[Avida-SVN] r2030 - in branches/collect/source: classification cpu main script tools
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Thu Aug 30 12:04:02 PDT 2007
Author: blwalker
Date: 2007-08-30 15:04:02 -0400 (Thu, 30 Aug 2007)
New Revision: 2030
Modified:
branches/collect/source/classification/cGenotypeControl.cc
branches/collect/source/cpu/cHardwareCPU.cc
branches/collect/source/cpu/cHardwareCPU.h
branches/collect/source/cpu/cInstSet.cc
branches/collect/source/cpu/cTestCPU.cc
branches/collect/source/main/cAvidaConfig.h
branches/collect/source/main/cOrganism.cc
branches/collect/source/main/cOrganism.h
branches/collect/source/main/cPopulation.cc
branches/collect/source/main/cPopulationCell.cc
branches/collect/source/main/cPopulationCell.h
branches/collect/source/script/ASTree.cc
branches/collect/source/script/ASTree.h
branches/collect/source/script/cASTDumpVisitor.cc
branches/collect/source/script/cASTDumpVisitor.h
branches/collect/source/script/cASTVisitor.h
branches/collect/source/script/cParser.cc
branches/collect/source/tools/tArray.h
Log:
Porting development r2014:2016, r2017:2019, r2020:2026, and r2027:2028 to collect branch, thus making it current.
Translation: I am done spamming you now. Sorry 'bout that.
Modified: branches/collect/source/classification/cGenotypeControl.cc
===================================================================
--- branches/collect/source/classification/cGenotypeControl.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/classification/cGenotypeControl.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -204,29 +204,22 @@
bool cGenotypeControl::Adjust(cGenotype & in_genotype)
{
- cGenotype * cur_genotype = in_genotype.GetPrev();
+ cGenotype* cur_genotype = in_genotype.GetPrev();
// Check to see if this genotype should be removed completely.
-
- if (in_genotype.GetNumOrganisms() == 0 &&
- in_genotype.GetDeferAdjust() == false) {
+ if (in_genotype.GetNumOrganisms() == 0 && in_genotype.GetDeferAdjust() == false) {
m_world->GetClassificationManager().RemoveGenotype(in_genotype);
return false;
}
// Do not adjust the position of this genotype if it was and still is the
// best genotype, or if it is otherwise in the proper spot...
+ if (CheckPos(in_genotype)) return true;
- if (CheckPos(in_genotype)) {
- return true;
- }
-
// Otherwise, remove it from the queue (for just the moment).
-
Remove(in_genotype);
// If this genotype is the best, put it there.
-
if (in_genotype.GetNumOrganisms() > best->GetNumOrganisms()) {
Insert(in_genotype, best->GetPrev());
best = &in_genotype;
Modified: branches/collect/source/cpu/cHardwareCPU.cc
===================================================================
--- branches/collect/source/cpu/cHardwareCPU.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/cpu/cHardwareCPU.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -355,9 +355,10 @@
tInstLibEntry<tMethod>("time", &cHardwareCPU::Inst_GetUpdate),
// Promoter Model
+ tInstLibEntry<tMethod>("promoter", &cHardwareCPU::Inst_Promoter),
tInstLibEntry<tMethod>("terminate", &cHardwareCPU::Inst_Terminate),
- tInstLibEntry<tMethod>("promoter", &cHardwareCPU::Inst_Promoter),
tInstLibEntry<tMethod>("regulate", &cHardwareCPU::Inst_Regulate),
+ tInstLibEntry<tMethod>("numberate", &cHardwareCPU::Inst_Numberate),
// Energy usage
tInstLibEntry<tMethod>("double-energy-usage", &cHardwareCPU::Inst_DoubleEnergyUsage),
@@ -466,20 +467,22 @@
}
#endif
+ // Promoter model
if (m_world->GetConfig().PROMOTERS_ENABLED.Get())
{
// Ideally, this shouldn't be hard-coded
cInstruction promoter_inst = m_world->GetHardwareManager().GetInstSet().GetInst(cStringUtil::Stringf("promoter"));
- promoter_search_pos = 0;
- promoter_inst_executed = 0;
- promoter_pos.Resize(0);
- promoter_active.Resize(0);
+
+ m_promoter_index = -1; // Meaning the last promoter was nothing
+ m_promoter_offset = 0;
+ m_promoter_regulation = 0;
+ m_promoters.Resize(0);
for (int i=0; i<GetMemory().GetSize(); i++)
{
if ( (GetMemory())[i] == promoter_inst)
{
- promoter_pos.Push(i);
- promoter_active.Push(true);
+ int code = Numberate(i-1, -1);
+ m_promoters.Push( cPromoter(i,code) );
}
}
}
@@ -505,27 +508,27 @@
cur_head = nHardware::HEAD_IP;
read_label.Clear();
next_label.Clear();
+
+ // Promoter model
+ m_promoter_inst_executed = 0;
}
-
-
// This function processes the very next command in the genome, and is made
// to be as optimized as possible. This is the heart of avida.
void cHardwareCPU::SingleProcess(cAvidaContext& ctx)
{
int last_IP_pos = IP().GetPosition();
-
+
// Mark this organism as running...
organism->SetRunning(true);
+ cPhenotype& phenotype = organism->GetPhenotype();
- cPhenotype & phenotype = organism->GetPhenotype();
+ // First instruction - check whether we should be starting at a promoter, when enabled.
