7 @@
trial_time_used = 0;
trial_cpu_cycles_used = 0;
cur_child_germline_propensity = m_world->GetConfig().DEMES_DEFAULT_GERMLINE_PROPENSITY.Get();
-
+
// Setup other miscellaneous values...
num_divides++;
generation++;
@@ -895,7 +895,7 @@
life_fitness = fitness;
exec_time_born += gestation_time; //@MRR See DivideReset
birth_update = m_world->GetStats().GetUpdate();
-
+
num_thresh_gb_donations_last = num_thresh_gb_donations;
num_thresh_gb_donations = 0;
num_quanta_thresh_gb_donations_last = num_quanta_thresh_gb_donations;
@@ -949,7 +949,7 @@
(void) parent_true;
(void) parent_sex;
(void) parent_cross_num;
-
+
// Reset child info...
(void) copy_true;
(void) divide_sex;
@@ -979,12 +979,12 @@
energy_tobe_applied = 0.0;
energy_testament = 0.0;
energy_received_buffer = 0.0;
-
+
if(m_world->GetConfig().INHERIT_EXE_RATE.Get() == 0)
executionRatio = 1.0;
else
executionRatio = clone_phenotype.executionRatio;
-
+
genome_length = clone_phenotype.genome_length;
copied_size = clone_phenotype.copied_size;
// copied_size = clone_phenotype.child_copied_size;
@@ -993,12 +993,12 @@
gestation_start = 0;
fitness = clone_phenotype.fitness;
div_type = clone_phenotype.div_type;
-
+
assert(genome_length > 0);
assert(copied_size > 0);
assert(gestation_time >= 0); //@JEB 0 valid for some fitness methods
assert(div_type > 0);
-
+
// Initialize current values, as neeeded.
cur_bonus = m_world->GetConfig().DEFAULT_BONUS.Get();
cpu_cycles_used = 0;
@@ -1016,14 +1016,14 @@
cur_sense_count.SetAll(0);
cur_task_time.SetAll(0.0);
for (int j = 0; j < sensed_resources.GetSize(); j++)
- sensed_resources[j] = clone_phenotype.sensed_resources[j];
+ sensed_resources[j] = clone_phenotype.sensed_resources[j];
cur_trial_fitnesses.Resize(0);
cur_trial_bonuses.Resize(0);
cur_trial_times_used.Resize(0);
trial_time_used = 0;
trial_cpu_cycles_used = 0;
cur_child_germline_propensity = m_world->GetConfig().DEMES_DEFAULT_GERMLINE_PROPENSITY.Get();
-
+
// Copy last values from parent
last_merit_base = clone_phenotype.last_merit_base;
last_bonus = clone_phenotype.last_bonus;
@@ -1041,7 +1041,7 @@
last_sense_count = clone_phenotype.last_sense_count;
last_fitness = CalcFitness(last_merit_base, last_bonus, gestation_time, last_cpu_cycles_used);
last_child_germline_propensity = clone_phenotype.last_child_germline_propensity;
-
+
// Setup other miscellaneous values...
num_divides = 0;
generation = clone_phenotype.generation;
@@ -1054,7 +1054,7 @@
life_fitness = fitness;
exec_time_born = 0;
birth_update = m_world->GetStats().GetUpdate();
-
+
num_thresh_gb_donations_last = clone_phenotype.num_thresh_gb_donations_last;
num_thresh_gb_donations = clone_phenotype.num_thresh_gb_donations;
num_quanta_thresh_gb_donations_last = clone_phenotype.num_quanta_thresh_gb_donations_last;
@@ -1116,7 +1116,7 @@
is_energy_receiver = false;
has_used_donated_energy = false;
has_open_energy_request = false;
-
+
// Setup child info...
copy_true = false;
divide_sex = false;
@@ -1126,7 +1126,7 @@
child_fertile = true;
child_copied_size = 0;
permanent_germline_propensity = clone_phenotype.permanent_germline_propensity;
-
+
initialized = true;
}
@@ -1141,35 +1141,35 @@
}
bool cPhenotype::TestOutput(cAvidaContext& ctx, cTaskContext& taskctx,
- const tArray<double>& res_in, const tArray<double>& rbins_in, tArray<double>& res_change,
- tArray<int>& insts_triggered)
+ const tArray<double>& res_in, const tArray<double>& rbins_in, tArray<double>& res_change,
+ tArray<int>& insts_triggered)
{
assert(initialized == true);
taskctx.SetTaskStates(&m_task_states);
-
+
const cEnvironment& env = m_world->GetEnvironment();
const int num_resources = env.GetResourceLib().GetSize();
const int num_tasks = env.GetNumTasks();
const int num_reactions = env.GetReactionLib().GetSize();
-
+
// For refractory period @WRE 03-20-07
const int cur_update_time = m_world->GetStats().GetUpdate();
const double biomimetic_refractory_period = m_world->GetConfig().BIOMIMETIC_REFRACTORY_PERIOD.Get();
double refract_factor;
-
+
if (!m_reaction_result) m_reaction_result = new cReactionResult(num_resources, num_tasks, num_reactions);
cReactionResult& result = *m_reaction_result;
// Run everything through the environment.
bool found = env.TestOutput(ctx, result, taskctx, eff_task_count, cur_reaction_count, res_in, rbins_in); //NEED different eff_task_count and cur_reaction_count for deme resource
-
+
// If nothing was found, stop here.
if (found == false) {
result.Invalidate();
res_change.SetAll(0.0);
return false; // Nothing happened.
}
-
+
// Update the phenotype with the results...
// Start with updating task and reaction counters
for (int i = 0; i < num_tasks; i++) {
@@ -1189,7 +1189,7 @@
//cerr << "eff: " << eff_task_count[i] << endl;
if(result.UsedEnvResource() == false) { cur_internal_task_count[i]++; }
}
-
+
if (result.TaskQuality(i) > 0)
{
cur_task_quality[i] += result.TaskQuality(i) * refract_factor;
@@ -1214,14 +1214,14 @@
m_world->GetStats().AddOtherTaskCounts(i, prev_num_tasks, cur_num_tasks);
}
}
-
+
for (int i = 0; i < num_reactions; i++) {
-// if (result.ReactionTriggered(i) == true) cur_reaction_count[i]++; // moved into cEnvironment::TestOutput to allow reaction requisites to be satisified at the time a reaction is completed
+ // if (result.ReactionTriggered(i) == true) cur_reaction_count[i]++; // moved into cEnvironment::TestOutput to allow reaction requisites to be satisified at the time a reaction is completed
cur_reaction_add_reward[i] += result.GetReactionAddBonus(i);
- if (result.ReactionTriggered(i) && last_reaction_count[i]==0)
- m_world->GetStats().AddNewReactionCount(i);
+ if (result.ReactionTriggered(i) && last_reaction_count[i]==0)
+ m_world->GetStats().AddNewReactionCount(i);
}
-
+
// Update the merit bonus
cur_bonus *= result.GetMultBonus();
cur_bonus += result.GetAddBonus();
@@ -1234,7 +1234,7 @@
// no deme object. Don't touch deme merit if there is no deme frac component.
cDeme* deme = taskctx.GetOrganism()->GetDeme();
if (deme) {
-
+
if (result.GetActiveDeme()) {
double deme_bonus = deme->GetHeritableDemeMerit().GetDouble();
deme_bonus *= result.GetMultDemeBonus();
@@ -1250,7 +1250,7 @@
if (result.ReactionTriggered(i) == true) deme->AddCurReaction(i);
}
}
-
+
// Update the energy bonus
cur_energy_bonus += result.GetAddEnergy();
@@ -1258,7 +1258,7 @@
for (int i = 0; i < res_in.GetSize(); i++) {
res_change[i] = result.GetProduced(i) - result.GetConsumed(i);
}
-
+
// Update rbins as necessary
if(result.UsedEnvResource() == false)
{
@@ -1270,18 +1270,18 @@
if(rbin_diff > 0) { cur_rbins_total[i] += rbin_diff; }
}
}
-
+
// Save the instructions that should be triggered...
insts_triggered = result.GetInstArray();
-
+
//Put in detected resources
for (int j = 0; j < res_in.GetSize(); j++)
if(result.GetDetected(j) != -1.0)
- sensed_resources[j] = result.GetDetected(j);
-
+ sensed_resources[j] = result.GetDetected(j);
+
//Kill any cells that did lethal reactions
to_die = result.GetLethal();
-
+
// Sterilize organisms that have performed a sterilizing task.
if(result.GetSterilize()) {
is_fertile = false;
@@ -1291,13 +1291,17 @@
return true;
}
+void cPhenotype::Sterilize()
+{
+ is_fertile = false;
+}
void cPhenotype::PrintStatus(ostream& fp) const
{
fp << " MeritBase:"
- << CalcSizeMerit()
- << " Bonus:" << cur_bonus
- << " Errors:" << cur_num_errors
- << " Donates:" << cur_num_donates;
+ << CalcSizeMerit()
+ << " Bonus:" << cur_bonus
+ << " Errors:" << cur_num_errors
+ << " Donates:" << cur_num_donates;
fp << endl;
fp << " Task Count (Quality):";
@@ -1326,48 +1330,48 @@
{
assert(genome_length > 0);
assert(copied_size > 0);
-
+
int out_size;
-
+
switch (m_world->GetConfig().BASE_MERIT_METHOD.Get()) {
- case BASE_MERIT_COPIED_SIZE:
- out_size = copied_size;
- break;
- case BASE_MERIT_EXE_SIZE:
- out_size = executed_size;
- break;
- case BASE_MERIT_FULL_SIZE:
- out_size = genome_length;
- break;
- case BASE_MERIT_LEAST_SIZE:
- out_size = genome_length;
- if (out_size > copied_size) out_size = copied_size;
- if (out_size > executed_size) out_size = executed_size;
- break;
- case BASE_MERIT_SQRT_LEAST_SIZE:
- out_size = genome_length;
- if (out_size > copied_size) out_size = copied_size;
- if (out_size > executed_size) out_size = executed_size;
- out_size = (int) sqrt((double) out_size);
- break;
- case BASE_MERIT_NUM_BONUS_INST:
- if(m_world->GetConfig().FITNESS_VALLEY.Get()){
- if (bonus_instruction_count >= m_world->GetConfig().FITNESS_VALLEY_START.Get() &&
- bonus_instruction_count <= m_world->GetConfig().FITNESS_VALLEY_STOP.Get()){
- out_size = 1;
- break;
- }
- }
- if (m_world->GetConfig().MERIT_BONUS_EFFECT.Get()>0) {out_size = 1 + bonus_instruction_count;}
- else if (m_world->GetConfig().MERIT_BONUS_EFFECT.Get()<0) {out_size = genome_length - (bonus_instruction_count -1);}
- else {out_size = 1;} //the extra 1 point in all these case is so the orgs are not jilted by the scheduler
- break;
- case BASE_MERIT_CONST:
- default:
- out_size = m_world->GetConfig().BASE_CONST_MERIT.Get();
- break;
+ case BASE_MERIT_COPIED_SIZE:
+ out_size = copied_size;
+ break;
+ case BASE_MERIT_EXE_SIZE:
+ out_size = executed_size;
+ break;
+ case BASE_MERIT_FULL_SIZE:
+ out_size = genome_length;
+ break;
+ case BASE_MERIT_LEAST_SIZE:
+ out_size = genome_length;
+ if (out_size > copied_size) out_size = copied_size;
+ if (out_size > executed_size) out_size = executed_size;
+ break;
+ case BASE_MERIT_SQRT_LEAST_SIZE:
+ out_size = genome_length;
+ if (out_size > copied_size) out_size = copied_size;
+ if (out_size > executed_size) out_size = executed_size;
+ out_size = (int) sqrt((double) out_size);
+ break;
+ case BASE_MERIT_NUM_BONUS_INST:
+ if(m_world->GetConfig().FITNESS_VALLEY.Get()){
+ if (bonus_instruction_count >= m_world->GetConfig().FITNESS_VALLEY_START.Get() &&
+ bonus_instruction_count <= m_world->GetConfig().FITNESS_VALLEY_STOP.Get()){
+ out_size = 1;
+ break;
+ }
+ }
+ if (m_world->GetConfig().MERIT_BONUS_EFFECT.Get()>0) {out_size = 1 + bonus_instruction_count;}
+ else if (m_world->GetConfig().MERIT_BONUS_EFFECT.Get()<0) {out_size = genome_length - (bonus_instruction_count -1);}
+ else {out_size = 1;} //the extra 1 point in all these case is so the orgs are not jilted by the scheduler
+ break;
+ case BASE_MERIT_CONST:
+ default:
+ out_size = m_world->GetConfig().BASE_CONST_MERIT.Get();
+ break;
}
-
+
return out_size;
}
@@ -1388,10 +1392,10 @@
switch (m_world->GetConfig().FITNESS_METHOD.Get())
{
case 0: // Normal
- assert(_gestation_time > 0);
- out_fitness = _merit_base * _bonus / _gestation_time;
- break;
-
+ assert(_gestation_time > 0);
+ out_fitness = _merit_base * _bonus / _gestation_time;
+ break;
+
case 1: // Sigmoidal returns (should be used with an additive reward)
{
assert(_gestation_time > 0);
@@ -1400,19 +1404,19 @@
double converted_bonus = (_bonus - m_world->GetConfig().DEFAULT_BONUS.Get()) * m_world->GetConfig().FITNESS_COEFF_2.Get() / (1 + _bonus * m_world->GetConfig().FITNESS_COEFF_2.Get() ) ;
out_fitness = _merit_base * exp(converted_bonus * log(m_world->GetConfig().FITNESS_COEFF_1.Get())) / _gestation_time;
}
- break;
-
+ break;
+
case 2: //Activity of one enzyme in pathway altered (with diminishing returns and a cost for each executed instruction)
{
out_fitness = 0;
double net_bonus = _bonus + - m_world->GetConfig().DEFAULT_BONUS.Get();
out_fitness = net_bonus / (net_bonus + 1)* exp (_gestation_time * log(1 - m_world->GetConfig().FITNESS_COEFF_1.Get()));
}
- break;
-
+ break;
+
default:
- cout << "Unknown FITNESS_METHOD!" << endl;
- exit(1);
+ cout << "Unknown FITNESS_METHOD!" << endl;
+ exit(1);
}
return out_fitness;
@@ -1440,7 +1444,7 @@
/**
-Credit organism with energy reward, but only update energy store if APPLY_ENERGY_METHOD = "on task completion" (1)
+ Credit organism with energy reward, but only update energy store if APPLY_ENERGY_METHOD = "on task completion" (1)
*/
void cPhenotype::RefreshEnergy() {
if(cur_energy_bonus > 0) {
@@ -1476,7 +1480,7 @@
void cPhenotype::ApplyDonatedEnergy() {
double energy_cap = m_world->GetConfig().ENERGY_CAP.Get();
-
+
if((energy_store + energy_received_buffer) >= energy_cap) {
IncreaseEnergyApplied(energy_cap - energy_store);
SetEnergy(energy_store + (energy_cap - energy_received_buffer));
@@ -1524,7 +1528,7 @@
assert(GetStoredEnergy()>0.0);
// adjust energy in parent
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(ConvertEnergyToMerit(GetStoredEnergy() * GetEnergyUsageRatio()));
if(parentMerit.GetDouble() > 0.0)
@@ -1547,7 +1551,7 @@
cur_trial_fitnesses.Push(fitness);
cur_trial_bonuses.Push(GetCurBonus());
cur_trial_times_used.Push(trial_time_used);
-
+
//The rest of the function, resets the phenotype like DivideReset(), but without
//incrementing the generation or child statistics.
