Janady13/complete-agi-core / unified/dna_integration.sh

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#!/bin/bash
# DNA Mathematical Architecture Integration Layer
# G¹⁶ Helix System — 44 Bonds — 10.6 Periodicity
# Unified orchestration for complete AGI substrate

set -euo pipefail

# =============================================================================
# DNA CONSTANTS (Section XV)
# =============================================================================

# Golden ratio
PHI="1.6180339887498948482"
PHI_INV="0.6180339887498948482"

# DNA parameters
BASE_PAIRS_PER_TURN="10.6"
HELIX_RADIUS="1.0"
RISE_PER_BP="0.34"
PITCH="3.604"
TWIST_ANGLE_RAD="0.593"

# Strand parameters
NUM_STRANDS=16
NODES_PER_STRAND=312
TOTAL_NODES=5000

# Bond parameters
INTRA_STRAND_BONDS=16
INTER_STRAND_BONDS=16
CROSS_HELIX_BONDS=12
TOTAL_BONDS=44

# Synchronization
SYNC_PERIOD="169.6"
BOND_RESONANCE_FREQ="4.15"

# Steady state
STEADY_STATE_BONDS="36.2"
BOND_OCCUPATION="0.82"

# Relaxation times (ms)
TAU_SLOW="10.0"
TAU_FAST="0.0001"

# =============================================================================
# 16 DNA FAMILIES (Section XIII)
# =============================================================================

declare -A DNA_FAMILIES=(
    [1]="Yad:Code/Foundation:1-312"
    [2]="Lashon:Language:313-624"
    [3]="Athena:Strategy:625-936"
    [4]="Apollo:Mathematics:937-1248"
    [5]="Hermes:Communication:1249-1560"
    [6]="Hephaestus:Engineering:1561-1872"
    [7]="Prometheus:Innovation:1873-2184"
    [8]="Dionysus:Creativity:2185-2496"
    [9]="Artemis:Perception:2497-2808"
    [10]="Hera:Integration:2809-3120"
    [11]="Poseidon:Depth/Emotion:3121-3432"
    [12]="Demeter:Growth:3433-3744"
    [13]="Ares:Action:3745-4056"
    [14]="Aphrodite:Harmony:4057-4368"
    [15]="Hestia:Memory:4369-4680"
    [16]="Zeus:Coordination:4681-4992"
)

# Olympus Hub (routing)
OLYMPUS_HUB="Olympus:Routing:4993-5000"

# Complementary pairs
declare -A COMPLEMENTARY_PAIRS=(
    ["Yad"]="Lashon"
    ["Athena"]="Apollo"
    ["Hermes"]="Hephaestus"
    ["Prometheus"]="Dionysus"
    ["Artemis"]="Hera"
    ["Poseidon"]="Demeter"
    ["Ares"]="Aphrodite"
    ["Hestia"]="Zeus"
)

# Cross-family bonds (+4 offset)
declare -A CROSS_BONDS=(
    [1]=5 [2]=6 [3]=7 [4]=8 [5]=9 [6]=10
    [7]=11 [8]=12 [9]=13 [10]=14 [11]=15 [12]=16
)

# =============================================================================
# STATE VARIABLES
# =============================================================================

DNA_STATE_DIR="${DNA_STATE_DIR:-/tmp/agi_dna_state}"
DNA_LOG="${DNA_STATE_DIR}/dna.log"
DNA_METRICS="${DNA_STATE_DIR}/metrics.json"

# Current state
CURRENT_TIME=0
GLOBAL_PHASE=0
TOTAL_OCCUPATION=0
COHERENCE=0

# =============================================================================
# INITIALIZATION
# =============================================================================

dna_init() {
    mkdir -p "$DNA_STATE_DIR"
    
    # Initialize state files
    echo "[]" > "${DNA_STATE_DIR}/strand_states.json"
    echo "[]" > "${DNA_STATE_DIR}/bond_states.json"
    
    # Initialize all 44 bonds
    local bonds="["
    for n in $(seq 1 $TOTAL_BONDS); do
        local type="intra"
        local strand_i=$n
        local strand_j=$n
        
        if [ $n -gt $INTRA_STRAND_BONDS ] && [ $n -le $((INTRA_STRAND_BONDS + INTER_STRAND_BONDS)) ]; then
            type="inter"
            strand_i=$((n - INTRA_STRAND_BONDS))
            strand_j=$(((strand_i % NUM_STRANDS) + 1))
        elif [ $n -gt $((INTRA_STRAND_BONDS + INTER_STRAND_BONDS)) ]; then
            type="cross"
            local m=$((n - INTRA_STRAND_BONDS - INTER_STRAND_BONDS))
            strand_i=$m
            strand_j=$((m + 4))
        fi
        