+ if (phenotype.GetCPUCyclesUsed() == 0 && m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1)
+ Inst_Terminate(m_world->GetDefaultContext());
- if (m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1) {
- //First instruction - check whether we should be starting at a promoter.
- if (phenotype.GetCPUCyclesUsed() == 0) Inst_Terminate(m_world->GetDefaultContext());
- }
-
+ // Count the cpu cycles used
phenotype.IncCPUCyclesUsed();
if (!m_world->GetConfig().NO_CPU_CYCLE_TIME.Get()) phenotype.IncTimeUsed();
@@ -557,6 +560,14 @@
// Test if costs have been paid and it is okay to execute this now...
bool exec = SingleProcess_PayCosts(ctx, cur_inst);
+ // If there are no active promoters and a certain mode is set, then don't execute any further instructions
+ if ((m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1)
+ && (m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 2)
+ && (m_promoter_index == -1) )
+ {
+ exec = false;
+ }
+
// Now execute the instruction...
if (exec == true) {
// NOTE: This call based on the cur_inst must occur prior to instruction
@@ -571,7 +582,7 @@
//Add to the promoter inst executed count before executing the inst (in case it is a terminator)
if (m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1) {
- promoter_inst_executed++;
+ m_threads[m_cur_thread].IncPromoterInstExecuted();
}
if (exec == true) SingleProcess_ExecuteInst(ctx, cur_inst);
@@ -582,29 +593,19 @@
// Pay the time cost of the instruction now
phenotype.IncTimeUsed(time_cost);
-
- // In the promoter model, there may be a chance of termination
- // that causes execution to start at a new instruction (per instruction executed)
- if ( m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1 ) {
- const double processivity = m_world->GetConfig().PROMOTER_PROCESSIVITY_INST.Get();
- if ( ctx.GetRandom().P(1-processivity) ) Inst_Terminate(ctx);
+
+ // In the promoter model, we may force termination after a certain number of inst have been executed
+ if ( m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1 )
+ {
+ const double processivity = m_world->GetConfig().PROMOTER_PROCESSIVITY.Get();
+ if ( ctx.GetRandom().P(1-processivity) )
+ Inst_Terminate(ctx);
+ if ( m_world->GetConfig().PROMOTER_INST_MAX.Get() && (m_threads[m_cur_thread].GetPromoterInstExecuted() >= m_world->GetConfig().PROMOTER_INST_MAX.Get()) )
+ Inst_Terminate(ctx);
}
-
+
} // if exec
-
- // In the promoter model, there may be a chance of termination
- // that causes execution to start at a new instruction (per cpu cycle executed)
- // @JEB - since processivities usually v. close to 1 it doesn't
- // improve speed much to combine with "per instruction" block
- if ( m_world->GetConfig().PROMOTERS_ENABLED.Get() == 1 )
- {
- const double processivity = m_world->GetConfig().PROMOTER_PROCESSIVITY.Get();
- if ( ctx.GetRandom().P(1-processivity) )
- Inst_Terminate(ctx);
- if ( m_world->GetConfig().PROMOTER_MAX_INST.Get() && (promoter_inst_executed >= m_world->GetConfig().PROMOTER_MAX_INST.Get()) )
- Inst_Terminate(ctx);
- }
-
+
} // Previous was executed once for each thread...
// Kill creatures who have reached their max num of instructions executed
@@ -723,13 +724,16 @@
if (m_world->GetConfig().PROMOTERS_ENABLED.Get())
{
- fp << "Promoters:";
- for (int i=0; i<promoter_pos.GetSize(); i++)
+ fp << "Promoters: index=" << m_promoter_index << " offset=" << m_promoter_offset;
+ fp << " exe_inst=" << m_threads[m_cur_thread].GetPromoterInstExecuted();
+ fp << " regulation=0x" << setbase(16) << setfill('0') << setw(8) << m_promoter_regulation << endl;
+ for (int i=0; i<m_promoters.GetSize(); i++)
{
- fp << " " << promoter_pos[i] << "-" << (promoter_active[i] ? "on" : "off");
+ fp << setfill(' ') << setbase(10) << i << "(" << m_promoters[i].m_pos << "):";
+ fp << "Ox" << setbase(16) << setfill('0') << setw(8) << (m_promoters[i].m_bit_code ^ m_promoter_regulation) << " ";
}
- fp << endl;
- fp << "Instructions executed past promoter: " << promoter_inst_executed << endl;
+ fp << endl;
+ fp << setfill(' ') << setbase(10) << endl;
}
fp.flush();
}
@@ -4371,56 +4375,188 @@
return true;
}
-// Move execution to a new promoter
+// Move the instruction ptr to the next active promoter
bool cHardwareCPU::Inst_Terminate(cAvidaContext& ctx)
{
- // Reset the CPU, clearing everything except R/W head positions.