@@ -1571,21 +1575,21 @@
energy_store += cur_energy_bonus;
energy_store = m_world->GetConfig().ENERGY_GIVEN_AT_BIRTH.Get(); // We reset to what they had at birth
cur_energy_bonus = 0;
- // to be perfectly accurate, this should be from a last_energy value??
-
+ // to be perfectly accurate, this should be from a last_energy value??
- // genome_length = _genome.GetSize(); //No child! @JEB
+
+ // genome_length = _genome.GetSize(); //No child! @JEB
(void) copied_size; // Unchanged
(void) executed_size; // Unchanged
gestation_time = time_used - gestation_start; //Keep gestation referring to actual replication time! @JEB
gestation_start = time_used; //Keep gestation referring to actual replication time! @JEB
- // fitness = merit.GetDouble() / gestation_time; //Use fitness measure that is per-trial @JEB
-
+ // fitness = merit.GetDouble() / gestation_time; //Use fitness measure that is per-trial @JEB
+
// Lock in cur values as last values.
last_merit_base = cur_merit_base;
last_bonus = cur_bonus;
last_cpu_cycles_used = cpu_cycles_used;
-//TODO? last_energy = cur_energy_bonus;
+ //TODO? last_energy = cur_energy_bonus;
last_num_errors = cur_num_errors;
last_num_donates = cur_num_donates;
last_task_count = cur_task_count;
@@ -1600,7 +1604,7 @@
last_reaction_add_reward = cur_reaction_add_reward;
last_inst_count = cur_inst_count;
last_sense_count = cur_sense_count;
-
+
// Reset cur values.
cur_bonus = m_world->GetConfig().DEFAULT_BONUS.Get();
cpu_cycles_used = 0;
@@ -1623,7 +1627,7 @@
//cur_trial_fitnesses.Resize(0); Don't throw out the trial fitnesses! @JEB
trial_time_used = 0;
trial_cpu_cycles_used = 0;
-
+
// Setup other miscellaneous values...
num_divides++;
(void) generation;
@@ -1633,7 +1637,7 @@
(void) neutral_metric;
life_fitness = fitness;
-
+
num_thresh_gb_donations_last = num_thresh_gb_donations;
num_thresh_gb_donations = 0;
num_quanta_thresh_gb_donations_last = num_quanta_thresh_gb_donations;
@@ -1696,11 +1700,11 @@
* This function is run to reset an organism whose task counts (etc) have already been moved from cur to last
* by another call (like NewTrial). It is a subset of DivideReset @JEB
**/
-
+
void cPhenotype::TrialDivideReset(const cGenome & _genome)
{
int cur_merit_base = CalcSizeMerit();
-
+
// If we are resetting the current merit, do it here
// and it will also be propagated to the child
const int merit_default_bonus = m_world->GetConfig().MERIT_DEFAULT_BONUS.Get();
@@ -1708,17 +1712,17 @@
cur_bonus = merit_default_bonus;
}
merit = cur_merit_base * cur_bonus;
-
+
SetEnergy(energy_store + cur_energy_bonus);
m_world->GetStats().SumEnergyTestamentAcceptedByOrganisms().Add(energy_testament);
energy_testament = 0.0;
-
+
genome_length = _genome.GetSize();
gestation_start = time_used;
cur_trial_fitnesses.Resize(0);
cur_trial_bonuses.Resize(0);
cur_trial_times_used.Resize(0);
-
+
// Reset child info...
(void) copy_true;
(void) divide_sex;
@@ -1727,16 +1731,16 @@
last_child_fertile = child_fertile;
child_fertile = true;
(void) child_copied_size;
-
+
// A few final changes if the parent was supposed to be be considered
// a second child on the divide.
- if (m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) {
+ if ((m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_SPLIT) || (m_world->GetConfig().DIVIDE_METHOD.Get() == DIVIDE_METHOD_BIRTH)) {
gestation_start = 0;
cpu_cycles_used = 0;
time_used = 0;
neutral_metric += m_world->GetRandom().GetRandNormal();
}
-
+
if (m_world->GetConfig().GENERATION_INC_METHOD.Get() == GENERATION_INC_BOTH) generation++;
}
Modified: branches/biounit/source/main/cPhenotype.h
===================================================================
--- branches/biounit/source/main/cPhenotype.h 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/main/cPhenotype.h 2009-12-16 16:01:42 UTC (rev 3559)
@@ -276,6 +276,7 @@
bool OK();
+ void Sterilize();
// Run when being setup *as* and offspring.
void SetupOffspring(const cPhenotype & parent_phenotype, const cGenome & _genome);
Modified: branches/biounit/source/main/cPopulation.cc
===================================================================
--- branches/biounit/source/main/cPopulation.cc 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/main/cPopulation.cc 2009-12-16 16:01:42 UTC (rev 3559)
@@ -122,7 +122,7 @@
case nGeometry::PARTIAL: { cout << "Geometry: Partial" << endl; break; }
case nGeometry::RANDOM_CONNECTED: { cout << "Geometry: Random connected" << endl; break; }
case nGeometry::SCALE_FREE: { cout << "Geometry: Scale-free" << endl; break; }
-
+
default:
cout << "Unknown geometry!" << endl;
assert(false);
@@ -221,10 +221,10 @@
break;
case nGeometry::SCALE_FREE:
build_scale_free(&cell_array.begin()[i], &cell_array.begin()[i+deme_size],
- world->GetConfig().SCALE_FREE_M.Get(),
- world->GetConfig().SCALE_FREE_ALPHA.Get(),
- world->GetConfig().SCALE_FREE_ZERO_APPEAL.Get(),
- m_world->GetRandom());
+ world->GetConfig().SCALE_FREE_M.Get(),
+ world->GetConfig().SCALE_FREE_ALPHA.Get(),
+ world->GetConfig().SCALE_FREE_ZERO_APPEAL.Get(),
+ m_world->GetRandom());
break;
default:
assert(false);
@@ -537,21 +537,103 @@
assert(parent_id >= 0 && parent_id < cell_array.GetSize());
cPopulationCell& parent_cell = cell_array[ parent_id ];
- int num_neighbors = parent.GetNeighborhoodSize();
- cOrganism* target_organism =
- parent_cell.ConnectionList().GetPos(m_world->GetRandom().GetUInt(num_neighbors))->GetOrganism();
+ cOrganism* target_organism = NULL;
+ if (m_world->GetConfig().BIRTH_METHOD.Get() == POSITION_OFFSPRING_FULL_SOUP_RANDOM)
+ {
+ target_organism = GetCell(m_world->GetRandom().GetUInt(cell_array.GetSize())).GetOrganism();
+ }
+ else
+ {
+ target_organism =
+ parent_cell.ConnectionList().GetPos(m_world->GetRandom().GetUInt(parent.GetNeighborhoodSize()))->GetOrganism();
+ }
+
if (target_organism == NULL) return false;
cHardwareBase& child_cpu = target_organism->GetHardware();
if (child_cpu.GetNumThreads() == m_world->GetConfig().MAX_CPU_THREADS.Get()) return false;
+ tArray<int> task_counts = target_organism->GetPhenotype().GetCurTaskCount();
+ int random_int = m_world->GetRandom().GetUInt(100);
+
+ if (m_world->GetConfig().INJECT_PROB_FROM_TASKS.Get())
+ {
+
+ int last_task_count = target_organism->GetPhenotype().GetLastTaskCount()[0];
+ int total_count;
+ int task_count = last_task_count;
+
+ if (task_count < task_counts[0])
+ {
+ task_count = task_counts[0];
+ }
+
+ total_count = task_count;
+
+ if (total_count > 0)
+ {
+ if (m_world->GetConfig().INJECT_PROB_SIGMOID.Get())
+ {
+ switch (total_count) {
+ case 1:
+ if(random_int > 10)
+ return false;
+ break;
+ case 2:
+ if(random_int > 30)
+ return false;
+ break;
+ case 3:
+ if(random_int > 50)
+ return false;
+ break;
+ case 4:
+ if(random_int > 70)
+ return false;
+ break;
+ case 5:
+ if (random_int > 75)
+ return false;
+ break;
+ case 6:
+ if (random_int > 80)
+ return false;
+ break;
+ case 7:
+ if(random_int > 85)
+ return false;
+ break;
+ case 8:
+ if(random_int > 90)
+ return false;
+ break;
+ case 9:
+ if(random_int > 95)
+ return false;
+ break;
+ case 10:
+ break;
+ }
+ }
+ else
+ {
+ if (random_int > (total_count * 10))
+ return false;
+ }
+ }
+
+ else
+ return false;
+
+ }
+
if (target_organism->InjectHost(label, injected_code)) {
cInjectGenotype* child_genotype = parent_genotype;
- // If the parent genotype is not correct for the child, adjust it.
+ // If the parent genotype is not correct for the child, adjust it.
if (parent_genotype == NULL || parent_genotype->GetGenome() != injected_code) {
child_genotype = m_world->GetClassificationManager().GetInjectGenotype(injected_code, parent_genotype);
}
@@ -560,6 +642,10 @@
child_genotype->AddParasite();
child_cpu.ThreadSetOwner(child_genotype);
m_world->GetClassificationManager().AdjustInjectGenotype(*child_genotype);
+
+ if(m_world->GetConfig().INJECT_STERILIZES_HOST.Get())
+ target_organism->GetPhenotype().Sterilize();
+
}
else
return false;
@@ -1338,7 +1424,7 @@
// better have more than deme tournament size, otherwise something is *really* screwed up:
if(m_world->GetConfig().DEMES_TOURNAMENT_SIZE.Get() > static_cast<int>(deme_ids.size())) {
- m_world->GetDriver().RaiseFatalException(-1, "The number of demes that can participate in a tournament is less than the deme tournament size.");
+ m_world->GetDriver().RaiseFatalException(-1, "The number of demes that can participate in a tournament is less than the deme tournament size.");
}
// Run the tournaments.
@@ -4830,7 +4916,7 @@
/* depth */ cur_line.PopWord();
cString name = cStringUtil::Stringf("org-%d", tmp.id_num);
cGenome genome(cur_line.PopWord());
-
+
// Process resident cell ids
cString cellstr(cur_line.PopWord());
while (cellstr.GetSize()) tmp.cells.Push(cellstr.Pop(',').AsInt());
Modified: branches/biounit/source/main/cPopulationInterface.cc
===================================================================
--- branches/biounit/source/main/cPopulationInterface.cc 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/main/cPopulationInterface.cc 2009-12-16 16:01:42 UTC (rev 3559)
@@ -651,6 +651,10 @@
HGTTrimmedFragmentSelection(ctx, offspring, cell.GetFragments(), selected, location);
break;
}
+ case 2: { // random selection and random placement
+ HGTRandomFragmentPlacement(ctx, offspring, cell.GetFragments(), selected, location);
+ break;
+ }
default: { // error
m_world->GetDriver().RaiseFatalException(1, "HGT_FRAGMENT_SELECTION is set to an invalid value.");
break;
@@ -682,7 +686,7 @@
substring_match& location) {
// randomly select the genome fragment for HGT:
selected=fragments.begin();
- std::advance(selected, ctx.GetRandom().GetInt(fragments.size()));
+ std::advance(selected, ctx.GetRandom().GetUInt(fragments.size()));
// find the location within the offspring's genome that best matches the selected fragment:
location = cGenomeUtil::FindUnbiasedCircularMatch(ctx, offspring, *selected);
@@ -703,7 +707,7 @@
substring_match& location) {
// randomly select the genome fragment for HGT:
selected=fragments.begin();
- std::advance(selected, ctx.GetRandom().GetInt(fragments.size()));
+ std::advance(selected, ctx.GetRandom().GetUInt(fragments.size()));
// copy the selected fragment, trimming redundant instructions at the end:
cGenome trimmed(*selected);
@@ -714,3 +718,26 @@
// find the location within the offspring's genome that best matches the selected fragment:
location = cGenomeUtil::FindUnbiasedCircularMatch(ctx, offspring, trimmed);
}
+
+
+/*! Random selection of the fragment used for HGT mutation, located at a random position.
+
+ Here we select a random fragment and a random location for that fragment within the offspring.
+ The beginning of the fragment location is selected at random, while the end is selected a
+ random distance (up to the length of the selected fragment * 2) instructions away.
+ */
+void cPopulationInterface::HGTRandomFragmentPlacement(cAvidaContext& ctx, const cGenome& offspring,
+ fragment_list_type& fragments, fragment_list_type::iterator& selected,
+ substring_match& location) {
+ // randomly select the genome fragment for HGT:
+ selected=fragments.begin();
+ std::advance(selected, ctx.GetRandom().GetUInt(fragments.size()));
+
+ // select a random location within the offspring's genome for this fragment to be
+ // inserted:
+ location.begin = ctx.GetRandom().GetUInt(offspring.GetSize());
+ location.end = location.begin + ctx.GetRandom().GetUInt(selected->GetSize()*2);
+ location.size = offspring.GetSize();
+ location.resize(offspring.GetSize());
+}
+
Modified: branches/biounit/source/main/cPopulationInterface.h
===================================================================
--- branches/biounit/source/main/cPopulationInterface.h 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/main/cPopulationInterface.h 2009-12-16 16:01:42 UTC (rev 3559)
@@ -148,8 +148,9 @@
typedef cGenomeUtil::substring_match substring_match;
//! Perform an HGT mutation on this offspring.
void DoHGTMutation(cAvidaContext& ctx, cGenome& offspring);
+
protected:
- //! Random selection of the fragment used for HGT mutation.
+ //! Random selection of the fragment used for HGT mutation, located at the best match.
void HGTRandomFragmentSelection(cAvidaContext& ctx, const cGenome& offspring,
fragment_list_type& fragments, fragment_list_type::iterator& selected,
substring_match& location);
@@ -157,6 +158,10 @@
void HGTTrimmedFragmentSelection(cAvidaContext& ctx, const cGenome& offspring,
fragment_list_type& fragments, fragment_list_type::iterator& selected,
substring_match& location);
+ //! Random selection of the fragment used for HGT mutation, located at a random position.
+ void HGTRandomFragmentPlacement(cAvidaContext& ctx, const cGenome& offspring,
+ fragment_list_type& fragments, fragment_list_type::iterator& selected,
+ substring_match& location);
};
Modified: branches/biounit/source/targets/avida-viewer/cSymbolUtil.cc
===================================================================
--- branches/biounit/source/targets/avida-viewer/cSymbolUtil.cc 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/source/targets/avida-viewer/cSymbolUtil.cc 2009-12-16 16:01:42 UTC (rev 3559)
@@ -29,7 +29,7 @@
{
if (cell.IsOccupied() == false) return ' ';
const cOrganism & organism = *(cell.GetOrganism());
-
+
cSpecies * cur_species = organism.GetGenotype()->GetSpecies();
if (cur_species == NULL) return '.'; // no species
return cur_species->GetSymbol(); // symbol!
