Janady13/complete-agi-core / mind_farm/include/dna_unified.hpp

1// DNA Mathematical Architecture: Unified System 2// Complete G¹⁶ Helix Integration — 44 Bonds — 10.6 Periodicity 3// Master header combining all DNA subsystems 4#pragma once 5 6#include "dna_helix.hpp" 7#include "dna_dynamics.hpp" 8#include "dna_eigenvalues.hpp" 9#include <string> 10#include <map> 11 12namespace agi::dna { 13 14// ============================================================================ 15// XIII. 16 DNA FAMILIES - C++ Implementation 16// ============================================================================ 17 18struct DNAFamily { 19 int strand; 20 std::string name; 21 std::string domain; 22 int node_start; 23 int node_end; 24 double phase; 25 std::function<double(double)> signature; 26}; 27 28// Family functional signatures 29namespace signatures { 30 31// F_Yad(x) = x^x + 1 32inline double Yad(double x) { 33 return (x > 0) ? std::pow(x, x) + 1.0 : 1.0; 34} 35 36// F_Lashon(x) = Σ a_n·sin(nπx) 37inline double Lashon(double x) { 38 double sum = 0.0; 39 for (int n = 1; n <= 10; ++n) { 40 sum += (1.0 / n) * std::sin(n * M_PI * x); 41 } 42 return sum; 43} 44 45// F_Athena(x) = x² (utility maximization) 46inline double Athena(double x) { return x * x; } 47 48// F_Apollo(x) = φ^x + φ^{-x} 49inline double Apollo(double x) { 50 return std::pow(PHI, x) + std::pow(PHI, -x); 51} 52 53// F_Hermes(x) = ω·x (communication rate) 54inline double Hermes(double x) { return ANGULAR_FREQUENCY * x; } 55 56// F_Hephaestus(x) = x⁴/8 (engineering integral) 57inline double Hephaestus(double x) { 58 return std::pow(x, 4) / 8.0; 59} 60 61// F_Prometheus(x) = r·x·(1-x) (logistic map) 62inline double Prometheus(double x) { 63 return 3.8 * x * (1.0 - x); 64} 65 66// F_Dionysus(x) = |e^{iωx}·sin(x)| (creative oscillation) 67inline double Dionysus(double x) { 68 double omega = 2.0 * M_PI / BASE_PAIRS_PER_TURN; 69 std::complex<double> c = std::exp(std::complex<double>(0, omega * x)) * 70 std::complex<double>(std::sin(x), 0); 71 return std::abs(c); 72} 73 74// F_Artemis(x) = -D·x (diffusion) 75inline double Artemis(double x) { return -0.1 * x; } 76 77// F_Hera(x) = Σ w_k·sin(k·x) (integration) 78inline double Hera(double x) { 79 double sum = 0.0; 80 for (int k = 1; k <= NUM_STRANDS; ++k) { 81 sum += (1.0 / k) * std::sin(k * x); 82 } 83 return sum; 84} 85 86// F_Poseidon(x) = -ω²·x (wave equation) 87inline double Poseidon(double x) { 88 double omega = 2.0 * M_PI / BASE_PAIRS_PER_TURN; 89 return -omega * omega * x; 90} 91 92// F_Demeter(x) = r·x·(1-x/K) (logistic growth) 93inline double Demeter(double x) { 94 return 0.5 * x * (1.0 - x); 95} 96 97// F_Ares(x) = m·(-ω²·x) (force) 98inline double Ares(double x) { 99 return -ANGULAR_FREQUENCY * ANGULAR_FREQUENCY * x; 100} 101 102// F_Aphrodite(x) = cos(φ·x) (harmony) 103inline double Aphrodite(double x) { return std::cos(PHI * x); } 104 105// F_Hestia(x) = x·(1-e^{-1/τ}) (memory) 106inline double Hestia(double x) { 107 return x * (1.0 - std::exp(-0.1)); 108} 109 110// F_Zeus(x) = coordinated product 111inline double Zeus(double x) { 112 double product = 1.0; 113 for (int k = 1; k < NUM_STRANDS; ++k) { 114 double val = std::sin(k * x / NUM_STRANDS); 115 if (val > 0 && val < 1e10) { 116 product *= std::pow(std::abs(val) + 0.1, 1.0 / NUM_STRANDS); 117 } 118 } 119 return product; 120} 