- const int write_head_pos = GetHead(nHardware::HEAD_WRITE).GetPosition();
- const int read_head_pos = GetHead(nHardware::HEAD_READ).GetPosition();
- m_threads[m_cur_thread].Reset(this, m_threads[m_cur_thread].GetID());
- GetHead(nHardware::HEAD_WRITE).Set(write_head_pos);
- GetHead(nHardware::HEAD_READ).Set(read_head_pos);
+ // Optionally,
+ // Reset the thread.
+ if (m_world->GetConfig().TERMINATION_RESETS.Get())
+ {
+ //const int write_head_pos = GetHead(nHardware::HEAD_WRITE).GetPosition();
+ //const int read_head_pos = GetHead(nHardware::HEAD_READ).GetPosition();
+ m_threads[m_cur_thread].Reset(this, m_threads[m_cur_thread].GetID());
+ //GetHead(nHardware::HEAD_WRITE).Set(write_head_pos);
+ //GetHead(nHardware::HEAD_READ).Set(read_head_pos);
+
+ //Setting this makes it harder to do things. You have to be modular.
+ organism->GetOrgInterface().ResetInputs(ctx); // Re-randomize the inputs this organism sees
+ organism->ClearInput(); // Also clear their input buffers, or they can still claim
+ // rewards for numbers no longer in their environment!
+ }
+
+ // Reset our count
+ m_threads[m_cur_thread].ResetPromoterInstExecuted();
+ m_advance_ip = false;
+ const int reg_used = REG_BX; // register to put chosen promoter code in, for now always BX
- // We want to execute the promoter that we land on.
- promoter_inst_executed = 0;
- m_advance_ip = false;
+ // Search for an active promoter
+ int start_offset = m_promoter_offset;
+ int start_index = m_promoter_index;
- //Setting this makes it harder to do things. You have to be modular.
- organism->GetOrgInterface().ResetInputs(ctx); // Re-randomize the inputs this organism sees
- organism->ClearInput(); // Also clear their input buffers, or they can still claim
- // rewards for numbers no longer in their environment!
-
- // Find the next active promoter
- int started_search_pos = promoter_search_pos;
-
- while (promoter_pos.GetSize() > 0) // conditional infinite loop, breaks out
+ bool no_promoter_found = true;
+ if ( m_promoters.GetSize() > 0 )
{
- promoter_search_pos++;
- promoter_search_pos %= promoter_active.GetSize();
- if (promoter_active[promoter_search_pos]) break;
- if (started_search_pos == promoter_search_pos) break;
- }
+ while( true )
+ {
+ // If the next promoter is active, then break out
+ NextPromoter();
+ if (IsActivePromoter())
+ {
+ no_promoter_found = false;
+ break;
+ }
+
+ // If we just checked the promoter that we were originally on, then there
+ // are no active promoters.
+ if ( (start_offset == m_promoter_offset) && (start_index == m_promoter_index) ) break;
+
+ // If we originally were not on a promoter, then stop once we check the
+ // first promoter and an offset of zero
+ if (start_index == -1)
+ {
+ start_index = 0;
+ }
+ }
+ }
- //Can't find a promoter -- start at the beginning of the genome (or die! or sleep!)
- if ((promoter_pos.GetSize() == 0) || ((promoter_search_pos == started_search_pos) && (!promoter_active[promoter_search_pos])))
+ if (no_promoter_found)
{
- IP().Set(0);
+ if ((m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 0) || (m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 2))
+ {
+ // Set defaults for when no active promoter is found
+ m_promoter_index = -1;
+ IP().Set(0);
+ GetRegister(reg_used) = 0;
+
+ // @JEB HACK! -- All kinds of bad stuff happens if execution length is zero. For now:
+ if (m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 2) GetMemory().SetFlagExecuted(0);
+ }
+ // Death to organisms that refuse to use promoters!
+ else if (m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() == 1)
+ {
+ organism->Die();
+ }
+ else
+ {
+ cout << "Unrecognized NO_ACTIVE_PROMOTER_EFFECT setting: " << m_world->GetConfig().NO_ACTIVE_PROMOTER_EFFECT.Get() << endl;
+ }
}
else
{
- IP().Set(promoter_pos[promoter_search_pos]);
+ // We found an active match, offset to just after it.