@@ -39,13 +39,13 @@
{
if (cell.IsOccupied() == false) return ' ';
const cOrganism & organism = *(cell.GetOrganism());
-
+
const bool modifier = organism.GetPhenotype().IsModifier();
const bool modified = organism.GetPhenotype().IsModified();
-
+
// 'I' = Injector 'H' = Host (Injected into)
// 'B' = Both '-' = Neither
-
+
if (modifier == true && modified == true) return 'B';
if (modifier == true) return 'I'-6;
if (modified == true) return 'H'-6;
@@ -63,14 +63,14 @@
{
if (cell.IsOccupied() == false) return ' ';
const cOrganism & organism = *(cell.GetOrganism());
-
+
const int age = organism.GetPhenotype().GetAge();
if (age < 0) return '-';
if (age < 10) return (char) ('0' + age);
if (age < 20) return 'X';
if (age < 80) return 'L';
if (age < 200) return 'C';
-
+
return '+';
}
@@ -78,7 +78,7 @@
{
if (cell.IsOccupied() == false) return ' ';
const cOrganism & organism = *(cell.GetOrganism());
-
+
if (organism.GetPhenotype().ParentTrue() == true) return '*';
return '-';
}
@@ -87,8 +87,8 @@
{
if (cell.IsOccupied() == false) return ' ';
const cOrganism & organism = *(cell.GetOrganism());
-
- if (organism.GetNumParasites()) return '*';
+
+ if (organism.GetNumParasites()) return 'A';
return '-';
}
@@ -96,7 +96,7 @@
{
if (cell.IsOccupied() == false) return ' ';
const cOrganism & organism = *(cell.GetOrganism());
-
+
if (organism.GetPhenotype().IsMutated() == true) return '*';
return '-';
}
@@ -111,7 +111,7 @@
{
if (cell.IsOccupied() == false) return ' ';
const cOrganism & organism = *(cell.GetOrganism());
-
+
return 'A' + (organism.GetLineageLabel() % 12);
}
Copied: branches/biounit/support/config/misc/Parasites (from rev 3558, branches/parasites/support/config/misc/Parasites)
Property changes on: branches/biounit/support/config/misc/Parasites
___________________________________________________________________
Name: svn:ignore
+ avida.cfg
default-smt.org
dominant-org.org
environment.cfg
events.cfg
instset-smt.cfg
parasite-smt.org
Deleted: branches/biounit/support/config/misc/Parasites/avida.cfg
===================================================================
--- branches/parasites/support/config/misc/Parasites/avida.cfg 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/support/config/misc/Parasites/avida.cfg 2009-12-16 16:01:42 UTC (rev 3559)
@@ -1,543 +0,0 @@
-#############################################################################
-# This file includes all the basic run-time defines for Avida.
-# For more information, see doc/config.html
-#############################################################################
-
-VERSION_ID 2.9.0 # Do not change this value.
-
-INJECT_PROB_FROM_TASKS 1
-INJECT_PROB_SIGMOID 1
-### GENERAL_GROUP ###
-# General Settings
-ANALYZE_MODE 0 # 0 = Disabled
- # 1 = Enabled
- # 2 = Interactive
-VIEW_MODE 1 # Initial viewer screen
-PAUSE_VIEWER_ON_START 0 #Pause the viewer on load
-MERIT_INC_APPLY_IMMEDIATE 1
-CLONE_FILE - # Clone file to load
-VERBOSITY 1 # 0 = No output at all
- # 1 = Normal output
- # 2 = Verbose output, detailing progress
- # 3 = High level of details, as available
- # 4 = Print Debug Information, as applicable
-
-### ARCH_GROUP ###
-# Architecture Variables
-WORLD_X 60 # Width of the Avida world
-WORLD_Y 60 # Height of the Avida world
-WORLD_Z 1 # Depth of the Avida world
-WORLD_GEOMETRY 3 # 1 = Bounded Grid
- # 2 = Torus
- # 3 = Clique
- # 4 = Hexagonal grid
- # 5 = Lattice
-RANDOM_SEED 0 # Random number seed (0 for based on time)
-HARDWARE_TYPE 2 # 0 = Original CPUs
- # 1 = New SMT CPUs
- # 2 = Transitional SMT
- # 3 = Experimental CPU
- # 4 = Gene Expression CPU
-SPECULATIVE 1 # Enable speculative execution
-TRACE_EXECUTION 0 # Trace the execution of all organisms in the population (default=off,SLOW!)
-BCAST_HOPS 1 # Number of hops to broadcast an alarm
-ALARM_SELF 0 # Does sending an alarm move sender IP to alarm label?
- # 0=no
- # 1=yes
-IO_EXPIRE 1 # Is the expiration functionality of '-expire' I/O instructions enabled?
-INSTRUCTION_CONSTANT 3 # The Constant to add when the add-const instruction is called
-
-### CONFIG_FILE_GROUP ###
-# Configuration Files
-DATA_DIR data # Directory in which config files are found
-INST_SET instset-smt.cfg # File containing instruction set
-INST_SET_FORMAT 0 # Instruction set file format.
- # 0 = Default
- # 1 = New Style
-EVENT_FILE events.cfg # File containing list of events during run
-ANALYZE_FILE analyze.cfg # File used for analysis mode
-ENVIRONMENT_FILE environment.cfg # File that describes the environment
-START_CREATURE dominant-org.org # Organism to seed the soup
-
-### DEME_GROUP ###
-# Demes and Germlines
-NUM_DEMES 1 # Number of independent groups in the
- # population (default=1).
-DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline (default=0).
-DEMES_PREVENT_STERILE 0 # Whether to prevent sterile demes from
- # replicating (default=0 or no).
-DEMES_RESET_RESOURCES 0 # Reset resources in demes on replication.
- # 0 = reset both demes
- # 1 = reset target deme
- # 2 = deme resources remain unchanged
-DEMES_REPLICATE_SIZE 1 # Number of identical organisms to create or copy from the
- # source deme to the target deme (default=1).
-LOG_DEMES_REPLICATE 0 # Log deme replications. 0/1 (off/on)
-DEMES_REPLICATE_LOG_START 0 # Update at which to start logging deme replications
-DEMES_PROB_ORG_TRANSFER 0.0 # Probablity of an organism being transferred from the
- # source deme to the target deme (default=0.0).
-DEMES_ORGANISM_SELECTION 0 # How organisms are selected for transfer from
- # source to target during deme replication.
- # 0=random with replacement (default).
- # 1=sequential.
-DEMES_ORGANISM_PLACEMENT 0 # How organisms are placed during deme replication.
- # 0=cell-array middle (default).
- # 1=deme center.
- # 2=random placement.
- # 3=sequential.
-DEMES_ORGANISM_FACING 0 # How organisms are facing during deme replication.
- # 0=unchanged (default).
- # 1=northwest.
- # 2=random.
-DEMES_MAX_AGE 500 # The maximum age of a deme (in updates) to be
- # used for age-based replication (default=500).
-DEMES_MAX_BIRTHS 100 # The maximum number of births that can occur
- # within a deme; used with birth-count
- # replication (default=100).
-DEMES_MIM_EVENTS_KILLED_RATIO 0.7 # Minimum ratio of events killed required for event period to be a success.
-DEMES_MIM_SUCCESSFUL_EVENT_PERIODS 1 # Minimum number of consecutive event periods that must be a success.
-GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
- # germline replication (default=0.0075).
-GERMLINE_INS_MUT 0.05 # Prob. of an insertion mutation occuring
- # during germline replication (default=0.05).
-GERMLINE_DEL_MUT 0.05 # Prob. of a deletion mutation occuring
- # during germline replication (default=0.05).
-DEMES_REPLICATE_CPU_CYCLES 0.0 # Replicate a deme immediately after it has used
- # this number of cpu cycles, normalized
- # by number of orgs in deme (0 = OFF).
-DEMES_REPLICATE_TIME 0.0 # Replicate a deme immediately after it has used
- # this number of cpu cycles, normalized
- # by number of orgs in deme and organism merit (0 = OFF).
-DEMES_REPLICATE_BIRTHS 0 # Replicate a deme immediately after it has
- # produced this many offspring (0 = OFF).
-DEMES_REPLICATE_ORGS 0 # Replicate a deme immediately once it reaches a
- # certain number of organisms (0 = OFF).
-DEMES_REPLICATION_ONLY_RESETS 0 # Kin selection mode. Deme replication really:
- # 1=resets deme resources
- # 2=rests deme resources and re-injects organisms
-DEMES_MIGRATION_RATE 0.0 # Probability of an offspring being born in a different deme.
-DEMES_MIGRATION_METHOD 0 # How do we choose what demes an org may land in when it migrates?
- # 0=all other demes
- # 1=eight adjacent neighbors
- # 2=two adjacent demes in list
- # 3=proportional based on the number of points
-DEMES_NUM_X 0 # Simulated number of demes in X dimension. Only used for migration.
-DEMES_SEED_METHOD 0 # Deme seeding method.
- # 0=maintain old consistency
- # 1=new method using genotypes
-DEMES_DIVIDE_METHOD 0 # Deme divide method. Only works with DEMES_SEED_METHOD 1
- # 0=replace and target demes
- # 1= replace target deme, reset source deme to founders
- # 2=replace target deme, leave source deme unchanged
-DEMES_DEFAULT_GERMLINE_PROPENSITY 0.0 # Default germline propensity of organisms in deme.
- # For use with DEMES_DIVIDE_METHOD 2.
-DEMES_FOUNDER_GERMLINE_PROPENSITY -1.0 # Default germline propensity of founder organisms in deme.
- # For use with DEMES_DIVIDE_METHOD 2.
- # <0 = OFF
-DEMES_PREFER_EMPTY 0 # Give empty demes preference as targets of deme replication?
-DEMES_PROTECTION_POINTS 0 # The number of points a deme receives for each suicide.
-POINT_DECAY_PERCENT 0 # The percentage of points decayed each time cActionDecayPoints is called.
-
-### REPRODUCTION_GROUP ###
-# Birth and Death
-BIRTH_METHOD 0 # Which organism should be replaced on birth?
- # 0 = Random organism in neighborhood
- # 1 = Oldest in neighborhood
- # 2 = Largest Age/Merit in neighborhood
- # 3 = None (use only empty cells in neighborhood)
- # 4 = Random from population (Mass Action)
- # 5 = Oldest in entire population
- # 6 = Random within deme
- # 7 = Organism faced by parent
- # 8 = Next grid cell (id+1)
- # 9 = Largest energy used in entire population
- # 10 = Largest energy used in neighborhood
-PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
-ALLOW_PARENT 1 # Allow births to replace the parent organism?
-DEATH_METHOD 2 # 0 = Never die of old age.
- # 1 = Die when inst executed = AGE_LIMIT (+deviation)
- # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
-AGE_LIMIT 20 # Modifies DEATH_METHOD
-AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
-ALLOC_METHOD 0 # (Orignal CPU Only)
- # 0 = Allocated space is set to default instruction.
- # 1 = Set to section of dead genome (Necrophilia)
- # 2 = Allocated space is set to random instruction.
-DIVIDE_METHOD 2 # 0 = Divide leaves state of mother untouched.
- # 1 = Divide resets state of mother
- # (after the divide, we have 2 children)
- # 2 = Divide resets state of current thread only
- # (does not touch possible parasite threads)
- # 3 = Divide resets mother stats, but not state.
- # 4 = 3 + child inherits mother registers and stack values.
-EPIGENETIC_METHOD 0 # Inheritance of state information other than genome
- # 0 = none
- # 1 = offspring inherits registers and stacks of first thread
- # 1 = parent maintains registers and stacks of first thread
- #
- # 1 = offspring and parent keep state information
-INJECT_METHOD 1 # 0 = Leaves the parasite thread state untouched.
- # 1 = Resets the calling thread state on inject
-GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
- # increased on divide.
- # 1 = Both the generation of the mother and child are
- # increased on divide (good with DIVIDE_METHOD 1).
-RESET_INPUTS_ON_DIVIDE 0 # Reset environment inputs of parent upon successful divide.
-REPRO_METHOD 1 # Replace existing organism: 1=yes
-
-### RECOMBINATION_GROUP ###
-# Sexual Recombination and Modularity
-RECOMBINATION_PROB 1.0 # probability of recombination in div-sex
-MAX_BIRTH_WAIT_TIME -1 # Updates incipiant orgs can wait for crossover
-MODULE_NUM 0 # number of modules in the genome
-CONT_REC_REGS 1 # are (modular) recombination regions continuous
-CORESPOND_REC_REGS 1 # are (modular) recombination regions swapped randomly
- # or with corresponding positions?
-TWO_FOLD_COST_SEX 0 # 1 = only one recombined offspring is born.
- # 2 = both offspring are born
-SAME_LENGTH_SEX 0 # 0 = recombine with any genome
- # 1 = only recombine w/ same length
-
-### DIVIDE_GROUP ###
-# Divide Restrictions
-CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
- # (Checked BEFORE mutations applied on divide.)
-MIN_COPIED_LINES 0.5 # Code fraction which must be copied before divide.
-MIN_EXE_LINES 0.5 # Code fraction which must be executed before divide.
-MIN_GENOME_SIZE 30 # Minimum number of instructions allowed in a genome. 0 = OFF
-MAX_GENOME_SIZE 0 # Maximum number of instructions allowed in a genome. 0 = OFF
-REQUIRE_ALLOCATE 1 # (Original CPU Only) Require allocate before divide?
-REQUIRED_TASK -1 # Task ID required for successful divide.
-IMMUNITY_TASK -1 # Task providing immunity from the required task.
-REQUIRED_REACTION -1 # Reaction ID required for successful divide.
-REQUIRED_BONUS 0.0 # Required bonus to divide.
-REQUIRE_EXACT_COPY 0 # Require offspring to be an exact copy (only divide mutations allowed).
-IMPLICIT_REPRO_BONUS 0 # Call Inst_Repro to divide upon achieving this bonus. 0 = OFF
-IMPLICIT_REPRO_CPU_CYCLES 0 # Call Inst_Repro after this many cpu cycles. 0 = OFF
-IMPLICIT_REPRO_TIME 0 # Call Inst_Repro after this time used. 0 = OFF
-IMPLICIT_REPRO_END 0 # Call Inst_Repro after executing the last instruction in the genome.
-IMPLICIT_REPRO_ENERGY 0.0 # Call Inst_Repro if organism accumulates this amount of energy.
-
-### MUTATION_GROUP ###
-# Mutations
-POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
-COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
-COPY_INS_PROB 0.0 # Insertion rate (per copy)
-COPY_DEL_PROB 0.0 # Deletion rate (per copy)
-COPY_UNIFORM_PROB 0.0 # Uniform mutation probability (per copy)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-COPY_SLIP_PROB 0.0 # Slip rate (per copy)
-DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
-DIV_INS_PROB 0.0 # Insertion rate (per site, applied on divide)
-DIV_DEL_PROB 0.0 # Deletion rate (per site, applied on divide)
-DIV_UNIFORM_PROB 0.0 # Uniform mutation probability (per site, applied on divide)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-DIV_SLIP_PROB 0.0 # Slip rate (per site, applied on divide)
-DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
-DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
-DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
-DIVIDE_UNIFORM_PROB 0.0 # Uniform mutation probability (per divide)
- # - Randomly applies any of the three classes of mutations (ins, del, point).
-DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
-INJECT_INS_PROB 0.00#006 # Insertion rate (per site, applied on inject)
-INJECT_DEL_PROB 0.00#006 # Deletion rate (per site, applied on inject)
-INJECT_MUT_PROB 0.00#8 # Mutation rate (per site, applied on inject)
-SLIP_FILL_MODE 0 # Fill insertions from slip mutations with 0=duplication, 1=nop-X, 2=random, 3=scrambled, 4=nop-C
-SLIP_COPY_MODE 0 # How to handle 'on-copy' slip mutations:
- # 0 = actual read head slip
- # 1 = instant large mutation (obeys slip mode)
-PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
-SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
-META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
-META_STD_DEV 0.0 # Standard deviation of meta mutation size.
-MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
- # 2 = Mutation rates inherited from parent.
-MIGRATION_RATE 0.0 # Uniform probability of offspring migrating to a new deme.
-
-### REVERSION_GROUP ###
-# Mutation Reversion
-# These slow down avida a lot, and should be set to 0.0 normally.
-REVERT_FATAL 0.0 # Should any mutations be reverted on birth?
-REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
-REVERT_NEUTRAL 0.0 #
-REVERT_BENEFICIAL 0.0 #
-STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
-STERILIZE_DETRIMENTAL 0.0 #
-STERILIZE_NEUTRAL 0.0 #
-STERILIZE_BENEFICIAL 0.0 #
-FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
- # be eliminated?
-NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness
- # to be considered neutral.
-NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness
- # to be considered neutral.
-
-### TIME_GROUP ###
-# Time Slicing
-AVE_TIME_SLICE 30 # Ave number of insts per org per update
-SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
- # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
- # 2 = INTEGRATED: Perfectly integrated deterministic.
- # 3 = DemeProbabalistic, each deme gets the same number of CPU cycles, which are awarded probabalistically within each deme.
- # 4 = ProbDemeProbabalistic, each deme gets CPU cycles proportional to its living population size, which are awarded probabalistically within each deme.
- # 5 = CONSTANT BURST: all organisms get default, in SLICING_BURST_SIZE chunks
-SLICING_BURST_SIZE 1 # Sets the scheduler burst size, when supported.
-BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
- # 1 = Merit proportional to copied size
- # 2 = Merit prop. to executed size
- # 3 = Merit prop. to full size
- # 4 = Merit prop. to min of executed or copied size
- # 5 = Merit prop. to sqrt of the minimum size
- # 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
-BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
-DEFAULT_BONUS 1.0 # Initial bonus before any tasks
-MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by this default bonus
- # rather than the accumulated bonus of the parent? 0 = off
-MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
- # (-1 = none, 0 = First in INST_SET.)
-MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
- # per instruction (-1 = penalty, 0 = no effect.)
-FITNESS_METHOD 0 # 0 = default, >=1 = experimental
-FITNESS_COEFF_1 1.0 # 1st FITNESS_METHOD parameter
-FITNESS_COEFF_2 1.0 # 2nd FITNESS_METHOD parameter
-FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from
- # FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # (0 = off, 1 = on)
-FITNESS_VALLEY_START 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
- # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # get fitness 1 (lowest)
-FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
- # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
- # get fitness 1 (lowest)
-MAX_CPU_THREADS 2 # Number of Threads a CPU can spawn
-THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
- # (num_threads-1) * THREAD_SLICING_METHOD + 1
- # 0 = One thread executed per time slice.
- # 1 = All threads executed each time slice.
-NO_CPU_CYCLE_TIME 0 # Don't count each CPU cycle as part of gestation time
-MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
-MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
-MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
-MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
-MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
-MIN_GB_DONATE_THRESHOLD -1 # threshold green beard donates only to orgs above this
- # donation attempt threshold; -1=no thresh
-DONATE_THRESH_QUANTA 10 # The size of steps between quanta donate thresholds
-MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
-PRECALC_PHENOTYPE 0 # 0 = Disabled
- # 1 = Assign precalculated merit at birth (unlimited resources only)
- # 2 = Assign precalculated gestation time
- # 3 = Assign precalculated merit AND gestation time.
- # Fitness will be evaluated for organism based on these settings.
-FASTFORWARD_UPDATES 0 # Fast-forward if the average generation has not changed in this many updates. (0 = off)
-FASTFORWARD_NUM_ORGS 0 # Fast-forward if population is equal to this
-
-### GENEOLOGY_GROUP ###
-# Geneology
-TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
- # 0=no, 1=yes, 2=yes,w/sexual population
-THRESHOLD 3 # Number of organisms in a genotype needed for it
- # to be considered viable.
-GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
-GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
- # this many updates. (0 = off)
-SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
-SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
-SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
-TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
-
-### LOG_GROUP ###
-# Log Files
-LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
-LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
-LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
-LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
-
-### LINEAGE_GROUP ###
-# Lineage
-# NOTE: This should probably be called "Clade"
-# This one can slow down avida a lot. It is used to get an idea of how
-# often an advantageous mutation arises, and where it goes afterwards.
-# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
-# 0 = manual creation (on inject, use successive integers as lineage labels).
-# 1 = when a child's (potential) fitness is higher than that of its parent.
-# 2 = when a child's (potential) fitness is higher than max in population.
-# 3 = when a child's (potential) fitness is higher than max in dom. lineage
-# *and* the child is in the dominant lineage, or (2)
-# 4 = when a child's (potential) fitness is higher than max in dom. lineage
-# (and that of its own lineage)
-# 5 = same as child's (potential) fitness is higher than that of the
-# currently dominant organism, and also than that of any organism
-# currently in the same lineage.
-# 6 = when a child's (potential) fitness is higher than any organism
-# currently in the same lineage.
-# 7 = when a child's (potential) fitness is higher than that of any
-# organism in its line of descent
-LOG_LINEAGES 0 #
-LINEAGE_CREATION_METHOD 0 #
-
-### ORGANISM_NETWORK_GROUP ###
-# Organism Network Communication
-NET_ENABLED 0 # Enable Network Communication Support
-NET_DROP_PROB 0.0 # Message drop rate
-NET_MUT_PROB 0.0 # Message corruption probability
-NET_MUT_TYPE 0 # Type of message corruption. 0 = Random Single Bit, 1 = Always Flip Last
-NET_STYLE 0 # Communication Style. 0 = Random Next, 1 = Receiver Facing
-
-### ORGANISM_MESSAGING_GROUP ###
-# Organism Message-Based Communication
-MESSAGE_TYPE 0 # Messaging Style. 0=Receiver Facing, 1=Broadcast
-MESSAGE_BCAST_RADIUS 1 # Broadcast message radius (cells)
-ORGANISMS_REMEMBER_MESSAGES 1 # Does an organism remember all messages it has sent or received? 0=false, 1=true (default)
-MESSAGE_QUEUE_SIZE -1 # Maximum number of unretrieved messages an organism can store (-1 for no limit is the default)
-MESSAGE_QUEUE_BEHAVIOR_WHEN_FULL 0 # 0 = Drop incoming message (default), 1 = Drop oldest unretrieved message
-
-### BUY_SELL_GROUP ###
-# Buying and Selling Parameters
-SAVE_RECEIVED 0 # Enable storage of all inputs bought from other orgs
-BUY_PRICE 0 # price offered by organisms attempting to buy
-SELL_PRICE 0 # price offered by organisms attempting to sell
-
-### HOARD_RESOURCE_GROUP ###
-# Resource Hoarding Parameters
-USE_RESOURCE_BINS 0 # Enable resource bin use. This serves as a guard on most resource hoarding code.
-ABSORB_RESOURCE_FRACTION .0025 # Fraction of available environmental resource an organism absorbs.
-MULTI_ABSORB_TYPE 0 # What to do if a collect instruction is called on a range of resources.
- # 0 = absorb a random resource in the range
- # 1 = absorb the first resource in the range
- # 2 = absorb the last resource in the range
- # 3 = absorb ABSORB_RESOURCE_FRACTION / (# of resources in range) of each resource in the range
-MAX_TOTAL_STORED -1 # Maximum total amount of all resources an organism can store.
- # <0 = no maximum
-USE_STORED_FRACTION 1.0 # The fraction of stored resource to use.
-ENV_FRACTION_THRESHOLD 1.0 # The fraction of available environmental resource to compare available stored resource to when deciding whether to use stored resource.
-RETURN_STORED_ON_DEATH 1 # Return an organism's stored resources to the world when it dies?
-
-### ANALYZE_GROUP ###
-# Analysis Settings
-MAX_CONCURRENCY -1 # Maximum number of analyze threads, -1 == use all available.
-ANALYZE_OPTION_1 # String variable accessible from analysis scripts
-ANALYZE_OPTION_2 # String variable accessible from analysis scripts
-
-### ENERGY_GROUP ###
-# Energy Settings
-ENERGY_ENABLED 0 # Enable Energy Model. 0/1 (off/on)
-ENERGY_GIVEN_ON_INJECT 100.0 # Energy given to organism upon injection.
-ENERGY_GIVEN_AT_BIRTH 10.0 # Energy given to offspring upon birth.
-FRAC_PARENT_ENERGY_GIVEN_TO_ORG_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring organism.
-FRAC_PARENT_ENERGY_GIVEN_TO_DEME_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring deme.
-FRAC_ENERGY_DECAY_AT_ORG_BIRTH 0.0 # Fraction of energy lost due to decay during organism reproduction.
-FRAC_ENERGY_DECAY_AT_DEME_BIRTH 0.0 # Fraction of energy lost due to decay during deme reproduction.
-NUM_CYCLES_EXC_BEFORE_0_ENERGY 1000 # Number of virtual CPU cycles executed before energy is exhausted.
-ENERGY_CAP -1.0 # Maximum amount of energy that can be stored in an organism. -1 means the cap is set to Max Double
-APPLY_ENERGY_METHOD 1 # When should rewarded energy be applied to current energy?
- # 0 = on divide
- # 1 = on completion of task
- # 2 = on sleep
-FIX_METABOLIC_RATE -1.0 # Fix organism metobolic rate to value. This value is static. Feature disabled by default (value == -1)
-FRAC_ENERGY_TRANSFER 0.0 # Fraction of replaced organism's energy take by new resident
-LOG_SLEEP_TIMES 0 # Log sleep start and end times. 0/1 (off/on)
- # WARNING: may use lots of memory.
-FRAC_ENERGY_RELINQUISH 1.0 # Fraction of organisms energy to relinquish
-ENERGY_PASSED_ON_DEME_REPLICATION_METHOD 0 # Who get energy passed from a parent deme
- # 0 = Energy divided among organisms injected to offspring deme
- # 1 = Energy divided among cells in offspring deme
-INHERIT_EXE_RATE 0 # Inherit energy rate from parent? 0=no 1=yes
-ATTACK_DECAY_RATE 0.0 # Percent of cell's energy decayed by attack
-ENERGY_THRESH_LOW .33 # Threshold percent below which energy level is considered low. Requires ENERGY_CAP.
-ENERGY_THRESH_HIGH .75 # Threshold percent above which energy level is considered high. Requires ENERGY_CAP.
-ENERGY_COMPARISON_EPSILON 0.0 # Percent difference (relative to executing organism) required in energy level comparisons
-
-### ENERGY_SHARING_GROUP ###
-# Energy Sharing Settings
-ENERGY_SHARING_METHOD 0 # Method for sharing energy. 0=receiver must actively receive/request, 1=energy pushed on receiver
-ENERGY_SHARING_PCT 0.0 # Percent of energy to share
-ENERGY_SHARING_INCREMENT 0.01 # Amount to change percent energy shared
-ENERGY_SHARING_LOSS 0.0 # Percent of shared energy lost in transfer
-ENERGY_SHARING_UPDATE_METABOLIC 0 # 0/1 (off/on) - Whether to update an organism's metabolic rate on donate or reception/application of energy
-LOG_ENERGY_SHARING 0 # Whether or not to log energy shares. 0/1 (off/on)
-
-### SECOND_PASS_GROUP ###
-# Tracking metrics known after the running experiment previously
-TRACK_CCLADES 0 # Enable tracking of coalescence clades
-TRACK_CCLADES_IDS coalescence.ids # File storing coalescence IDs
-
-### GX_GROUP ###
-# Gene Expression CPU Settings
-MAX_PROGRAMIDS 16 # Maximum number of programids an organism can create.
-MAX_PROGRAMID_AGE 2000 # Max number of CPU cycles a programid executes before it is removed.
-IMPLICIT_GENE_EXPRESSION 0 # Create executable programids from the genome without explicit allocation and copying?
-IMPLICIT_BG_PROMOTER_RATE 0.0 # Relative rate of non-promoter sites creating programids.
-IMPLICIT_TURNOVER_RATE 0.0 # Number of programids recycled per CPU cycle. 0 = OFF
-IMPLICIT_MAX_PROGRAMID_LENGTH 0 # Creation of an executable programid terminates after this many instructions. 0 = disabled
-
-### PROMOTER_GROUP ###
-# Promoters
-PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
- # Certain instructions must also be included.
-PROMOTER_INST_MAX 0 # Maximum number of instructions to execute before terminating. 0 = off
-PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating after each cpu cycle.
-PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after each instruction.
-PROMOTER_TO_REGISTER 0 # Place a promoter's base bit code in register BX when starting execution from it?
-TERMINATION_RESETS 0 # Does termination reset the thread's state?
-NO_ACTIVE_PROMOTER_EFFECT 0 # What happens when there are no active promoters?
- # 0 = Start execution at the beginning of the genome.
- # 1 = Kill the organism.
- # 2 = Stop the organism from executing any further instructions.
-PROMOTER_CODE_SIZE 24 # Size of a promoter code in bits. (Maximum value is 32)
-PROMOTER_EXE_LENGTH 3 # Length of promoter windows used to determine execution.
-PROMOTER_EXE_THRESHOLD 2 # Minimum number of bits that must be set in a promoter window to allow execution.
-INST_CODE_LENGTH 3 # Instruction binary code length (number of bits)
-INST_CODE_DEFAULT_TYPE 0 # Default value of instruction binary code value.
- # 0 = All zeros
- # 1 = Based off the instruction number
-CONSTITUTIVE_REGULATION 0 # Sense a new regulation value before each CPU cycle?
-
-### COLORS_GROUP ###
-# Output colors for when data files are printed in HTML mode.
-# There are two sets of these; the first are for lineages,
-# and the second are for mutation tests.
-COLOR_DIFF CCCCFF # Color to flag stat that has changed since parent.
-COLOR_SAME FFFFFF # Color to flag stat that has NOT changed since parent.
-COLOR_NEG2 FF0000 # Color to flag stat that is significantly worse than parent.
-COLOR_NEG1 FFCCCC # Color to flag stat that is minorly worse than parent.
-COLOR_POS1 CCFFCC # Color to flag stat that is minorly better than parent.
-COLOR_POS2 00FF00 # Color to flag stat that is significantly better than parent.
-COLOR_MUT_POS 00FF00 # Color to flag stat that has changed since parent.
-COLOR_MUT_NEUT FFFFFF # Color to flag stat that has changed since parent.
-COLOR_MUT_NEG FFFF00 # Color to flag stat that has changed since parent.
-COLOR_MUT_LETHAL FF0000 # Color to flag stat that has changed since parent.