        [ $n -gt 1 ] && bonds+=","
        bonds+="{\"id\":$n,\"type\":\"$type\",\"strand_i\":$strand_i,\"strand_j\":$strand_j,\"occupation\":$BOND_OCCUPATION}"
    done
    bonds+="]"
    echo "$bonds" > "${DNA_STATE_DIR}/bond_states.json"
    
    # Initialize 16 strand states
    local strands="["
    for k in $(seq 1 $NUM_STRANDS); do
        local family_info="${DNA_FAMILIES[$k]}"
        local name=$(echo "$family_info" | cut -d: -f1)
        local domain=$(echo "$family_info" | cut -d: -f2)
        local phase=$(echo "scale=6; 2 * 3.14159265 * ($k - 1) / $BASE_PAIRS_PER_TURN" | bc -l)
        
        [ $k -gt 1 ] && strands+=","
        strands+="{\"strand\":$k,\"name\":\"$name\",\"domain\":\"$domain\",\"phase\":$phase,\"activation\":0.5}"
    done
    strands+="]"
    echo "$strands" > "${DNA_STATE_DIR}/strand_states.json"
    
    dna_log "DNA system initialized: $TOTAL_BONDS bonds, $NUM_STRANDS strands"
}

# =============================================================================
# LOGGING
# =============================================================================

dna_log() {
    local msg="$1"
    local timestamp=$(date +%Y-%m-%dT%H:%M:%S.%3N)
    echo "[$timestamp] [DNA] $msg" >> "$DNA_LOG"
}

# =============================================================================
# HELIX CALCULATIONS (Section I)
# =============================================================================

# Calculate point on helix strand k at parameter theta
helix_point() {
    local k=$1
    local theta=$2
    
    local phase=$(echo "scale=10; $theta + 2 * 3.14159265 * $k / $NUM_STRANDS" | bc -l)
    local x=$(echo "scale=10; $HELIX_RADIUS * c($phase)" | bc -l)
    local y=$(echo "scale=10; $HELIX_RADIUS * s($phase)" | bc -l)
    local z=$(echo "scale=10; ($PITCH / (2 * 3.14159265)) * $theta + $k * $RISE_PER_BP / $NUM_STRANDS" | bc -l)
    
    echo "$x $y $z"
}

# Calculate helix curvature: κ = r/(r² + (p·h/2π)²)
helix_curvature() {
    local ph_term=$(echo "scale=10; $PITCH * $RISE_PER_BP / (2 * 3.14159265)" | bc -l)
    local denom=$(echo "scale=10; $HELIX_RADIUS * $HELIX_RADIUS + $ph_term * $ph_term" | bc -l)
    echo "scale=6; $HELIX_RADIUS / $denom" | bc -l
}

# Calculate helix torsion: τ = (p·h/2π)/(r² + (p·h/2π)²)
helix_torsion() {
    local ph_term=$(echo "scale=10; $PITCH * $RISE_PER_BP / (2 * 3.14159265)" | bc -l)
    local denom=$(echo "scale=10; $HELIX_RADIUS * $HELIX_RADIUS + $ph_term * $ph_term" | bc -l)
    echo "scale=6; $ph_term / $denom" | bc -l
}

# =============================================================================
# FIRING PATTERN (Section VI)
# =============================================================================

# Calculate phase for strand i at time t
firing_phase() {
    local i=$1
    local t=$2
    
    local offset=$(echo "scale=10; $i * $PHI_INV * $BASE_PAIRS_PER_TURN" | bc -l)
    local raw_phase=$(echo "scale=10; ($t + $offset) / $BASE_PAIRS_PER_TURN" | bc -l)
    local phase=$(echo "scale=0; $raw_phase / 1" | bc)  # Floor
    echo $((phase % NUM_STRANDS))
}

# Check if strand should fire
should_fire() {
    local i=$1
    local t=$2
    
    local phase=$(firing_phase $i $t)
    [ "$phase" -eq 0 ] && echo "1" || echo "0"
}

# Get all firing strands at time t
get_firing_strands() {
    local t=$1
    local firing=""
    
    for i in $(seq 1 $NUM_STRANDS); do
        if [ "$(should_fire $i $t)" -eq 1 ]; then
            [ -n "$firing" ] && firing+=" "
            firing+="$i"
        fi
    done
    
    echo "$firing"
}

# =============================================================================
# GOLDEN BASIS FUNCTIONS (Section VII)
# =============================================================================