+ // and put its bit code in BX for the organism to have
+ // cHeadCPU will do the mod genome size for us
+ IP().Set(m_promoters[m_promoter_index].m_pos + 1);
+ GetRegister(reg_used) = m_promoters[m_promoter_index].m_bit_code;
}
-
return true;
}
-// To be implemented...
+// Get a new regulation code (which is XOR'ed with promoter codes).
bool cHardwareCPU::Inst_Regulate(cAvidaContext& ctx)
{
+ const int reg_used = FindModifiedRegister(REG_BX);
+ m_promoter_regulation = GetRegister(reg_used);
return true;
}
+// Create a number from inst bit codes
+bool cHardwareCPU::Inst_Numberate(cAvidaContext& ctx)
+{
+ const int reg_used = FindModifiedRegister(REG_BX);
+
+ // advance the IP now, so that it rests on the beginning of our number
+ IP().Advance();
+ m_advance_ip = false;
+
+ int num = Numberate(IP().GetPosition(), +1);
+ GetRegister(reg_used) = num;
+ return true;
+}
+// Move to the next promoter.
+void cHardwareCPU::NextPromoter()
+{
+ // Move promoter index, rolling over if necessary
+ m_promoter_index++;
+ if (m_promoter_index == m_promoters.GetSize())
+ {
+ m_promoter_index = 0;
+
+ // Move offset, rolling over when there are not enough bits before we would have to wrap around left
+ m_promoter_offset+=m_world->GetConfig().PROMOTER_EXE_LENGTH.Get();
+ if (m_promoter_offset + m_world->GetConfig().PROMOTER_EXE_LENGTH.Get() >= cHardwareCPU::PROMOTER_CODE_SIZE)
+ {
+ m_promoter_offset = 0;
+ }
+ }
+}
+
+
+// Check whether the current promoter is active.
+bool cHardwareCPU::IsActivePromoter()
+{
+ assert( m_promoters.GetSize() != 0 );
+ int count = 0;
+ unsigned int code = m_promoters[m_promoter_index].m_bit_code ^ m_promoter_regulation;
+ for(int i=0; i<m_world->GetConfig().PROMOTER_EXE_LENGTH.Get(); i++)
+ {
+ int offset = m_promoter_offset + i;
+ offset %= cHardwareCPU::PROMOTER_CODE_SIZE;
+ int state = code >> offset;
+ count += (state & 1);
+ }
+
+ return (count >= m_world->GetConfig().PROMOTER_EXE_THRESHOLD.Get());
+}
+
+// Construct a promoter bit code from instruction bit codes
+int cHardwareCPU::Numberate(int _pos, int _dir)
+{
+ int code_size = 0;
+ unsigned int code = 0;
+ int j = _pos;
+ j %= GetMemory().GetSize();
+ while (code_size < cHardwareCPU::PROMOTER_CODE_SIZE)
+ {
+ unsigned int inst_code = (unsigned int) GetInstSet().GetInstructionCode( (GetMemory())[j] );
+ // shift bits in, one by one ... excuse the counter pun
+ for (int code_on = 0; (code_size < cHardwareCPU::PROMOTER_CODE_SIZE) && (code_on < m_world->GetConfig().INST_CODE_LENGTH.Get()); code_on++)
+ {
+ if (_dir < 0)
+ {
+ code >>= 1; // shift first so we don't go one too far at the end
+ code += (1 << (cHardwareCPU::PROMOTER_CODE_SIZE - 1)) * (inst_code & 1);
+ inst_code >>= 1;
+ }
+ else
+ {
+ code <<= 1; // shift first so we don't go one too far at the end;
+ code += (inst_code >> (m_world->GetConfig().INST_CODE_LENGTH.Get() - 1)) & 1;
+ inst_code <<= 1;
+ }
+ code_size++;
+ }
+
+ // move back one inst
+ j += GetMemory().GetSize() + _dir;
+ j %= GetMemory().GetSize();
+
+ }
+ return code;
+}
+
+
/*! Send a message to the organism that is currently faced by this cell,
where the label field of sent message is from register ?BX?, and the data field
is from register ~?BX?.
@@ -4436,7 +4572,6 @@
return organism->SendMessage(ctx, msg);
}
-
/*! This method /attempts/ to retrieve a message -- It may not be possible, as in
the case of an empty receive buffer.