-
-### BIOMIMETIC_GROUP ###
-# Biomimetic Features Settings
-BIOMIMETIC_REFRACTORY_PERIOD 0.0 # Number of updates affected by refractory period
-BIOMIMETIC_MOVEMENT_STEP 1 # Number of cells to move Avidian on move instruction
-BIOMIMETIC_MOVEMENT_LOG 0 # Log detailed movement information (WARNING: large data file)
-BIOMIMETIC_MOVEMENT_FACTOR 1.0 # Scale merit bonus due to movement (m<1.0 applies a cost)
-BIOMIMETIC_EVAL_ON_MOVEMENT 0 # Force task evaluation on each movement step
-BIOMIMETIC_K 0 # Carrying capacity in number of organisms
-
-### PHEROMONE_GROUP ###
-# Pheromone Settings
-PHEROMONE_ENABLED 0 # Enable pheromone usage. 0/1 (off/on)
-PHEROMONE_AMOUNT 1.0 # Amount of pheromone to add per drop
-PHEROMONE_DROP_MODE 0 # Where to drop pheromone
- # 0 = Half amount at src, half at dest
- # 1 = All at source
- # 2 = All at dest
-EXPLOIT_EXPLORE_PROB 0.00 # Probability of random exploration
- # instead of pheromone trail following
-LOG_PHEROMONE 0 # Log pheromone drops. 0/1 (off/on)
-PHEROMONE_LOG_START 0 # Update at which to start logging pheromone drops
-EXPLOIT_LOG_START 0 # Update at which to start logging exploit moves
-EXPLORE_LOG_START 0 # Update at which to start logging explore moves
-MOVETARGET_LOG_START 0 # Update at which to start logging movetarget moves
-LOG_INJECT 0 # Log injection of organisms. 0/1 (off/on)
-INJECT_LOG_START 0 # Update at which to start logging injection of
- # organisms
-
-### SYNCHRONIZATION_GROUP ###
-# Synchronization settings
-SYNC_FITNESS_WINDOW 100 # Number of updates over which to calculate fitness (default=100).
-SYNC_FLASH_LOSSRATE 0.0 # P() to lose a flash send (0.0==off).
-SYNC_TEST_FLASH_ARRIVAL -1 # CPU cycle at which an organism will receive a flash (off=-1, default=-1, analyze mode only.)
Copied: branches/biounit/support/config/misc/Parasites/avida.cfg (from rev 3558, branches/parasites/support/config/misc/Parasites/avida.cfg)
===================================================================
--- branches/biounit/support/config/misc/Parasites/avida.cfg (rev 0)
+++ branches/biounit/support/config/misc/Parasites/avida.cfg 2009-12-16 16:01:42 UTC (rev 3559)
@@ -0,0 +1,543 @@
+#############################################################################
+# This file includes all the basic run-time defines for Avida.
+# For more information, see doc/config.html
+#############################################################################
+
+VERSION_ID 2.9.0 # Do not change this value.
+
+INJECT_PROB_FROM_TASKS 1
+INJECT_PROB_SIGMOID 1
+### GENERAL_GROUP ###
+# General Settings
+ANALYZE_MODE 0 # 0 = Disabled
+ # 1 = Enabled
+ # 2 = Interactive
+VIEW_MODE 1 # Initial viewer screen
+PAUSE_VIEWER_ON_START 0 #Pause the viewer on load
+MERIT_INC_APPLY_IMMEDIATE 1
+CLONE_FILE - # Clone file to load
+VERBOSITY 1 # 0 = No output at all
+ # 1 = Normal output
+ # 2 = Verbose output, detailing progress
+ # 3 = High level of details, as available
+ # 4 = Print Debug Information, as applicable
+
+### ARCH_GROUP ###
+# Architecture Variables
+WORLD_X 60 # Width of the Avida world
+WORLD_Y 60 # Height of the Avida world
+WORLD_Z 1 # Depth of the Avida world
+WORLD_GEOMETRY 3 # 1 = Bounded Grid
+ # 2 = Torus
+ # 3 = Clique
+ # 4 = Hexagonal grid
+ # 5 = Lattice
+RANDOM_SEED 0 # Random number seed (0 for based on time)
+HARDWARE_TYPE 2 # 0 = Original CPUs
+ # 1 = New SMT CPUs
+ # 2 = Transitional SMT
+ # 3 = Experimental CPU
+ # 4 = Gene Expression CPU
+SPECULATIVE 1 # Enable speculative execution
+TRACE_EXECUTION 0 # Trace the execution of all organisms in the population (default=off,SLOW!)
+BCAST_HOPS 1 # Number of hops to broadcast an alarm
+ALARM_SELF 0 # Does sending an alarm move sender IP to alarm label?
+ # 0=no
+ # 1=yes
+IO_EXPIRE 1 # Is the expiration functionality of '-expire' I/O instructions enabled?
+INSTRUCTION_CONSTANT 3 # The Constant to add when the add-const instruction is called
+
+### CONFIG_FILE_GROUP ###
+# Configuration Files
+DATA_DIR data # Directory in which config files are found
+INST_SET instset-smt.cfg # File containing instruction set
+INST_SET_FORMAT 0 # Instruction set file format.
+ # 0 = Default
+ # 1 = New Style
+EVENT_FILE events.cfg # File containing list of events during run
+ANALYZE_FILE analyze.cfg # File used for analysis mode
+ENVIRONMENT_FILE environment.cfg # File that describes the environment
+START_CREATURE dominant-org.org # Organism to seed the soup
+
+### DEME_GROUP ###
+# Demes and Germlines
+NUM_DEMES 1 # Number of independent groups in the
+ # population (default=1).
+DEMES_USE_GERMLINE 0 # Whether demes use a distinct germline (default=0).
+DEMES_PREVENT_STERILE 0 # Whether to prevent sterile demes from
+ # replicating (default=0 or no).
+DEMES_RESET_RESOURCES 0 # Reset resources in demes on replication.
+ # 0 = reset both demes
+ # 1 = reset target deme
+ # 2 = deme resources remain unchanged
+DEMES_REPLICATE_SIZE 1 # Number of identical organisms to create or copy from the
+ # source deme to the target deme (default=1).
+LOG_DEMES_REPLICATE 0 # Log deme replications. 0/1 (off/on)
+DEMES_REPLICATE_LOG_START 0 # Update at which to start logging deme replications
+DEMES_PROB_ORG_TRANSFER 0.0 # Probablity of an organism being transferred from the
+ # source deme to the target deme (default=0.0).
+DEMES_ORGANISM_SELECTION 0 # How organisms are selected for transfer from
+ # source to target during deme replication.
+ # 0=random with replacement (default).
+ # 1=sequential.
+DEMES_ORGANISM_PLACEMENT 0 # How organisms are placed during deme replication.
+ # 0=cell-array middle (default).
+ # 1=deme center.
+ # 2=random placement.
+ # 3=sequential.
+DEMES_ORGANISM_FACING 0 # How organisms are facing during deme replication.
+ # 0=unchanged (default).
+ # 1=northwest.
+ # 2=random.
+DEMES_MAX_AGE 500 # The maximum age of a deme (in updates) to be
+ # used for age-based replication (default=500).
+DEMES_MAX_BIRTHS 100 # The maximum number of births that can occur
+ # within a deme; used with birth-count
+ # replication (default=100).
+DEMES_MIM_EVENTS_KILLED_RATIO 0.7 # Minimum ratio of events killed required for event period to be a success.
+DEMES_MIM_SUCCESSFUL_EVENT_PERIODS 1 # Minimum number of consecutive event periods that must be a success.
+GERMLINE_COPY_MUT 0.0075 # Prob. of copy mutations occuring during
+ # germline replication (default=0.0075).
+GERMLINE_INS_MUT 0.05 # Prob. of an insertion mutation occuring
+ # during germline replication (default=0.05).
+GERMLINE_DEL_MUT 0.05 # Prob. of a deletion mutation occuring
+ # during germline replication (default=0.05).
+DEMES_REPLICATE_CPU_CYCLES 0.0 # Replicate a deme immediately after it has used
+ # this number of cpu cycles, normalized
+ # by number of orgs in deme (0 = OFF).
+DEMES_REPLICATE_TIME 0.0 # Replicate a deme immediately after it has used
+ # this number of cpu cycles, normalized
+ # by number of orgs in deme and organism merit (0 = OFF).
+DEMES_REPLICATE_BIRTHS 0 # Replicate a deme immediately after it has
+ # produced this many offspring (0 = OFF).
+DEMES_REPLICATE_ORGS 0 # Replicate a deme immediately once it reaches a
+ # certain number of organisms (0 = OFF).
+DEMES_REPLICATION_ONLY_RESETS 0 # Kin selection mode. Deme replication really:
+ # 1=resets deme resources
+ # 2=rests deme resources and re-injects organisms
+DEMES_MIGRATION_RATE 0.0 # Probability of an offspring being born in a different deme.
+DEMES_MIGRATION_METHOD 0 # How do we choose what demes an org may land in when it migrates?
+ # 0=all other demes
+ # 1=eight adjacent neighbors
+ # 2=two adjacent demes in list
+ # 3=proportional based on the number of points
+DEMES_NUM_X 0 # Simulated number of demes in X dimension. Only used for migration.
+DEMES_SEED_METHOD 0 # Deme seeding method.
+ # 0=maintain old consistency
+ # 1=new method using genotypes
+DEMES_DIVIDE_METHOD 0 # Deme divide method. Only works with DEMES_SEED_METHOD 1
+ # 0=replace and target demes
+ # 1= replace target deme, reset source deme to founders
+ # 2=replace target deme, leave source deme unchanged
+DEMES_DEFAULT_GERMLINE_PROPENSITY 0.0 # Default germline propensity of organisms in deme.
+ # For use with DEMES_DIVIDE_METHOD 2.
+DEMES_FOUNDER_GERMLINE_PROPENSITY -1.0 # Default germline propensity of founder organisms in deme.
+ # For use with DEMES_DIVIDE_METHOD 2.
+ # <0 = OFF
+DEMES_PREFER_EMPTY 0 # Give empty demes preference as targets of deme replication?
+DEMES_PROTECTION_POINTS 0 # The number of points a deme receives for each suicide.
+POINT_DECAY_PERCENT 0 # The percentage of points decayed each time cActionDecayPoints is called.
+
+### REPRODUCTION_GROUP ###
+# Birth and Death
+BIRTH_METHOD 0 # Which organism should be replaced on birth?
+ # 0 = Random organism in neighborhood
+ # 1 = Oldest in neighborhood
+ # 2 = Largest Age/Merit in neighborhood
+ # 3 = None (use only empty cells in neighborhood)
+ # 4 = Random from population (Mass Action)
+ # 5 = Oldest in entire population
+ # 6 = Random within deme
+ # 7 = Organism faced by parent
+ # 8 = Next grid cell (id+1)
+ # 9 = Largest energy used in entire population
+ # 10 = Largest energy used in neighborhood
+PREFER_EMPTY 1 # Give empty cells preference in offsping placement?
+ALLOW_PARENT 1 # Allow births to replace the parent organism?
+DEATH_METHOD 2 # 0 = Never die of old age.
+ # 1 = Die when inst executed = AGE_LIMIT (+deviation)
+ # 2 = Die when inst executed = length*AGE_LIMIT (+dev)
+AGE_LIMIT 20 # Modifies DEATH_METHOD
+AGE_DEVIATION 0 # Creates a distribution around AGE_LIMIT
+ALLOC_METHOD 0 # (Orignal CPU Only)
+ # 0 = Allocated space is set to default instruction.
+ # 1 = Set to section of dead genome (Necrophilia)
+ # 2 = Allocated space is set to random instruction.
+DIVIDE_METHOD 2 # 0 = Divide leaves state of mother untouched.
+ # 1 = Divide resets state of mother
+ # (after the divide, we have 2 children)
+ # 2 = Divide resets state of current thread only
+ # (does not touch possible parasite threads)
+ # 3 = Divide resets mother stats, but not state.
+ # 4 = 3 + child inherits mother registers and stack values.
+EPIGENETIC_METHOD 0 # Inheritance of state information other than genome
+ # 0 = none
+ # 1 = offspring inherits registers and stacks of first thread
+ # 1 = parent maintains registers and stacks of first thread
+ #
+ # 1 = offspring and parent keep state information
+INJECT_METHOD 1 # 0 = Leaves the parasite thread state untouched.
+ # 1 = Resets the calling thread state on inject
+GENERATION_INC_METHOD 1 # 0 = Only the generation of the child is
+ # increased on divide.
+ # 1 = Both the generation of the mother and child are
+ # increased on divide (good with DIVIDE_METHOD 1).
+RESET_INPUTS_ON_DIVIDE 0 # Reset environment inputs of parent upon successful divide.
+REPRO_METHOD 1 # Replace existing organism: 1=yes
+
+### RECOMBINATION_GROUP ###
+# Sexual Recombination and Modularity
+RECOMBINATION_PROB 1.0 # probability of recombination in div-sex
+MAX_BIRTH_WAIT_TIME -1 # Updates incipiant orgs can wait for crossover
+MODULE_NUM 0 # number of modules in the genome
+CONT_REC_REGS 1 # are (modular) recombination regions continuous
+CORESPOND_REC_REGS 1 # are (modular) recombination regions swapped randomly
+ # or with corresponding positions?
+TWO_FOLD_COST_SEX 0 # 1 = only one recombined offspring is born.
+ # 2 = both offspring are born
+SAME_LENGTH_SEX 0 # 0 = recombine with any genome
+ # 1 = only recombine w/ same length
+
+### DIVIDE_GROUP ###
+# Divide Restrictions
+CHILD_SIZE_RANGE 2.0 # Maximal differential between child and parent sizes.
+ # (Checked BEFORE mutations applied on divide.)
+MIN_COPIED_LINES 0.5 # Code fraction which must be copied before divide.
+MIN_EXE_LINES 0.5 # Code fraction which must be executed before divide.
+MIN_GENOME_SIZE 30 # Minimum number of instructions allowed in a genome. 0 = OFF
+MAX_GENOME_SIZE 0 # Maximum number of instructions allowed in a genome. 0 = OFF
+REQUIRE_ALLOCATE 1 # (Original CPU Only) Require allocate before divide?
+REQUIRED_TASK -1 # Task ID required for successful divide.
+IMMUNITY_TASK -1 # Task providing immunity from the required task.
+REQUIRED_REACTION -1 # Reaction ID required for successful divide.
+REQUIRED_BONUS 0.0 # Required bonus to divide.
+REQUIRE_EXACT_COPY 0 # Require offspring to be an exact copy (only divide mutations allowed).
+IMPLICIT_REPRO_BONUS 0 # Call Inst_Repro to divide upon achieving this bonus. 0 = OFF
+IMPLICIT_REPRO_CPU_CYCLES 0 # Call Inst_Repro after this many cpu cycles. 0 = OFF
+IMPLICIT_REPRO_TIME 0 # Call Inst_Repro after this time used. 0 = OFF
+IMPLICIT_REPRO_END 0 # Call Inst_Repro after executing the last instruction in the genome.
+IMPLICIT_REPRO_ENERGY 0.0 # Call Inst_Repro if organism accumulates this amount of energy.
+
+### MUTATION_GROUP ###
+# Mutations
+POINT_MUT_PROB 0.0 # Mutation rate (per-location per update)
+COPY_MUT_PROB 0.0075 # Mutation rate (per copy)
+COPY_INS_PROB 0.0 # Insertion rate (per copy)
+COPY_DEL_PROB 0.0 # Deletion rate (per copy)
+COPY_UNIFORM_PROB 0.0 # Uniform mutation probability (per copy)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+COPY_SLIP_PROB 0.0 # Slip rate (per copy)
+DIV_MUT_PROB 0.0 # Mutation rate (per site, applied on divide)
+DIV_INS_PROB 0.0 # Insertion rate (per site, applied on divide)
+DIV_DEL_PROB 0.0 # Deletion rate (per site, applied on divide)
+DIV_UNIFORM_PROB 0.0 # Uniform mutation probability (per site, applied on divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+DIV_SLIP_PROB 0.0 # Slip rate (per site, applied on divide)
+DIVIDE_MUT_PROB 0.0 # Mutation rate (per divide)
+DIVIDE_INS_PROB 0.05 # Insertion rate (per divide)
+DIVIDE_DEL_PROB 0.05 # Deletion rate (per divide)
+DIVIDE_UNIFORM_PROB 0.0 # Uniform mutation probability (per divide)
+ # - Randomly applies any of the three classes of mutations (ins, del, point).