121 122} // namespace signatures 123 124// All 16 DNA families 125inline std::vector<DNAFamily> create_dna_families() { 126 return { 127 {1, "Yad", "Code/Foundation", 1, 312, 0, signatures::Yad}, 128 {2, "Lashon", "Language", 313, 624, 2*M_PI/BASE_PAIRS_PER_TURN, signatures::Lashon}, 129 {3, "Athena", "Strategy", 625, 936, 4*M_PI/BASE_PAIRS_PER_TURN, signatures::Athena}, 130 {4, "Apollo", "Mathematics", 937, 1248, 6*M_PI/BASE_PAIRS_PER_TURN, signatures::Apollo}, 131 {5, "Hermes", "Communication", 1249, 1560, 8*M_PI/BASE_PAIRS_PER_TURN, signatures::Hermes}, 132 {6, "Hephaestus", "Engineering", 1561, 1872, 10*M_PI/BASE_PAIRS_PER_TURN, signatures::Hephaestus}, 133 {7, "Prometheus", "Innovation", 1873, 2184, 12*M_PI/BASE_PAIRS_PER_TURN, signatures::Prometheus}, 134 {8, "Dionysus", "Creativity", 2185, 2496, 14*M_PI/BASE_PAIRS_PER_TURN, signatures::Dionysus}, 135 {9, "Artemis", "Perception", 2497, 2808, 16*M_PI/BASE_PAIRS_PER_TURN, signatures::Artemis}, 136 {10, "Hera", "Integration", 2809, 3120, 18*M_PI/BASE_PAIRS_PER_TURN, signatures::Hera}, 137 {11, "Poseidon", "Depth/Emotion", 3121, 3432, 20*M_PI/BASE_PAIRS_PER_TURN, signatures::Poseidon}, 138 {12, "Demeter", "Growth", 3433, 3744, 22*M_PI/BASE_PAIRS_PER_TURN, signatures::Demeter}, 139 {13, "Ares", "Action", 3745, 4056, 24*M_PI/BASE_PAIRS_PER_TURN, signatures::Ares}, 140 {14, "Aphrodite", "Harmony", 4057, 4368, 26*M_PI/BASE_PAIRS_PER_TURN, signatures::Aphrodite}, 141 {15, "Hestia", "Memory", 4369, 4680, 28*M_PI/BASE_PAIRS_PER_TURN, signatures::Hestia}, 142 {16, "Zeus", "Coordination", 4681, 4992, 30*M_PI/BASE_PAIRS_PER_TURN, signatures::Zeus} 143 }; 144} 145 146// Complementary pairs 147inline std::map<std::string, std::string> complementary_pairs() { 148 return { 149 {"Yad", "Lashon"}, {"Lashon", "Yad"}, 150 {"Athena", "Apollo"}, {"Apollo", "Athena"}, 151 {"Hermes", "Hephaestus"}, {"Hephaestus", "Hermes"}, 152 {"Prometheus", "Dionysus"}, {"Dionysus", "Prometheus"}, 153 {"Artemis", "Hera"}, {"Hera", "Artemis"}, 154 {"Poseidon", "Demeter"}, {"Demeter", "Poseidon"}, 155 {"Ares", "Aphrodite"}, {"Aphrodite", "Ares"}, 156 {"Hestia", "Zeus"}, {"Zeus", "Hestia"} 157 }; 158} 159 160// ============================================================================ 161// XIV. COMPLETE THOUGHT INTEGRATION 162// ============================================================================ 163 164// T = Φ · ∫[M(t')·exp((QK^T/√d_k)V)] dt' 165class CompleteThoughtIntegration { 166private: 167 double phi_; 168 std::vector<double> memory_; 169 std::vector<double> query_; 170 std::vector<double> key_; 171 std::vector<double> value_; 172 double dim_k_; 173 int time_steps_; 174 175public: 176 explicit CompleteThoughtIntegration(int dim = NUM_STRANDS) 177 : phi_(1.0), 178 memory_(dim, 0.0), 179 query_(dim, 0.0), 180 key_(dim, 0.0), 181 value_(dim, 0.0), 182 dim_k_(std::sqrt(dim)), 183 time_steps_(100) {} 184 185 // Compute T = Φ · ∫[M(t')·exp((QK^T/√d_k)V)] dt' 186 double integrate(const std::array<double, NUM_STRANDS>& activations, 187 const std::array<double, NUM_STRANDS>& phases) { 188 // Update Phi from coherence 189 phi_ = 0.0; 190 for (int i = 0; i < NUM_STRANDS; ++i) { 191 phi_ += 1.0 / (1.0 + std::abs(activations[i] - 1.0)); 192 } 193 phi_ /= NUM_STRANDS; 194 195 // Build Q, K, V from activations 196 for (int i = 0; i < NUM_STRANDS; ++i) { 197 