@@ -4457,7 +4592,6 @@
return true;
}
-
//// Placebo insts ////
bool cHardwareCPU::Inst_Skip(cAvidaContext& ctx)
{
Modified: branches/collect/source/cpu/cHardwareCPU.h
===================================================================
--- branches/collect/source/cpu/cHardwareCPU.h 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/cpu/cHardwareCPU.h 2007-08-30 19:04:02 UTC (rev 2030)
@@ -89,13 +89,14 @@
static const int NUM_HEADS = nHardware::NUM_HEADS >= NUM_REGISTERS ? nHardware::NUM_HEADS : NUM_REGISTERS;
enum tRegisters { REG_AX = 0, REG_BX, REG_CX, REG_DX, REG_EX, REG_FX };
static const int NUM_NOPS = 3;
+ static const int PROMOTER_CODE_SIZE = sizeof(int) * 8; // Number of bits in promoter codes
// -------- Data Structures --------
struct cLocalThread
{
private:
int m_id;
-
+ int m_promoter_inst_executed;
public:
int reg[NUM_REGISTERS];
cHeadCPU heads[NUM_HEADS];
@@ -115,6 +116,9 @@
void Reset(cHardwareBase* in_hardware, int in_id);
int GetID() const { return m_id; }
void SetID(int in_id) { m_id = in_id; }
+ int GetPromoterInstExecuted() { return m_promoter_inst_executed; }
+ void IncPromoterInstExecuted() { m_promoter_inst_executed++; }
+ void ResetPromoterInstExecuted() { m_promoter_inst_executed = 0; }
};
@@ -137,13 +141,24 @@
bool m_mal_active; // Has an allocate occured since last divide?
bool m_advance_ip; // Should the IP advance after this instruction?
bool m_executedmatchstrings; // Have we already executed the match strings instruction?
+
+ // <-- Promoter model
+ int m_promoter_index; //site to begin looking for the next active promoter from
+ int m_promoter_offset; //bit offset when testing whether a promoter is on
+ int m_promoter_regulation; //bit code that modifies current execution, via an XOR
- // Promoter model
- int promoter_search_pos; //site to begin looking for the next active promoter from
- int promoter_inst_executed; //num inst executed since last termination
- tArray<int> promoter_pos; //positions with promoter instructions
- tArray<bool> promoter_active; //whether each promoter is active (same size as promoter_pos)
-
+ struct cPromoter
+ {
+ public:
+ int m_pos; //position within genome
+ int m_bit_code; //bit code of promoter
+ public:
+ cPromoter(int _pos = 0, int _bit_code = 0) { m_pos = _pos; m_bit_code = _bit_code; }
+ ~cPromoter() { ; }
+ };
+ tArray<cPromoter> m_promoters;
+ // Promoter Model -->
+
bool SingleProcess_ExecuteInst(cAvidaContext& ctx, const cInstruction& cur_inst);
// -------- Stack Manipulation... --------
@@ -536,7 +551,13 @@
bool Inst_Promoter(cAvidaContext& ctx);
bool Inst_Terminate(cAvidaContext& ctx);
bool Inst_Regulate(cAvidaContext& ctx);
+ bool Inst_Numberate(cAvidaContext& ctx);
+ // Helper functions //
+ bool IsActivePromoter();
+ void NextPromoter();
+ int Numberate(int _pos, int _dir);
+
//// Messaging ////
bool Inst_SendMessage(cAvidaContext& ctx);
bool Inst_RetrieveMessage(cAvidaContext& ctx);
Modified: branches/collect/source/cpu/cInstSet.cc
===================================================================
--- branches/collect/source/cpu/cInstSet.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/cpu/cInstSet.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -249,12 +249,11 @@
break;
}
} else {
- const int iclidx = inst_code.GetSize() - 1;
int inst_code_val = 0;
- for (int i = 0; i < inst_code_len && i <= iclidx; i++) {
+ for (int i = 0; i < inst_code_len && i < inst_code.GetSize(); i++) {
inst_code_val <<= 1;
- if (inst_code[iclidx - i] == '1') inst_code_val |= 1;
- else if (inst_code[iclidx - i] != '0') {
+ if (inst_code[i] == '1') inst_code_val |= 1;
+ else if (inst_code[i] != '0') {
errors.PushRear(new cString("Invalid character in instruction code, must be 0 or 1."));
success = false;
break;
Modified: branches/collect/source/cpu/cTestCPU.cc
===================================================================
--- branches/collect/source/cpu/cTestCPU.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/cpu/cTestCPU.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -221,7 +221,7 @@
organism.GetHardware().SetTrace(tracer);
while (time_used < time_allocated && organism.GetHardware().GetMemory().GetSize() &&
- organism.GetPhenotype().GetNumDivides() == 0)
+ organism.GetPhenotype().GetNumDivides() == 0 && !organism.IsDead())
{
time_used++;
Modified: branches/collect/source/main/cAvidaConfig.h
===================================================================
--- branches/collect/source/main/cAvidaConfig.h 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/main/cAvidaConfig.h 2007-08-30 19:04:02 UTC (rev 2030)
@@ -474,14 +474,15 @@
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_MAX_INST, int, 20, "Maximum number of instructions to execute before terminating.");
+ CONFIG_ADD_VAR(PROMOTER_INST_MAX, int, 0, "Maximum number of instructions to execute before terminating. 0 = off");