+DIVIDE_SLIP_PROB 0.0 # Slip rate (per divide) - creates large deletions/duplications
+INJECT_INS_PROB 0.00#006 # Insertion rate (per site, applied on inject)
+INJECT_DEL_PROB 0.00#006 # Deletion rate (per site, applied on inject)
+INJECT_MUT_PROB 0.00#8 # Mutation rate (per site, applied on inject)
+SLIP_FILL_MODE 0 # Fill insertions from slip mutations with 0=duplication, 1=nop-X, 2=random, 3=scrambled, 4=nop-C
+SLIP_COPY_MODE 0 # How to handle 'on-copy' slip mutations:
+ # 0 = actual read head slip
+ # 1 = instant large mutation (obeys slip mode)
+PARENT_MUT_PROB 0.0 # Per-site, in parent, on divide
+SPECIAL_MUT_LINE -1 # If this is >= 0, ONLY this line is mutated
+META_COPY_MUT 0.0 # Prob. of copy mutation rate changing (per gen)
+META_STD_DEV 0.0 # Standard deviation of meta mutation size.
+MUT_RATE_SOURCE 1 # 1 = Mutation rates determined by environment.
+ # 2 = Mutation rates inherited from parent.
+MIGRATION_RATE 0.0 # Uniform probability of offspring migrating to a new deme.
+
+### REVERSION_GROUP ###
+# Mutation Reversion
+# These slow down avida a lot, and should be set to 0.0 normally.
+REVERT_FATAL 0.0 # Should any mutations be reverted on birth?
+REVERT_DETRIMENTAL 0.0 # 0.0 to 1.0; Probability of reversion.
+REVERT_NEUTRAL 0.0 #
+REVERT_BENEFICIAL 0.0 #
+STERILIZE_FATAL 0.0 # Should any mutations clear (kill) the organism?
+STERILIZE_DETRIMENTAL 0.0 #
+STERILIZE_NEUTRAL 0.0 #
+STERILIZE_BENEFICIAL 0.0 #
+FAIL_IMPLICIT 0 # Should copies that failed *not* due to mutations
+ # be eliminated?
+NEUTRAL_MAX 0.0 # The percent benifical change from parent fitness
+ # to be considered neutral.
+NEUTRAL_MIN 0.0 # The percent deleterious change from parent fitness
+ # to be considered neutral.
+
+### TIME_GROUP ###
+# Time Slicing
+AVE_TIME_SLICE 30 # Ave number of insts per org per update
+SLICING_METHOD 1 # 0 = CONSTANT: all organisms get default...
+ # 1 = PROBABILISTIC: Run _prob_ proportional to merit.
+ # 2 = INTEGRATED: Perfectly integrated deterministic.
+ # 3 = DemeProbabalistic, each deme gets the same number of CPU cycles, which are awarded probabalistically within each deme.
+ # 4 = ProbDemeProbabalistic, each deme gets CPU cycles proportional to its living population size, which are awarded probabalistically within each deme.
+ # 5 = CONSTANT BURST: all organisms get default, in SLICING_BURST_SIZE chunks
+SLICING_BURST_SIZE 1 # Sets the scheduler burst size, when supported.
+BASE_MERIT_METHOD 4 # 0 = Constant (merit independent of size)
+ # 1 = Merit proportional to copied size
+ # 2 = Merit prop. to executed size
+ # 3 = Merit prop. to full size
+ # 4 = Merit prop. to min of executed or copied size
+ # 5 = Merit prop. to sqrt of the minimum size
+ # 6 = Merit prop. to num times MERIT_BONUS_INST is in genome.
+BASE_CONST_MERIT 100 # Base merit when BASE_MERIT_METHOD set to 0
+DEFAULT_BONUS 1.0 # Initial bonus before any tasks
+MERIT_DEFAULT_BONUS 0 # Scale the merit of an offspring by this default bonus
+ # rather than the accumulated bonus of the parent? 0 = off
+MERIT_BONUS_INST 0 # in BASE_MERIT_METHOD 6, this sets which instruction counts
+ # (-1 = none, 0 = First in INST_SET.)
+MERIT_BONUS_EFFECT 0 # in BASE_MERIT_METHOD 6, this sets how much merit is earned
+ # per instruction (-1 = penalty, 0 = no effect.)
+FITNESS_METHOD 0 # 0 = default, >=1 = experimental
+FITNESS_COEFF_1 1.0 # 1st FITNESS_METHOD parameter
+FITNESS_COEFF_2 1.0 # 2nd FITNESS_METHOD parameter
+FITNESS_VALLEY 0 # in BASE_MERIT_METHOD 6, this creates valleys from
+ # FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # (0 = off, 1 = on)
+FITNESS_VALLEY_START 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+FITNESS_VALLEY_STOP 0 # if FITNESS_VALLEY = 1, orgs with num_key_instructions
+ # from FITNESS_VALLEY_START to FITNESS_VALLEY_STOP
+ # get fitness 1 (lowest)
+MAX_CPU_THREADS 2 # Number of Threads a CPU can spawn
+THREAD_SLICING_METHOD 0 # Formula for and organism's thread slicing
+ # (num_threads-1) * THREAD_SLICING_METHOD + 1
+ # 0 = One thread executed per time slice.
+ # 1 = All threads executed each time slice.
+NO_CPU_CYCLE_TIME 0 # Don't count each CPU cycle as part of gestation time
+MAX_LABEL_EXE_SIZE 1 # Max nops marked as executed when labels are used
+MERIT_GIVEN 0.0 # Fraction of merit donated with 'donate' command
+MERIT_RECEIVED 0.0 # Multiplier of merit given with 'donate' command
+MAX_DONATE_KIN_DIST -1 # Limit on distance of relation for donate; -1=no max
+MAX_DONATE_EDIT_DIST -1 # Limit on genetic (edit) distance for donate; -1=no max
+MIN_GB_DONATE_THRESHOLD -1 # threshold green beard donates only to orgs above this
+ # donation attempt threshold; -1=no thresh
+DONATE_THRESH_QUANTA 10 # The size of steps between quanta donate thresholds
+MAX_DONATES 1000000 # Limit on number of donates organisms are allowed.
+PRECALC_PHENOTYPE 0 # 0 = Disabled
+ # 1 = Assign precalculated merit at birth (unlimited resources only)
+ # 2 = Assign precalculated gestation time
+ # 3 = Assign precalculated merit AND gestation time.
+ # Fitness will be evaluated for organism based on these settings.
+FASTFORWARD_UPDATES 0 # Fast-forward if the average generation has not changed in this many updates. (0 = off)
+FASTFORWARD_NUM_ORGS 0 # Fast-forward if population is equal to this
+
+### GENEOLOGY_GROUP ###
+# Geneology
+TRACK_MAIN_LINEAGE 1 # Keep all ancestors of the active population?
+ # 0=no, 1=yes, 2=yes,w/sexual population
+THRESHOLD 3 # Number of organisms in a genotype needed for it
+ # to be considered viable.
+GENOTYPE_PRINT 0 # 0/1 (off/on) Print out all threshold genotypes?
+GENOTYPE_PRINT_DOM 0 # Print out a genotype if it stays dominant for
+ # this many updates. (0 = off)
+SPECIES_THRESHOLD 2 # max failure count for organisms to be same species
+SPECIES_RECORDING 0 # 1 = full, 2 = limited search (parent only)
+SPECIES_PRINT 0 # 0/1 (off/on) Print out all species?
+TEST_CPU_TIME_MOD 20 # Time allocated in test CPUs (multiple of length)
+
+### LOG_GROUP ###
+# Log Files
+LOG_CREATURES 0 # 0/1 (off/on) toggle to print file.
+LOG_GENOTYPES 0 # 0 = off, 1 = print ALL, 2 = print threshold ONLY.
+LOG_THRESHOLD 0 # 0/1 (off/on) toggle to print file.
+LOG_SPECIES 0 # 0/1 (off/on) toggle to print file.
+
+### LINEAGE_GROUP ###
+# Lineage
+# NOTE: This should probably be called "Clade"
+# This one can slow down avida a lot. It is used to get an idea of how
+# often an advantageous mutation arises, and where it goes afterwards.
+# Lineage creation options are. Works only when LOG_LINEAGES is set to 1.
+# 0 = manual creation (on inject, use successive integers as lineage labels).
+# 1 = when a child's (potential) fitness is higher than that of its parent.
+# 2 = when a child's (potential) fitness is higher than max in population.
+# 3 = when a child's (potential) fitness is higher than max in dom. lineage
+# *and* the child is in the dominant lineage, or (2)
+# 4 = when a child's (potential) fitness is higher than max in dom. lineage
+# (and that of its own lineage)
+# 5 = same as child's (potential) fitness is higher than that of the
+# currently dominant organism, and also than that of any organism
+# currently in the same lineage.
+# 6 = when a child's (potential) fitness is higher than any organism
+# currently in the same lineage.
+# 7 = when a child's (potential) fitness is higher than that of any
+# organism in its line of descent
+LOG_LINEAGES 0 #
+LINEAGE_CREATION_METHOD 0 #
+
+### ORGANISM_NETWORK_GROUP ###
+# Organism Network Communication
+NET_ENABLED 0 # Enable Network Communication Support
+NET_DROP_PROB 0.0 # Message drop rate
+NET_MUT_PROB 0.0 # Message corruption probability
+NET_MUT_TYPE 0 # Type of message corruption. 0 = Random Single Bit, 1 = Always Flip Last
+NET_STYLE 0 # Communication Style. 0 = Random Next, 1 = Receiver Facing
+
+### ORGANISM_MESSAGING_GROUP ###
+# Organism Message-Based Communication
+MESSAGE_TYPE 0 # Messaging Style. 0=Receiver Facing, 1=Broadcast
+MESSAGE_BCAST_RADIUS 1 # Broadcast message radius (cells)
+ORGANISMS_REMEMBER_MESSAGES 1 # Does an organism remember all messages it has sent or received? 0=false, 1=true (default)
+MESSAGE_QUEUE_SIZE -1 # Maximum number of unretrieved messages an organism can store (-1 for no limit is the default)
+MESSAGE_QUEUE_BEHAVIOR_WHEN_FULL 0 # 0 = Drop incoming message (default), 1 = Drop oldest unretrieved message
+
+### BUY_SELL_GROUP ###
+# Buying and Selling Parameters
+SAVE_RECEIVED 0 # Enable storage of all inputs bought from other orgs
+BUY_PRICE 0 # price offered by organisms attempting to buy
+SELL_PRICE 0 # price offered by organisms attempting to sell
+
+### HOARD_RESOURCE_GROUP ###
+# Resource Hoarding Parameters
+USE_RESOURCE_BINS 0 # Enable resource bin use. This serves as a guard on most resource hoarding code.
+ABSORB_RESOURCE_FRACTION .0025 # Fraction of available environmental resource an organism absorbs.
+MULTI_ABSORB_TYPE 0 # What to do if a collect instruction is called on a range of resources.
+ # 0 = absorb a random resource in the range
+ # 1 = absorb the first resource in the range
+ # 2 = absorb the last resource in the range
+ # 3 = absorb ABSORB_RESOURCE_FRACTION / (# of resources in range) of each resource in the range
+MAX_TOTAL_STORED -1 # Maximum total amount of all resources an organism can store.
+ # <0 = no maximum
+USE_STORED_FRACTION 1.0 # The fraction of stored resource to use.
+ENV_FRACTION_THRESHOLD 1.0 # The fraction of available environmental resource to compare available stored resource to when deciding whether to use stored resource.
+RETURN_STORED_ON_DEATH 1 # Return an organism's stored resources to the world when it dies?
+
+### ANALYZE_GROUP ###
+# Analysis Settings
+MAX_CONCURRENCY -1 # Maximum number of analyze threads, -1 == use all available.
+ANALYZE_OPTION_1 # String variable accessible from analysis scripts
+ANALYZE_OPTION_2 # String variable accessible from analysis scripts
+
+### ENERGY_GROUP ###
+# Energy Settings
+ENERGY_ENABLED 0 # Enable Energy Model. 0/1 (off/on)
+ENERGY_GIVEN_ON_INJECT 100.0 # Energy given to organism upon injection.
+ENERGY_GIVEN_AT_BIRTH 10.0 # Energy given to offspring upon birth.
+FRAC_PARENT_ENERGY_GIVEN_TO_ORG_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring organism.
+FRAC_PARENT_ENERGY_GIVEN_TO_DEME_AT_BIRTH 0.5 # Fraction of parent's energy given to offspring deme.
+FRAC_ENERGY_DECAY_AT_ORG_BIRTH 0.0 # Fraction of energy lost due to decay during organism reproduction.
+FRAC_ENERGY_DECAY_AT_DEME_BIRTH 0.0 # Fraction of energy lost due to decay during deme reproduction.
+NUM_CYCLES_EXC_BEFORE_0_ENERGY 1000 # Number of virtual CPU cycles executed before energy is exhausted.
+ENERGY_CAP -1.0 # Maximum amount of energy that can be stored in an organism. -1 means the cap is set to Max Double
+APPLY_ENERGY_METHOD 1 # When should rewarded energy be applied to current energy?
+ # 0 = on divide
+ # 1 = on completion of task
+ # 2 = on sleep
+FIX_METABOLIC_RATE -1.0 # Fix organism metobolic rate to value. This value is static. Feature disabled by default (value == -1)
+FRAC_ENERGY_TRANSFER 0.0 # Fraction of replaced organism's energy take by new resident
+LOG_SLEEP_TIMES 0 # Log sleep start and end times. 0/1 (off/on)
+ # WARNING: may use lots of memory.
+FRAC_ENERGY_RELINQUISH 1.0 # Fraction of organisms energy to relinquish
+ENERGY_PASSED_ON_DEME_REPLICATION_METHOD 0 # Who get energy passed from a parent deme
+ # 0 = Energy divided among organisms injected to offspring deme
+ # 1 = Energy divided among cells in offspring deme
+INHERIT_EXE_RATE 0 # Inherit energy rate from parent? 0=no 1=yes
+ATTACK_DECAY_RATE 0.0 # Percent of cell's energy decayed by attack
+ENERGY_THRESH_LOW .33 # Threshold percent below which energy level is considered low. Requires ENERGY_CAP.
+ENERGY_THRESH_HIGH .75 # Threshold percent above which energy level is considered high. Requires ENERGY_CAP.
+ENERGY_COMPARISON_EPSILON 0.0 # Percent difference (relative to executing organism) required in energy level comparisons
+
+### ENERGY_SHARING_GROUP ###
+# Energy Sharing Settings
+ENERGY_SHARING_METHOD 0 # Method for sharing energy. 0=receiver must actively receive/request, 1=energy pushed on receiver
+ENERGY_SHARING_PCT 0.0 # Percent of energy to share
+ENERGY_SHARING_INCREMENT 0.01 # Amount to change percent energy shared
+ENERGY_SHARING_LOSS 0.0 # Percent of shared energy lost in transfer
+ENERGY_SHARING_UPDATE_METABOLIC 0 # 0/1 (off/on) - Whether to update an organism's metabolic rate on donate or reception/application of energy
+LOG_ENERGY_SHARING 0 # Whether or not to log energy shares. 0/1 (off/on)
+
+### SECOND_PASS_GROUP ###
+# Tracking metrics known after the running experiment previously
+TRACK_CCLADES 0 # Enable tracking of coalescence clades
+TRACK_CCLADES_IDS coalescence.ids # File storing coalescence IDs
+
+### GX_GROUP ###
+# Gene Expression CPU Settings
+MAX_PROGRAMIDS 16 # Maximum number of programids an organism can create.