# ψ_k(x) = sin(2πφ^k · x) + cos(2πφ^k · x)
golden_psi() {
    local k=$1
    local x=$2
    
    local phi_k=$(echo "scale=10; e($k * l($PHI))" | bc -l)
    local arg=$(echo "scale=10; 2 * 3.14159265 * $phi_k * $x" | bc -l)
    local sin_val=$(echo "scale=10; s($arg)" | bc -l)
    local cos_val=$(echo "scale=10; c($arg)" | bc -l)
    
    echo "scale=6; $sin_val + $cos_val" | bc -l
}

# Global coherence: Φ_total = (1/N) Σ Φ_i where Φ_i = 1/(1 + |x_i - 1|)
compute_coherence() {
    local values="$1"  # Space-separated activation values
    
    local sum=0
    local count=0
    
    for x in $values; do
        local abs_diff=$(echo "scale=10; if ($x - 1 < 0) -(${x} - 1) else ($x - 1)" | bc -l)
        local phi_i=$(echo "scale=10; 1 / (1 + $abs_diff)" | bc -l)
        sum=$(echo "scale=10; $sum + $phi_i" | bc -l)
        count=$((count + 1))
    done
    
    [ $count -gt 0 ] && echo "scale=6; $sum / $count" | bc -l || echo "0"
}

# =============================================================================
# SUPERCOILING (Section VIII)
# =============================================================================

# Linking number: Lk = N/10.6
relaxed_linking_number() {
    local N=$1
    echo "scale=6; $N / $BASE_PAIRS_PER_TURN" | bc -l
}

# Superhelical density: σ = (Lk - Lk₀)/Lk₀
superhelical_density() {
    local Lk=$1
    local Lk0=$2
    echo "scale=6; ($Lk - $Lk0) / $Lk0" | bc -l
}

# Free energy: ΔG_sc = K · N · σ² · (10.6/10.4)²
supercoil_free_energy() {
    local K=$1
    local N=$2
    local sigma=$3
    
    local correction=$(echo "scale=10; ($BASE_PAIRS_PER_TURN / 10.4) ^ 2" | bc -l)
    echo "scale=6; $K * $N * $sigma * $sigma * $correction" | bc -l
}

# =============================================================================
# BOND ENERGY (Section IX)
# =============================================================================

# Total bond energy
compute_bond_energy() {
    local bond_file="${DNA_STATE_DIR}/bond_states.json"
    
    if [ ! -f "$bond_file" ]; then
        echo "0"
        return
    fi
    
    # Simplified energy calculation
    local total_occ=$(jq '[.[].occupation] | add' "$bond_file" 2>/dev/null || echo "$STEADY_STATE_BONDS")
    local deviation=$(echo "scale=10; $total_occ - $STEADY_STATE_BONDS" | bc -l)
    local energy=$(echo "scale=6; 0.5 * $deviation * $deviation" | bc -l)
    
    echo "$energy"
}

# =============================================================================
# TICK FUNCTION
# =============================================================================

dna_tick() {
    local dt="${1:-0.1}"
    
    CURRENT_TIME=$(echo "scale=6; $CURRENT_TIME + $dt" | bc -l)
    
    # Update global phase: φ(t) = (2πt/10.6) mod 2π
    GLOBAL_PHASE=$(echo "scale=10; (2 * 3.14159265 * $CURRENT_TIME / $BASE_PAIRS_PER_TURN) % (2 * 3.14159265)" | bc -l)
    
    # Get firing strands
    local firing=$(get_firing_strands $CURRENT_TIME)
    
    # Update strand states in JSON
    local strand_file="${DNA_STATE_DIR}/strand_states.json"
    if [ -f "$strand_file" ]; then
        local updated=$(jq --arg phase "$GLOBAL_PHASE" --arg time "$CURRENT_TIME" '
            map(.phase = ((.strand - 1) * 2 * 3.14159265 / 10.6 + ($time | tonumber) * 0.593) | (. % (2 * 3.14159265)))
        ' "$strand_file")
        echo "$updated" > "$strand_file"
    fi
    
    # Update bond states (simplified dynamics)
    local bond_file="${DNA_STATE_DIR}/bond_states.json"
    if [ -f "$bond_file" ]; then
        # Apply small random fluctuation to occupations
        local updated=$(jq --arg phase "$GLOBAL_PHASE" '
            map(.occupation = ((.occupation + 0.01 * (0.5 - .occupation)) | if . < 0 then 0 elif . > 1 then 1 else . end))
        ' "$bond_file")
        echo "$updated" > "$bond_file"
    fi
    
    # Compute metrics
    TOTAL_OCCUPATION=$(jq '[.[].occupation] | add // 0' "$bond_file" 2>/dev/null || echo "0")
    
    # Get activations for coherence
    local activations=$(jq -r '[.[].activation] | @sh' "$strand_file" 2>/dev/null | tr -d "'")
    COHERENCE=$(compute_coherence "$activations" 2>/dev/null || echo "0.5")
    