CONFIG_ADD_VAR(PROMOTER_PROCESSIVITY, double, 1.0, "Chance of not terminating after each cpu cycle.");
CONFIG_ADD_VAR(PROMOTER_PROCESSIVITY_INST, double, 1.0, "Chance of not terminating after each instruction.");
- CONFIG_ADD_VAR(PROMOTER_BG_STRENGTH, double, 0, "Probability of positions that are not promoter\ninstructions initiating execution (promoters are 1).");
- CONFIG_ADD_VAR(REGULATION_STRENGTH, double, 1, "Strength added or subtracted to a promoter by regulation.");
- CONFIG_ADD_VAR(REGULATION_DECAY_FRAC, double, 0.1, "Fraction of regulation that decays away. \nMax regulation = 2^(REGULATION_STRENGTH/REGULATION_DECAY_FRAC)");
+ CONFIG_ADD_VAR(TERMINATION_RESETS, int, 0, "Does termination reset the thread's state?");
+ CONFIG_ADD_VAR(NO_ACTIVE_PROMOTER_EFFECT, int, 0, "What happens when there are no active promoters?\n0 = Start execution at the beginning of the genome.\n1 = Kill the organism.\n2 = Stop the organism from executing any further instructions.");
+ CONFIG_ADD_VAR(PROMOTER_EXE_LENGTH, int, 4, "Length of promoter windows used to determine execution.");
+ CONFIG_ADD_VAR(PROMOTER_EXE_THRESHOLD, int, 3, "Minimum number of bits that must be set in a promoter window to allow execution.");
CONFIG_ADD_VAR(INST_CODE_LENGTH, int, 4, "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 of the instruction number");
+ 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_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.");
Modified: branches/collect/source/main/cOrganism.cc
===================================================================
--- branches/collect/source/main/cOrganism.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/main/cOrganism.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -70,6 +70,7 @@
, m_max_executed(-1)
, m_is_running(false)
, m_is_sleeping(false)
+ , m_is_dead(false)
, m_net(NULL)
, m_msg(0)
{
Modified: branches/collect/source/main/cOrganism.h
===================================================================
--- branches/collect/source/main/cOrganism.h 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/main/cOrganism.h 2007-08-30 19:04:02 UTC (rev 2030)
@@ -123,6 +123,7 @@
int m_max_executed; // Max number of instruction executed before death.
bool m_is_running; // Does this organism have the CPU?
bool m_is_sleeping; // Is this organisms sleeping?
+ bool m_is_dead; // Is this organism dead?
class cNetSupport
{
@@ -190,6 +191,7 @@
void SetSleeping(bool in_sleeping) { m_is_sleeping = in_sleeping; }
bool IsSleeping() { return m_is_sleeping; }
+ bool IsDead() { return m_is_dead; }
// -------- cOrgInterface Methods --------
cHardwareBase& GetHardware() { return *m_hardware; }
@@ -202,7 +204,7 @@
int GetNextInput(int& in_input_pointer) { return m_interface->GetInputAt(in_input_pointer); } //@JEB alternate for GX
tBuffer<int>& GetInputBuf() { return m_input_buf; }
tBuffer<int>& GetOutputBuf() { return m_output_buf; }
- void Die() { m_interface->Die(); }
+ void Die() { m_interface->Die(); m_is_dead = true; }
void Kaboom(int dist) { m_interface->Kaboom(dist);}
void SpawnDeme() { m_interface->SpawnDeme(); }
int GetCellID() { return m_interface->GetCellID(); }
Modified: branches/collect/source/main/cPopulation.cc
===================================================================
--- branches/collect/source/main/cPopulation.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/main/cPopulation.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -2040,7 +2040,7 @@
cPopulationCell& cell = GetCell(cell_id);
assert(cell.IsOccupied()); // Unoccupied cell getting processor time!
cOrganism* cur_org = cell.GetOrganism();
- cur_org->GetHardware().SingleProcess(ctx);
+ cell.GetHardware()->SingleProcess(ctx);
if (cur_org->GetPhenotype().GetToDelete() == true) {
delete cur_org;
}
Modified: branches/collect/source/main/cPopulationCell.cc
===================================================================
--- branches/collect/source/main/cPopulationCell.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/main/cPopulationCell.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -40,6 +40,7 @@
cPopulationCell::cPopulationCell(const cPopulationCell& in_cell)
: m_world(in_cell.m_world)
, m_organism(in_cell.m_organism)
+ , m_hardware(in_cell.m_hardware)
, m_inputs(in_cell.m_inputs)
, m_cell_id(in_cell.m_cell_id)
, m_deme_id(in_cell.m_deme_id)
@@ -58,6 +59,7 @@
{
m_world = in_cell.m_world;
m_organism = in_cell.m_organism;
+ m_hardware = in_cell.m_hardware;
m_inputs = in_cell.m_inputs;
m_cell_id = in_cell.m_cell_id;
m_deme_id = in_cell.m_deme_id;
@@ -164,6 +166,7 @@
// Adjust this cell's attributes to account for the new organism.
m_organism = new_org;
+ m_hardware = &new_org->GetHardware();
m_organism_count++;
// Adjust the organism's attributes to match this cell.
