#include "substrate_engine.h"
#include <math.h>
float substrate_resonance(uint32_t similarity) { float x = (float)similarity; return 1.0f / (1.0f + expf(-RESONANCE_K * (x - RESONANCE_MU))); }
float substrate_stability(float t) { return expf(-STABILITY_LAMBDA * t); }
float substrate_stability_from_mutations(uint32_t mutation_count) { return expf(-STABILITY_LAMBDA * (float)mutation_count); }
float substrate_coherence(const uint8_t *data, size_t len) {
    if (len < 2) return 1.0f; float total_diff = 0.0f;
    for (size_t i = 1; i < len; i++) { float diff = (float)data[i] - (float)data[i - 1]; if (diff < 0) diff = -diff; total_diff += diff; }
    float avg_diff = total_diff / (float)(len - 1); float c = 1.0f - (avg_diff / 128.0f); if (c < 0.0f) c = 0.0f; if (c > 1.0f) c = 1.0f; return c;
}
TraitMask substrate_traits_propagate(TraitMask a, TraitMask b) { TraitMask shared = a & b; TraitMask emergent = a ^ b; return shared | (emergent & 0x00000000FFFFFFFFULL); }
int substrate_traits_compatible(TraitMask filter, TraitMask candidate) { if (filter == 0) return 1; return (filter & candidate) != 0 ? 1 : 0; }
float substrate_neural_energy(const uint8_t *a, const uint8_t *b, size_t len) {
    if (len == 0) return 0.0f; float sum = 0.0f;
    for (size_t i = 0; i < len; i++) { float diff = (float)a[i] - (float)b[i]; sum += diff * diff; } return sum / (float)len;
}
int substrate_lineage_propagates(float correlation) { return correlation >= LINEAGE_THRESHOLD ? 1 : 0; }
int substrate_lineage_compatible(uint32_t lineage_a, uint32_t lineage_b) { if (lineage_a == 0 || lineage_b == 0) return 1; return lineage_a == lineage_b ? 1 : 0; }