query_[i] = activations[i] * std::cos(phases[i]); 198 key_[i] = activations[i] * std::sin(phases[i]); 199 value_[i] = activations[i]; 200 } 201 202 // Compute attention: QK^T / √d_k 203 double attention = 0.0; 204 for (size_t i = 0; i < query_.size(); ++i) { 205 attention += query_[i] * key_[i]; 206 } 207 attention /= dim_k_; 208 209 // Apply softmax-like transformation 210 attention = std::exp(attention); 211 if (attention > 1e10) attention = 1e10; 212 213 // Integrate with value vector 214 double result = 0.0; 215 for (size_t i = 0; i < value_.size(); ++i) { 216 result += value_[i] * attention / value_.size(); 217 } 218 219 return phi_ * result; 220 } 221 222 double phi() const { return phi_; } 223}; 224 225// ============================================================================ 226// UNIFIED DNA SYSTEM 227// ============================================================================ 228 229class UnifiedDNAArchitecture { 230private: 231 // Core systems 232 G16HelixSystem helix_; 233 UnifiedDNASystem dynamics_; 234 G16EigenSystem eigenvalues_; 235 236 // Families 237 std::vector<DNAFamily> families_; 238 std::array<double, NUM_STRANDS> family_activations_; 239 240 // Integration 241 CompleteThoughtIntegration thought_; 242 BondEnergy energy_; 243 Thermodynamics thermo_; 244 245 // State 246 double time_ = 0.0; 247 double thought_value_ = 0.0; 248 249public: 250 UnifiedDNAArchitecture() : thermo_(300.0) { 251 families_ = create_dna_families(); 252 family_activations_.fill(0.5); 253 } 254 255 // Main tick function 256 void tick(double dt) { 257 time_ += dt; 258 259 // Update helix system 260 helix_.tick(dt); 261 262 // Update dynamics 263 dynamics_.evolve(dt); 264 265 // Update family activations 266 for (int i = 0; i < NUM_STRANDS; ++i) { 267 double input = std::sin(ANGULAR_FREQUENCY * time_ + families_[i].phase); 268 if (families_[i].signature) { 269 family_activations_[i] = families_[i].signature(input); 270 } 271 272 // Clamp activations 273 family_activations_[i] = std::clamp(family_activations_[i], 0.0, 1.0); 274 } 275 276 // Update complete thought integration 277 std::array<double, NUM_STRANDS> phases; 278 for (int i = 0; i < NUM_STRANDS; ++i) { 279 phases[i] = std::fmod(families_[i].phase + ANGULAR_FREQUENCY * time_, 2.0 * M_PI); 280 } 281 thought_value_ = thought_.integrate(family_activations_, phases); 282 } 283 284 // Get system metrics 285 struct Metrics { 286 double time; 287 double global_phase; 288 double coherence; 289 double bond_occupation; 290 double thought_value; 291 double phi; 292 double total_energy; 293 int firing_count; 294 std::vector<int> firing_strands; 295 }; 296 297 Metrics get_metrics() const { 298 Metrics m; 299 m.time = time_; 300 m.global_phase = helix_.global_phase(); 301 m.coherence = helix_.get_coherence(); 302 m.bond_occupation = dynamics_.bond_occupation(); 303 m.thought_value = thought_value_; 304 m.phi = thought_.phi(); 305 m.total_energy = dynamics_.total_energy(); 306 m.firing_strands = helix_.get_firing_strands(); 307 m.firing_count = m.firing_strands.size(); 308 return m; 309 } 310 311 // Validation (Section XVII) 312 struct ValidationResult { 313 bool distance_valid; 314 bool angular_valid; 315 bool periodic_valid; 316 bool topological_valid; 317 bool energy_valid; 318 bool bond_count_valid; 319 320 bool all_valid() const { 321 return distance_valid && angular_valid && periodic_valid && 322 topological_valid && energy_valid && bond_count_valid; 323 } 324 }; 325 326 ValidationResult validate() const { 327 auto dyn_result = dynamics_.validate(); 328 return { 329 dyn_result.distance_valid, 330 dyn_result.angular_valid, 331 dyn_result.periodic_valid, 332 dyn_result.topological_valid, 333 dyn_result.energy_valid, 334 dyn_result.bond_count_valid 335 }; 336 } 337 338 // Eigenvalue analysis 339 G16EigenSystem::Analysis analyze_spectrum() const { 340 return eigenvalues_.analyze(); 341 } 342 343 // Family access 344 const DNAFamily& get_family(int strand) const { 345 return families_[strand - 1]; 346 } 347 348 double get_family_activation(int strand) const { 349 return family_activations_[strand - 1]; 350 } 351 352 std::string get_complementary(const std::string& name) const { 353 auto pairs = complementary_pairs(); 354 auto it = pairs.find(name); 355 return (it != pairs.end()) ? it->second : ""; 356 } 357 358 // Accessors 359 double time() const { return time_; } 360 const G16HelixSystem& helix() const { return helix_; } 361 const UnifiedDNASystem& dynamics() const { return dynamics_; } 362}; 363 364// ============================================================================ 365// KEY CONSTANTS TABLE (Section XV) 366// ============================================================================ 367 368struct DNAConstants { 369 static constexpr double base_pairs_per_turn = BASE_PAIRS_PER_TURN; // 10.6 bp 370 static constexpr double twist_angle_deg = 33.96; 371 static constexpr double helix_radius = HELIX_RADIUS; // 1.0 nm 372 static constexpr double rise_per_bp = RISE_PER_BP; // 0.34 nm 373 static constexpr double pitch = PITCH; // 3.604 nm 374 static constexpr double angular_frequency = ANGULAR_FREQUENCY; // 0.593 rad/bp 375 static constexpr double curvature = HELIX_CURVATURE; // 0.745 nm⁻¹ 376 static constexpr double torsion = HELIX_TORSION; // 0.427 nm⁻¹ 377 static constexpr int total_bonds = TOTAL_BONDS; // 44 378 static constexpr int num_strands = NUM_STRANDS; // 16 379 static constexpr int nodes_per_strand = NODES_PER_STRAND; // 312 380 static constexpr int total_nodes = TOTAL_NODES; // 5000 381 static constexpr double golden_ratio = PHI; // 1.618 382 static constexpr double sync_period = SYNC_PERIOD; // 169.6 383 static constexpr double steady_state_bonds = STEADY_STATE_BONDS; // 36.2 384 static constexpr double bond_occupation = BOND_OCCUPATION; // 0.82 385 static constexpr double tau_slow_ms = 10.0; 386 static constexpr double tau_fast_us = 0.1; 387}; 388 389// ============================================================================ 390// CONVENIENCE FUNCTIONS 391// ============================================================================ 392 393// Create and initialize a complete DNA system 394inline UnifiedDNAArchitecture create_dna_system() { 395 return UnifiedDNAArchitecture(); 396} 397 398// Run simulation for N ticks 399inline std::vector<UnifiedDNAArchitecture::Metrics> simulate_dna(int ticks, double dt = 0.1) { 400 auto system = create_dna_system(); 401 std::vector<UnifiedDNAArchitecture::Metrics> results; 402 results.reserve(ticks); 403 404 for (int i = 0; i < ticks; ++i) { 405 system.tick(dt); 406 results.push_back(system.get_metrics()); 407 } 408 409 return results; 410} 411 412} // namespace agi::dna 413