@@ -191,6 +194,7 @@
m_world->GetPopulation().GetDeme(m_deme_id).GiveBackCellEnergy(m_cell_id, m_organism->GetPhenotype().GetStoredEnergy() * m_world->GetConfig().FRAC_ENERGY_TRANSFER.Get());
}
m_organism = NULL;
+ m_hardware = NULL;
return out_organism;
}
Modified: branches/collect/source/main/cPopulationCell.h
===================================================================
--- branches/collect/source/main/cPopulationCell.h 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/main/cPopulationCell.h 2007-08-30 19:04:02 UTC (rev 2030)
@@ -38,6 +38,7 @@
#include "tList.h"
#endif
+class cHardwareBase;
class cPopulation;
class cOrganism;
class cPopulationCell;
@@ -50,6 +51,7 @@
private:
cWorld* m_world;
cOrganism* m_organism; // The occupent of this cell.
+ cHardwareBase* m_hardware;
tList<cPopulationCell> m_connections; // A list of neighboring cells.
cMutationRates* m_mut_rates; // Mutation rates at this cell.
tArray<int> m_inputs; // Environmental Inputs...
@@ -68,7 +70,7 @@
public:
- cPopulationCell() : m_world(NULL), m_organism(NULL), m_mut_rates(NULL), m_organism_count(0) { ; }
+ cPopulationCell() : m_world(NULL), m_organism(NULL), m_hardware(NULL), m_mut_rates(NULL), m_organism_count(0) { ; }
cPopulationCell(const cPopulationCell& in_cell);
~cPopulationCell() { delete m_mut_rates; }
@@ -79,6 +81,7 @@
void Rotate(cPopulationCell& new_facing);
inline cOrganism* GetOrganism() const { return m_organism; }
+ inline cHardwareBase* GetHardware() const { return m_hardware; }
inline tList<cPopulationCell>& ConnectionList() { return m_connections; }
inline cPopulationCell& GetCellFaced() { return *(m_connections.GetFirst()); }
int GetFacing(); // Returns the facing of this cell.
Modified: branches/collect/source/script/ASTree.cc
===================================================================
--- branches/collect/source/script/ASTree.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/script/ASTree.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -48,6 +48,7 @@
void cASTLiteral::Accept(cASTVisitor& visitor) { visitor.visitLiteral(*this); }
void cASTLiteralArray::Accept(cASTVisitor& visitor) { visitor.visitLiteralArray(*this); }
void cASTVariableReference::Accept(cASTVisitor& visitor) { visitor.visitVariableReference(*this); }
+void cASTUnpackTarget::Accept(cASTVisitor& visitor) { visitor.visitUnpackTarget(*this); }
cASTStatementList::~cASTStatementList()
Modified: branches/collect/source/script/ASTree.h
===================================================================
--- branches/collect/source/script/ASTree.h 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/script/ASTree.h 2007-08-30 19:04:02 UTC (rev 2030)
@@ -37,6 +37,9 @@
#ifndef tList_h
#include "tList.h"
#endif
+#ifndef tManagedPointerArray_h
+#include "tManagedPointerArray.h"
+#endif
class cASTVisitor;
@@ -88,6 +91,7 @@
class cASTLiteral;
class cASTLiteralArray;
class cASTVariableReference;
+class cASTUnpackTarget;
@@ -436,4 +440,33 @@
};
+class cASTUnpackTarget : public cASTNode
+{
+private:
+ tManagedPointerArray<cString> m_nodes;
+ bool m_last_wild;
+ bool m_last_named;
+ cASTNode* m_expr;
+
+public:
+ cASTUnpackTarget() : m_last_wild(false), m_last_named(false), m_expr(NULL) { ; }
+ ~cASTUnpackTarget() { delete m_expr; }
+
+ inline void AddVar(const cString& name) { m_nodes.Push(name); }
+ inline int GetSize() const { return m_nodes.GetSize(); }
+ inline const cString& GetVar(int idx) const { return m_nodes[idx]; }
+
+ inline bool IsLastNamed() const { return m_last_named; }
+ inline bool IsLastWild() const { return m_last_wild; }
+
+ inline void SetLastNamed() { m_last_wild = true; m_last_named = true; }
+ inline void SetLastWild() { m_last_wild = true; m_last_named = false; }
+
+ cASTNode* GetExpression() const { return m_expr; }
+ void SetExpression(cASTNode* expr) { delete m_expr; m_expr = expr; }
+
+ void Accept(cASTVisitor& visitor);
+};
+
+
#endif
Modified: branches/collect/source/script/cASTDumpVisitor.cc