+MAX_PROGRAMID_AGE 2000 # Max number of CPU cycles a programid executes before it is removed.
+IMPLICIT_GENE_EXPRESSION 0 # Create executable programids from the genome without explicit allocation and copying?
+IMPLICIT_BG_PROMOTER_RATE 0.0 # Relative rate of non-promoter sites creating programids.
+IMPLICIT_TURNOVER_RATE 0.0 # Number of programids recycled per CPU cycle. 0 = OFF
+IMPLICIT_MAX_PROGRAMID_LENGTH 0 # Creation of an executable programid terminates after this many instructions. 0 = disabled
+
+### PROMOTER_GROUP ###
+# Promoters
+PROMOTERS_ENABLED 0 # Use the promoter/terminator execution scheme.
+ # Certain instructions must also be included.
+PROMOTER_INST_MAX 0 # Maximum number of instructions to execute before terminating. 0 = off
+PROMOTER_PROCESSIVITY 1.0 # Chance of not terminating after each cpu cycle.
+PROMOTER_PROCESSIVITY_INST 1.0 # Chance of not terminating after each instruction.
+PROMOTER_TO_REGISTER 0 # Place a promoter's base bit code in register BX when starting execution from it?
+TERMINATION_RESETS 0 # Does termination reset the thread's state?
+NO_ACTIVE_PROMOTER_EFFECT 0 # What happens when there are no active promoters?
+ # 0 = Start execution at the beginning of the genome.
+ # 1 = Kill the organism.
+ # 2 = Stop the organism from executing any further instructions.
+PROMOTER_CODE_SIZE 24 # Size of a promoter code in bits. (Maximum value is 32)
+PROMOTER_EXE_LENGTH 3 # Length of promoter windows used to determine execution.
+PROMOTER_EXE_THRESHOLD 2 # Minimum number of bits that must be set in a promoter window to allow execution.
+INST_CODE_LENGTH 3 # Instruction binary code length (number of bits)
+INST_CODE_DEFAULT_TYPE 0 # Default value of instruction binary code value.
+ # 0 = All zeros
+ # 1 = Based off the instruction number
+CONSTITUTIVE_REGULATION 0 # Sense a new regulation value before each CPU cycle?
+
+### COLORS_GROUP ###
+# Output colors for when data files are printed in HTML mode.
+# There are two sets of these; the first are for lineages,
+# and the second are for mutation tests.
+COLOR_DIFF CCCCFF # Color to flag stat that has changed since parent.
+COLOR_SAME FFFFFF # Color to flag stat that has NOT changed since parent.
+COLOR_NEG2 FF0000 # Color to flag stat that is significantly worse than parent.
+COLOR_NEG1 FFCCCC # Color to flag stat that is minorly worse than parent.
+COLOR_POS1 CCFFCC # Color to flag stat that is minorly better than parent.
+COLOR_POS2 00FF00 # Color to flag stat that is significantly better than parent.
+COLOR_MUT_POS 00FF00 # Color to flag stat that has changed since parent.
+COLOR_MUT_NEUT FFFFFF # Color to flag stat that has changed since parent.
+COLOR_MUT_NEG FFFF00 # Color to flag stat that has changed since parent.
+COLOR_MUT_LETHAL FF0000 # Color to flag stat that has changed since parent.
+
+### BIOMIMETIC_GROUP ###
+# Biomimetic Features Settings
+BIOMIMETIC_REFRACTORY_PERIOD 0.0 # Number of updates affected by refractory period
+BIOMIMETIC_MOVEMENT_STEP 1 # Number of cells to move Avidian on move instruction
+BIOMIMETIC_MOVEMENT_LOG 0 # Log detailed movement information (WARNING: large data file)
+BIOMIMETIC_MOVEMENT_FACTOR 1.0 # Scale merit bonus due to movement (m<1.0 applies a cost)
+BIOMIMETIC_EVAL_ON_MOVEMENT 0 # Force task evaluation on each movement step
+BIOMIMETIC_K 0 # Carrying capacity in number of organisms
+
+### PHEROMONE_GROUP ###
+# Pheromone Settings
+PHEROMONE_ENABLED 0 # Enable pheromone usage. 0/1 (off/on)
+PHEROMONE_AMOUNT 1.0 # Amount of pheromone to add per drop
+PHEROMONE_DROP_MODE 0 # Where to drop pheromone
+ # 0 = Half amount at src, half at dest
+ # 1 = All at source
+ # 2 = All at dest
+EXPLOIT_EXPLORE_PROB 0.00 # Probability of random exploration
+ # instead of pheromone trail following
+LOG_PHEROMONE 0 # Log pheromone drops. 0/1 (off/on)
+PHEROMONE_LOG_START 0 # Update at which to start logging pheromone drops
+EXPLOIT_LOG_START 0 # Update at which to start logging exploit moves
+EXPLORE_LOG_START 0 # Update at which to start logging explore moves
+MOVETARGET_LOG_START 0 # Update at which to start logging movetarget moves
+LOG_INJECT 0 # Log injection of organisms. 0/1 (off/on)
+INJECT_LOG_START 0 # Update at which to start logging injection of
+ # organisms
+
+### SYNCHRONIZATION_GROUP ###
+# Synchronization settings
+SYNC_FITNESS_WINDOW 100 # Number of updates over which to calculate fitness (default=100).
+SYNC_FLASH_LOSSRATE 0.0 # P() to lose a flash send (0.0==off).
+SYNC_TEST_FLASH_ARRIVAL -1 # CPU cycle at which an organism will receive a flash (off=-1, default=-1, analyze mode only.)
Deleted: branches/biounit/support/config/misc/Parasites/default-smt.org
===================================================================
--- branches/parasites/support/config/misc/Parasites/default-smt.org 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/support/config/misc/Parasites/default-smt.org 2009-12-16 16:01:42 UTC (rev 3559)
@@ -1,160 +0,0 @@
-Search # 1: Find organism end.
-Nop-C # 2: - Match CB:AD
-Nop-B
-Push-Prev # 5: Move end position to Stack-A
-SetMemory # 6: Place FLOW-head in memory space for offspring
-Nop-B # - Memory space labeled Nop-A Nop-A Nop-A
-Head-Move # 7: Move Write head to flow head position
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-Search # 9: Drop flow head at start of copy loop
-Inst-Read # 10:
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-Head-Push # 12: Get current position of...
-Nop-C # 13: - Read-Head
-If-Equal # 14: Test if we are done copying...
-Divide # 15: ...If so, divide.
-Head-Move # 16: ...If not, continue with loop.
-Nop-A # 17:
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\ No newline at end of file
Copied: branches/biounit/support/config/misc/Parasites/default-smt.org (from rev 3558, branches/parasites/support/config/misc/Parasites/default-smt.org)
===================================================================
--- branches/biounit/support/config/misc/Parasites/default-smt.org (rev 0)
+++ branches/biounit/support/config/misc/Parasites/default-smt.org 2009-12-16 16:01:42 UTC (rev 3559)
@@ -0,0 +1,160 @@
+Search # 1: Find organism end.
+Nop-C # 2: - Match CB:AD
+Nop-B
+Push-Prev # 5: Move end position to Stack-A
+SetMemory # 6: Place FLOW-head in memory space for offspring
+Nop-B # - Memory space labeled Nop-A Nop-A Nop-A
+Head-Move # 7: Move Write head to flow head position
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+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C
+Search # 9: Drop flow head at start of copy loop
+Inst-Read # 10:
+Inst-Write # 11:
+Head-Push # 12: Get current position of...
+Nop-C # 13: - Read-Head
+If-Equal # 14: Test if we are done copying...
+Divide # 15: ...If so, divide.
+Head-Move # 16: ...If not, continue with loop.
+Nop-A # 17:
+Nop-D
\ No newline at end of file
Deleted: branches/biounit/support/config/misc/Parasites/dominant-org.org
===================================================================
--- branches/parasites/support/config/misc/Parasites/dominant-org.org 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/support/config/misc/Parasites/dominant-org.org 2009-12-16 16:01:42 UTC (rev 3559)
@@ -1,176 +0,0 @@
-# Thu Sep 24 20:03:43 2009
-# Filename........: 155-aabmh
-# Update Output...: N/A
-# Is Viable.......: 1
-# Repro Cycle Size: 0
-# Depth to Viable.: 0
-#
-# Generation: 0
-# Merit...........: 4672.000000
-# Gestation Time..: 996
-# Fitness.........: 4.690763
-# Errors..........: 0
-# Genome Size.....: 155
-# Copied Size.....: 155
-# Executed Size...: 146
-# Offspring.......: SELF
-#
-# Tasks Performed:
-# not 10 (10.000000)
-
-
-Search
-Nop-C
-Nop-B
-Push-Prev
-SetMemory
-Nop-B
-Head-Move
-Nop-C
-Nop-C
-If-Not-Equal
-Val-Inc
-Nop-C
-Push-Comp
-Nop-C
-Val-Nand
-Nop-C
-Val-Add
-If-Equal
-Nop-C
-Inst-Write
-Val-Shift-L
-Val-Sub
-Val-Dec
-Nop-C
-Val-Dec
-If-Less
-Search
-Nop-C
-Val-Mult
-IO
-Nop-B
-Val-Delete
-IO
-Nop-C
-Nop-C
-Val-Div
-Val-Inc
-IO
-If-Equal
-Search
-Nop-C
-Nop-C
-Val-Dec
-Val-Nand
-Nop-C
-Nop-C
-Nop-C
-IO
-Nop-C
-Val-Delete
-Search
-Val-Shift-R
-Push-Comp
-Nop-C
-SetMemory
-Nop-C
-Search
-Val-Copy
-Nop-C
-Push-Comp
-Nop-C
-IO
-IO
-Nop-C
-Val-Mod
-Nop-C
-SetMemory
-Val-Mult
-IO
-Nop-C
-Nop-D
-Search
-Val-Shift-R
-Val-Shift-L
-SetMemory
-Nop-D
-If-Less
-Val-Inc
-If-Not-Equal
-Val-Div
-Val-Nand
-Push-Comp
-Nop-C
-Val-Inc
-Val-Div
-Nop-C
-If-Less
-Val-Shift-L
-Val-Nand
-Nop-C
-Val-Shift-R
-Nop-C
-SetMemory
-Nop-C
-SetMemory
-Val-Inc
-Nop-C
-Inst-Read
-Nop-C
-Nop-C
-Val-Nand
-Nop-C
-If-Less
-Head-Move
-Val-Div
-Nop-C
-If-Less
-Nop-A
-Inst-Write
-Val-Add
-Val-Delete
-Nop-C
-Val-Sub
-Val-Mult
-Search
-Val-Nand
-SetMemory
-IO
-Nop-C
-Nop-D
-Nop-C
-Nop-C
-Val-Sub
-Nop-C
-SetMemory
-Nop-D
-Nop-C
-Nop-C
-If-Greater
-Nop-A
-IO
-Nop-C
-Push-Comp
-Nop-C
-Push-Next
-Nop-C
-Val-Add
-Nop-C
-Search
-Head-Push
-IO
-Nop-B
-Nop-C
-Val-Copy
-Nop-C
-Search
-Inst-Read
-Inst-Write
-Head-Push
-Nop-C
-If-Equal
-Divide
-Head-Move
-Nop-A
-Nop-D
Copied: branches/biounit/support/config/misc/Parasites/dominant-org.org (from rev 3558, branches/parasites/support/config/misc/Parasites/dominant-org.org)
===================================================================
--- branches/biounit/support/config/misc/Parasites/dominant-org.org (rev 0)
+++ branches/biounit/support/config/misc/Parasites/dominant-org.org 2009-12-16 16:01:42 UTC (rev 3559)
@@ -0,0 +1,176 @@
+# Thu Sep 24 20:03:43 2009
+# Filename........: 155-aabmh
+# Update Output...: N/A
+# Is Viable.......: 1
+# Repro Cycle Size: 0
+# Depth to Viable.: 0
+#
+# Generation: 0
+# Merit...........: 4672.000000
+# Gestation Time..: 996
+# Fitness.........: 4.690763
+# Errors..........: 0
+# Genome Size.....: 155
+# Copied Size.....: 155
+# Executed Size...: 146
+# Offspring.......: SELF
+#
+# Tasks Performed:
+# not 10 (10.000000)
+
+
+Search
+Nop-C
+Nop-B
+Push-Prev
+SetMemory
+Nop-B
+Head-Move
+Nop-C
+Nop-C
+If-Not-Equal
+Val-Inc
+Nop-C
+Push-Comp
+Nop-C
+Val-Nand
+Nop-C
+Val-Add
+If-Equal
+Nop-C
+Inst-Write
+Val-Shift-L
+Val-Sub
+Val-Dec
+Nop-C
+Val-Dec
+If-Less
+Search
+Nop-C
+Val-Mult
+IO
+Nop-B
+Val-Delete
+IO
+Nop-C
+Nop-C
+Val-Div
+Val-Inc
+IO
+If-Equal
+Search
+Nop-C
+Nop-C
+Val-Dec
+Val-Nand
+Nop-C
+Nop-C
+Nop-C
+IO
+Nop-C
+Val-Delete
+Search
+Val-Shift-R
+Push-Comp
+Nop-C
+SetMemory
+Nop-C
+Search
+Val-Copy
+Nop-C
+Push-Comp
+Nop-C
+IO
+IO
+Nop-C
+Val-Mod
+Nop-C
+SetMemory
+Val-Mult
+IO
+Nop-C
+Nop-D
+Search
+Val-Shift-R
+Val-Shift-L
+SetMemory
+Nop-D
+If-Less
+Val-Inc
+If-Not-Equal
+Val-Div
+Val-Nand
+Push-Comp
+Nop-C
+Val-Inc
+Val-Div
+Nop-C
+If-Less
+Val-Shift-L
+Val-Nand
+Nop-C
+Val-Shift-R
+Nop-C
+SetMemory
+Nop-C
+SetMemory
+Val-Inc
+Nop-C
+Inst-Read
+Nop-C
+Nop-C
+Val-Nand
+Nop-C
+If-Less
+Head-Move
+Val-Div
+Nop-C
+If-Less
+Nop-A
+Inst-Write
+Val-Add
+Val-Delete
+Nop-C
+Val-Sub
+Val-Mult
+Search
+Val-Nand
+SetMemory
+IO
+Nop-C
+Nop-D
+Nop-C
+Nop-C
+Val-Sub
+Nop-C
+SetMemory
+Nop-D
+Nop-C
+Nop-C
+If-Greater
+Nop-A
+IO
+Nop-C
+Push-Comp
+Nop-C
+Push-Next
+Nop-C
+Val-Add
+Nop-C
+Search
+Head-Push
+IO
+Nop-B
+Nop-C
+Val-Copy
+Nop-C
+Search
+Inst-Read
+Inst-Write
+Head-Push
+Nop-C
+If-Equal
+Divide
+Head-Move
+Nop-A
+Nop-D
Deleted: branches/biounit/support/config/misc/Parasites/environment.cfg
===================================================================
--- branches/parasites/support/config/misc/Parasites/environment.cfg 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/support/config/misc/Parasites/environment.cfg 2009-12-16 16:01:42 UTC (rev 3559)
@@ -1,18 +0,0 @@
-##############################################################################
-#
-# This is the setup file for the task/resource system. From here, you can
-# setup the available resources (including their inflow and outflow rates) as
-# well as the reactions that the organisms can trigger by performing tasks.