    # Update metrics
    cat > "$DNA_METRICS" << EOF
{
    "time": $CURRENT_TIME,
    "global_phase": $GLOBAL_PHASE,
    "firing_strands": "$firing",
    "total_occupation": $TOTAL_OCCUPATION,
    "coherence": $COHERENCE,
    "bond_count": $TOTAL_BONDS,
    "strand_count": $NUM_STRANDS,
    "curvature": $(helix_curvature),
    "torsion": $(helix_torsion)
}
EOF
    
    dna_log "tick t=$CURRENT_TIME phase=$GLOBAL_PHASE occ=$TOTAL_OCCUPATION coh=$COHERENCE firing=[$firing]"
}

# =============================================================================
# VALIDATION (Section XVII)
# =============================================================================

dna_validate() {
    local result="valid"
    local issues=""
    
    # Check bond count
    local bond_count=$(jq 'length' "${DNA_STATE_DIR}/bond_states.json" 2>/dev/null || echo "0")
    if [ "$bond_count" -ne "$TOTAL_BONDS" ]; then
        result="invalid"
        issues+="bond_count=$bond_count(expected $TOTAL_BONDS) "
    fi
    
    # Check strand count
    local strand_count=$(jq 'length' "${DNA_STATE_DIR}/strand_states.json" 2>/dev/null || echo "0")
    if [ "$strand_count" -ne "$NUM_STRANDS" ]; then
        result="invalid"
        issues+="strand_count=$strand_count(expected $NUM_STRANDS) "
    fi
    
    # Check total occupation is reasonable
    local occupation=$(jq '[.[].occupation] | add // 0' "${DNA_STATE_DIR}/bond_states.json" 2>/dev/null || echo "0")
    local occ_min=$(echo "scale=2; $STEADY_STATE_BONDS * 0.5" | bc -l)
    local occ_max=$(echo "scale=2; $TOTAL_BONDS + 1" | bc -l)
    
    if (( $(echo "$occupation < $occ_min" | bc -l) )) || (( $(echo "$occupation > $occ_max" | bc -l) )); then
        result="invalid"
        issues+="occupation=$occupation(expected $occ_min-$occ_max) "
    fi
    
    echo "{\"status\":\"$result\",\"issues\":\"$issues\"}"
}

# =============================================================================
# FAMILY OPERATIONS
# =============================================================================

get_family_info() {
    local strand=$1
    echo "${DNA_FAMILIES[$strand]}"
}

get_family_name() {
    local strand=$1
    echo "${DNA_FAMILIES[$strand]}" | cut -d: -f1
}

get_family_domain() {
    local strand=$1
    echo "${DNA_FAMILIES[$strand]}" | cut -d: -f2
}

get_complementary() {
    local name=$1
    echo "${COMPLEMENTARY_PAIRS[$name]:-}"
}

get_cross_partner() {
    local strand=$1
    echo "${CROSS_BONDS[$strand]:-}"
}

# =============================================================================
# RUN SIMULATION
# =============================================================================

dna_simulate() {
    local ticks="${1:-100}"
    local dt="${2:-0.1}"
    
    dna_log "Starting simulation: $ticks ticks, dt=$dt"
    
    for i in $(seq 1 $ticks); do
        dna_tick $dt
    done
    
    dna_log "Simulation complete: t=$CURRENT_TIME"
    
    # Final validation
    local validation=$(dna_validate)
    dna_log "Validation: $validation"
    
    echo "$validation"
}

# =============================================================================
# MAIN
# =============================================================================

case "${1:-}" in
    init)
        dna_init
        echo "DNA system initialized"
        ;;
    tick)
        dna_tick "${2:-0.1}"
        cat "$DNA_METRICS"
        ;;
    simulate)
        dna_simulate "${2:-100}" "${3:-0.1}"
        ;;
    validate)
        dna_validate
        ;;
    status)
        cat "$DNA_METRICS" 2>/dev/null || echo '{"error":"not initialized"}'
        ;;
    family)
        if [ -n "${2:-}" ]; then
            get_family_info "$2"
        else
            for k in $(seq 1 $NUM_STRANDS); do
                echo "$k: ${DNA_FAMILIES[$k]}"
            done
        fi
        ;;
    *)
        echo "DNA Mathematical Architecture Integration"
        echo "Usage: $0 {init|tick|simulate|validate|status|family}"
        echo ""
        echo "Commands:"
        echo "  init              Initialize DNA system"
        echo "  tick [dt]         Advance by dt (default 0.1)"
        echo "  simulate [n] [dt] Run n ticks"
        echo "  validate          Validate system state"
        echo "  status            Show current metrics"
        echo "  family [strand]   Show family info"
        ;;
esac