===================================================================
--- branches/collect/source/script/cASTDumpVisitor.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/script/cASTDumpVisitor.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -384,3 +384,42 @@
indent();
cout << node.GetName() << endl;
}
+
+
+void cASTDumpVisitor::visitUnpackTarget(cASTUnpackTarget& node)
+{
+ m_depth++;
+
+ // Array unpack portion
+ indent();
+ cout << "@{";
+ m_depth++;
+
+ for (int i = 0; i < node.GetSize(); i++) {
+ cout << endl;
+ indent();
+ cout << node.GetVar(i);
+ }
+ if (node.IsLastNamed()) {
+ cout << "..";
+ } else if (node.IsLastWild()) {
+ cout << endl;
+ indent();
+ cout << "..";
+ }
+ cout << endl;
+ m_depth--;
+ indent();
+ cout << "}" << endl;
+
+ // Equals
+ m_depth--;
+ indent();
+ cout << "=" << endl;
+ m_depth++;
+
+ // Expression portion
+ node.GetExpression()->Accept(*this);
+
+ m_depth--;
+}
Modified: branches/collect/source/script/cASTDumpVisitor.h
===================================================================
--- branches/collect/source/script/cASTDumpVisitor.h 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/script/cASTDumpVisitor.h 2007-08-30 19:04:02 UTC (rev 2030)
@@ -59,6 +59,7 @@
void visitLiteral(cASTLiteral&);
void visitLiteralArray(cASTLiteralArray&);
void visitVariableReference(cASTVariableReference&);
+ void visitUnpackTarget(cASTUnpackTarget&);
private:
inline void indent();
Modified: branches/collect/source/script/cASTVisitor.h
===================================================================
--- branches/collect/source/script/cASTVisitor.h 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/script/cASTVisitor.h 2007-08-30 19:04:02 UTC (rev 2030)
@@ -58,6 +58,7 @@
virtual void visitLiteral(cASTLiteral&) = 0;
virtual void visitLiteralArray(cASTLiteralArray&) = 0;
virtual void visitVariableReference(cASTVariableReference&) = 0;
+ virtual void visitUnpackTarget(cASTUnpackTarget&) = 0;
};
#endif
Modified: branches/collect/source/script/cParser.cc
===================================================================
--- branches/collect/source/script/cParser.cc 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/script/cParser.cc 2007-08-30 19:04:02 UTC (rev 2030)
@@ -265,31 +265,40 @@
cASTNode* cParser::parseArrayUnpack()
{
PARSE_TRACE("parseArrayUnpack");
- cASTNode* au = NULL;
- // @todo - array unpack
-
if (nextToken() != TOKEN(ID)) PARSE_UNEXPECT();
+
+ tAutoRelease<cASTUnpackTarget> ut(new cASTUnpackTarget());
+ (*ut).AddVar(currentText());
while (nextToken()) {
if (currentToken() == TOKEN(COMMA)) {
nextToken();
if (currentToken() == TOKEN(ID)) {
+ (*ut).AddVar(currentText());
continue;
} else if (currentToken() == TOKEN(ARR_WILD)) {
+ (*ut).SetLastWild();
break;
} else {
PARSE_ERROR(UNEXPECTED_TOKEN);
break;
}
} else if (currentToken() == TOKEN(ARR_WILD)) {
+ (*ut).SetLastNamed();
break;
} else {
PARSE_UNEXPECT();
}
}
+
+ if (nextToken() != TOKEN(ARR_CLOSE)) PARSE_UNEXPECT();
+ if (nextToken() != TOKEN(ASSIGN)) PARSE_UNEXPECT();
+ nextToken(); // consume '='
+
+ (*ut).SetExpression(parseExpression());
- return au;
+ return ut.Release();
}
cASTArgumentList* cParser::parseArgumentList()
Modified: branches/collect/source/tools/tArray.h
===================================================================
--- branches/collect/source/tools/tArray.h 2007-08-30 18:26:42 UTC (rev 2029)
+++ branches/collect/source/tools/tArray.h 2007-08-30 19:04:02 UTC (rev 2030)
@@ -83,15 +83,15 @@
return tmp;
}
- tArray Subset(int start, int end) {
+ inline tArray Subset(int start, int end) const {
assert(start <= end);
assert(0 <= start && start <= GetSize());
assert(0 <= end && end <= GetSize());
- tArray tmp(0);
- for(int i = start; i < end; i++) {
- tmp.Push(m_data[i]);
- }
+ const int new_size = end - start;
+ tArray tmp(end - start);
+ for(int i = 0; i < new_size; i++) tmp[i] = m_data[i + start];
+
return tmp;
}
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