-#
-# This file is currently setup to reward 9 tasks, all of which use the
-# "infinite" resource, which is undepletable.
-#
-# For information on how to use this file, see: doc/environment.html
-# For other sample environments, see: source/support/config/
-#
-##############################################################################
-
-
-REACTION NOT not process:value=0.15:type=pow requisite:max_count=10
-#REACTION NAND nand process:value=0.9:type=mult requisite:max_count=10
-
Copied: branches/biounit/support/config/misc/Parasites/environment.cfg (from rev 3558, branches/parasites/support/config/misc/Parasites/environment.cfg)
===================================================================
--- branches/biounit/support/config/misc/Parasites/environment.cfg (rev 0)
+++ branches/biounit/support/config/misc/Parasites/environment.cfg 2009-12-16 16:01:42 UTC (rev 3559)
@@ -0,0 +1,18 @@
+##############################################################################
+#
+# This is the setup file for the task/resource system. From here, you can
+# setup the available resources (including their inflow and outflow rates) as
+# well as the reactions that the organisms can trigger by performing tasks.
+#
+# This file is currently setup to reward 9 tasks, all of which use the
+# "infinite" resource, which is undepletable.
+#
+# For information on how to use this file, see: doc/environment.html
+# For other sample environments, see: source/support/config/
+#
+##############################################################################
+
+
+REACTION NOT not process:value=0.15:type=pow requisite:max_count=10
+#REACTION NAND nand process:value=0.9:type=mult requisite:max_count=10
+
Deleted: branches/biounit/support/config/misc/Parasites/events.cfg
===================================================================
--- branches/parasites/support/config/misc/Parasites/events.cfg 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/support/config/misc/Parasites/events.cfg 2009-12-16 16:01:42 UTC (rev 3559)
@@ -1,56 +0,0 @@
-##############################################################################
-#
-# This is the setup file for the events system. From here, you can
-# configure any actions that you want to have happen during the course of
-# an experiment, including setting the times for data collection.
-#
-# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
-#
-# This file is currently setup to record key information every 100 updates.
-#
-# For information on how to use this file, see: doc/events.html
-# For other sample event configurations, see: support/config/
-#
-##############################################################################
-
-# Print all of the standard data files...
-#u 0 InjectAll dominant-org.org
-#u 20:20 dump_genotype_grid
-u 700 InjectParasite parasite-smt.org ADC 0 400
-
-#i ZeroMuts
-u 0:100:end PrintAverageData # Save info about they average genotypes
-u 0:100:end PrintDominantData # Save info about most abundant genotypes
-u 0:100:end PrintStatsData # Collect satistics about entire pop.
-u 0:100:end PrintParasiteData ParasiteData.dat
-u 0:100:end PrintCountData # Count organisms, genotypes, species, etc.
-u 0:100:end PrintTasksData # Save organisms counts for each task.
-u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
-u 0:100:end PrintResourceData # Track resource abundance.
-
-# A few data files not printed by default
-# u 0:100 PrintDominantGenotype # Save the most abundant genotypes
-# u 100:100:end PrintErrorData # Std. Error on averages.
-# u 100:100:end PrintVarianceData # Variance on averages.
-# u 100:100:end PrintTotalsData # Total counts over entire run.
-# u 100:100:end PrintTasksExeData # Num. times tasks have been executed.
-# u 100:100:end PrintTasksQualData # Task quality information
-
-u 2000 ChangeEnvironment "REACTION NOT not process:value=0.08:type=pow requisite:max_count=10"
-u 4000 ChangeEnvironment "REACTION NOT not process:value=0.15:type=pow requisite:max_count=10"
-u 6000 ChangeEnvironment "REACTION NOT not process:value=0.08:type=pow requisite:max_count=10"
-# Setup the exit time and full population data collection.
-u 5000:5000 SavePopulation # Save current state of population.
-#u 5000:5000 SaveParasitePopulation
-u 5000:5000 SaveHistoricPopulation # Save ancestors of current population.
-u 5000:5000 SaveParasitePopulation
-u 5000 PrintParasiteData
-
-u 5000 PrintDominantGenotype dominant-genotype.50k.dat
-u 5000 PrintDominantParasiteGenotype dominant-parasite.50k.dat
-
-u 10000 PrintDominantGenotype dominant-genotype.dat
-u 10000 PrintDominantParasiteGenotype dominant-parasite.dat
-
-
-u 100000 exit
Copied: branches/biounit/support/config/misc/Parasites/events.cfg (from rev 3558, branches/parasites/support/config/misc/Parasites/events.cfg)
===================================================================
--- branches/biounit/support/config/misc/Parasites/events.cfg (rev 0)
+++ branches/biounit/support/config/misc/Parasites/events.cfg 2009-12-16 16:01:42 UTC (rev 3559)
@@ -0,0 +1,56 @@
+##############################################################################
+#
+# This is the setup file for the events system. From here, you can
+# configure any actions that you want to have happen during the course of
+# an experiment, including setting the times for data collection.
+#
+# basic syntax: [trigger] [start:interval:stop] [action/event] [arguments...]
+#
+# This file is currently setup to record key information every 100 updates.
+#
+# For information on how to use this file, see: doc/events.html
+# For other sample event configurations, see: support/config/
+#
+##############################################################################
+
+# Print all of the standard data files...
+#u 0 InjectAll dominant-org.org
+#u 20:20 dump_genotype_grid
+u 700 InjectParasite parasite-smt.org ADC 0 400
+
+#i ZeroMuts
+u 0:100:end PrintAverageData # Save info about they average genotypes
+u 0:100:end PrintDominantData # Save info about most abundant genotypes
+u 0:100:end PrintStatsData # Collect satistics about entire pop.
+u 0:100:end PrintParasiteData ParasiteData.dat
+u 0:100:end PrintCountData # Count organisms, genotypes, species, etc.
+u 0:100:end PrintTasksData # Save organisms counts for each task.
+u 0:100:end PrintTimeData # Track time conversion (generations, etc.)
+u 0:100:end PrintResourceData # Track resource abundance.
+
+# A few data files not printed by default
+# u 0:100 PrintDominantGenotype # Save the most abundant genotypes
+# u 100:100:end PrintErrorData # Std. Error on averages.
+# u 100:100:end PrintVarianceData # Variance on averages.
+# u 100:100:end PrintTotalsData # Total counts over entire run.
+# u 100:100:end PrintTasksExeData # Num. times tasks have been executed.
+# u 100:100:end PrintTasksQualData # Task quality information
+
+u 2000 ChangeEnvironment "REACTION NOT not process:value=0.08:type=pow requisite:max_count=10"
+u 4000 ChangeEnvironment "REACTION NOT not process:value=0.15:type=pow requisite:max_count=10"
+u 6000 ChangeEnvironment "REACTION NOT not process:value=0.08:type=pow requisite:max_count=10"
+# Setup the exit time and full population data collection.
+u 5000:5000 SavePopulation # Save current state of population.
+#u 5000:5000 SaveParasitePopulation
+u 5000:5000 SaveHistoricPopulation # Save ancestors of current population.
+u 5000:5000 SaveParasitePopulation
+u 5000 PrintParasiteData
+
+u 5000 PrintDominantGenotype dominant-genotype.50k.dat
+u 5000 PrintDominantParasiteGenotype dominant-parasite.50k.dat
+
+u 10000 PrintDominantGenotype dominant-genotype.dat
+u 10000 PrintDominantParasiteGenotype dominant-parasite.dat
+
+
+u 100000 exit
Deleted: branches/biounit/support/config/misc/Parasites/instset-smt.cfg
===================================================================
--- branches/parasites/support/config/misc/Parasites/instset-smt.cfg 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/support/config/misc/Parasites/instset-smt.cfg 2009-12-16 16:01:42 UTC (rev 3559)
@@ -1,50 +0,0 @@
-# Core Instruction Set
-Nop-A 1#1(a)
-Nop-B 1#2 (b)
-Nop-C 1#3 (c)
-Nop-D 1#4 (d)
-Val-Shift-R 1#5 (e)
-Val-Shift-L 1#6 (f)
-Val-Nand 1#7 (g)
-Val-Add 1#8 (h)
-Val-Sub 1#9 (i)
-Val-Mult 1#10 (j)
-Val-Div 1#11 (k)
-Val-Mod 1#12 (l)
-Val-Inc 1#13 (m)
-Val-Dec 1#14 (n)
-SetMemory 1#15 (o)
-Divide 1#16 (p)
-Inst-Read 1#17 (q)
-Inst-Write 1#18 (r)
-If-Equal 1#19 (s)
-If-Not-Equal 1#20 (t)
-If-Less 1#21 (u)
-If-Greater 1#22 (v)
-Head-Push 1#23 (w)
-Head-Pop 1#24 (x)
-Head-Move 1#25 (y)
-Search 1#26 (z)
-Push-Next 1#27 (A)
-Push-Prev 1#28 (B)
-Push-Comp 1#29 (C)
-Val-Delete 1#30 (D)
-Val-Copy 1#31 (E)
-IO 1#32 (F)
-
-# Additional Instructions - Disabled by Default
-Nop-X 0#33 ()
-#Thread-Create 1#34 ()
-#Thread-Cancel 1#35 ()
-#Thread-Kill 1#36 ()
-Inject 0#37 ()
-#Apoptosis 1#38 ()
-#Net-Get 1#39 ()
-#Net-Send 1#40 ()
-#Net-Receive 1#41 ()
-#Net-Last 1#42 ()
-#Rotate-Left 1#43 ()
-#Rotate-Right 1#44 ()
-#Call-Flow 1#45 ()
-#Call-Label 1#46 ()
-#Return 1#47 ()
Copied: branches/biounit/support/config/misc/Parasites/instset-smt.cfg (from rev 3558, branches/parasites/support/config/misc/Parasites/instset-smt.cfg)
===================================================================
--- branches/biounit/support/config/misc/Parasites/instset-smt.cfg (rev 0)
+++ branches/biounit/support/config/misc/Parasites/instset-smt.cfg 2009-12-16 16:01:42 UTC (rev 3559)
@@ -0,0 +1,50 @@
+# Core Instruction Set
+Nop-A 1#1(a)
+Nop-B 1#2 (b)
+Nop-C 1#3 (c)
+Nop-D 1#4 (d)
+Val-Shift-R 1#5 (e)
+Val-Shift-L 1#6 (f)
+Val-Nand 1#7 (g)
+Val-Add 1#8 (h)
+Val-Sub 1#9 (i)
+Val-Mult 1#10 (j)
+Val-Div 1#11 (k)
+Val-Mod 1#12 (l)
+Val-Inc 1#13 (m)
+Val-Dec 1#14 (n)
+SetMemory 1#15 (o)
+Divide 1#16 (p)
+Inst-Read 1#17 (q)
+Inst-Write 1#18 (r)
+If-Equal 1#19 (s)
+If-Not-Equal 1#20 (t)
+If-Less 1#21 (u)
+If-Greater 1#22 (v)
+Head-Push 1#23 (w)
+Head-Pop 1#24 (x)
+Head-Move 1#25 (y)
+Search 1#26 (z)
+Push-Next 1#27 (A)
+Push-Prev 1#28 (B)
+Push-Comp 1#29 (C)
+Val-Delete 1#30 (D)
+Val-Copy 1#31 (E)
+IO 1#32 (F)
+
+# Additional Instructions - Disabled by Default
+Nop-X 0#33 ()
+#Thread-Create 1#34 ()
+#Thread-Cancel 1#35 ()
+#Thread-Kill 1#36 ()
+Inject 0#37 ()
+#Apoptosis 1#38 ()
+#Net-Get 1#39 ()
+#Net-Send 1#40 ()
+#Net-Receive 1#41 ()
+#Net-Last 1#42 ()
+#Rotate-Left 1#43 ()
+#Rotate-Right 1#44 ()
+#Call-Flow 1#45 ()
+#Call-Label 1#46 ()
+#Return 1#47 ()
Deleted: branches/biounit/support/config/misc/Parasites/parasite-smt.org
===================================================================
--- branches/parasites/support/config/misc/Parasites/parasite-smt.org 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/support/config/misc/Parasites/parasite-smt.org 2009-12-16 16:01:42 UTC (rev 3559)
@@ -1,36 +0,0 @@
-Search # 1: Find organism end.
-Nop-C # 2: - Match CD:AB
-Nop-D
-Push-Prev # 5: Move end position to Stack-A
-SetMemory # 6: Place FLOW-head in memory space for offspring
-Nop-D
-Nop-A
-Head-Move # 7: Move Write head to flow head position
-Nop-C # 8:
-Nop-C
-Nop-C # 8:
-Nop-C #IO
-Nop-C # 8:
-Nop-C # 8:
-Nop-C # 8:
-Nop-C #IO
-Nop-C # 8:
-Nop-C
-Nop-C # 8:
-Nop-C #Val-Nand
-Nop-C
-Nop-C # 8:
-Nop-C # 8:
-Nop-C
-Search # 9: Drop flow head at start of copy loop
-Inst-Read # 10:
-Inst-Write # 11:
-Head-Push # 12: Get current position of...
-Nop-C # 13: - Read-Head
-If-Equal # 14: Test if we are done copying...
-Inject
-Nop-D
-Nop-C
-Head-Move # 16: ...If not, continue with loop.
-Nop-A # 17:
-Nop-B
Copied: branches/biounit/support/config/misc/Parasites/parasite-smt.org (from rev 3558, branches/parasites/support/config/misc/Parasites/parasite-smt.org)
===================================================================
--- branches/biounit/support/config/misc/Parasites/parasite-smt.org (rev 0)
+++ branches/biounit/support/config/misc/Parasites/parasite-smt.org 2009-12-16 16:01:42 UTC (rev 3559)
@@ -0,0 +1,36 @@
+Search # 1: Find organism end.
+Nop-C # 2: - Match CD:AB
+Nop-D
+Push-Prev # 5: Move end position to Stack-A
+SetMemory # 6: Place FLOW-head in memory space for offspring
+Nop-D
+Nop-A
+Head-Move # 7: Move Write head to flow head position
+Nop-C # 8:
+Nop-C
+Nop-C # 8:
+Nop-C #IO
+Nop-C # 8:
+Nop-C # 8:
+Nop-C # 8:
+Nop-C #IO
+Nop-C # 8:
+Nop-C
+Nop-C # 8:
+Nop-C #Val-Nand
+Nop-C
+Nop-C # 8:
+Nop-C # 8:
+Nop-C
+Search # 9: Drop flow head at start of copy loop
+Inst-Read # 10:
+Inst-Write # 11:
+Head-Push # 12: Get current position of...
+Nop-C # 13: - Read-Head
+If-Equal # 14: Test if we are done copying...
+Inject
+Nop-D
+Nop-C
+Head-Move # 16: ...If not, continue with loop.
+Nop-A # 17:
+Nop-B
Modified: branches/biounit/tests/default_transsmt_100u/test_list
===================================================================
--- branches/biounit/tests/default_transsmt_100u/test_list 2009-12-16 15:51:37 UTC (rev 3558)
+++ branches/biounit/tests/default_transsmt_100u/test_list 2009-12-16 16:01:42 UTC (rev 3559)
@@ -12,7 +12,7 @@
email = brysonda at egr.msu.edu ; Email address for the test's creator
[consistency]
-enabled = yes ; Is this test a consistency test?
+enabled = no ; Is this test a consistency test?
long = no ; Is this test a long test?
[performance]
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