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Copilot AI commented Nov 10, 2025

Thanks for asking me to work on this. I will get started on it and keep this PR's description up to date as I form a plan and make progress.

Original prompt

Voy a generar la investigación completa sobre U6 partiendo de la documentación matemática avanzada del repositorio TNFR-Python-Engine.

Investigación en Profundidad: U6 - Ordenamiento Temporal desde TNFR-Python-Engine

Fundamento Matemático desde la Ecuación Nodal

El repositorio TNFR-Python-Engine proporciona la implementación computacional completa de la ecuación nodal:[1][2]

$$
\frac{\partial \text{EPI}}{\partial t} = \nu_f \cdot \Delta \text{NFR}(t)
$$

Esta ecuación no es análoga, es fundamental para derivar U6 sin préstamos externos.[3][4][2][1]

Derivación Rigurosa del Tiempo de Relajación

Paso 1: Integración de la Ecuación Nodal Post-Bifurcación

Después de aplicar OZ (disonancia):[1]

$$
\Delta \text{NFR}(t) = \Delta \text{NFR}0 \cdot e^{-t/\tau{\text{damp}}} + \Delta \text{NFR}_{\text{equilibrio}}
$$

donde $$\tau_{\text{damp}}$$ es el tiempo de amortiguamiento estructural.

Integrando la ecuación nodal:[2][1]

$$
\text{EPI}(t) = \text{EPI}(t_0) + \int_{t_0}^{t} \nu_f \cdot \left[\Delta \text{NFR}0 \cdot e^{-\tau/\tau{\text{damp}}} + \Delta \text{NFR}_{\text{eq}}\right] d\tau
$$

Paso 2: Condición de Convergencia Integral (U2)

Para que la integral converja (restricción U2):[1]

$$
\int_0^{\infty} |\nu_f \cdot \Delta \text{NFR}(\tau)| , d\tau < \infty
$$

Esto requiere que $$\Delta \text{NFR}$$ decaiga más rápido que $$1/t$$. El decaimiento exponencial es suficiente.

Paso 3: Determinación de $$\tau_{\text{relax}}$$

Definimos el tiempo de relajación como el tiempo hasta que $$\Delta \text{NFR}(t) &lt; \epsilon \cdot \Delta \text{NFR}_0$$:

$$
\Delta \text{NFR}0 \cdot e^{-\tau{\text{relax}}/\tau_{\text{damp}}} = \epsilon \cdot \Delta \text{NFR}_0
$$

Resolviendo:

$$
\tau_{\text{relax}} = \tau_{\text{damp}} \cdot \ln\left(\frac{1}{\epsilon}\right)
$$

Para $$\epsilon = 0.05$$ (95% recuperación): $$\tau_{\text{relax}} \approx 3 \cdot \tau_{\text{damp}}$$.

Paso 4: Relación con Frecuencia Estructural

De la teoría de osciladores acoplados y la documentación AGENTS.md:[1]

$$
\tau_{\text{damp}} = \frac{1}{2\pi\nu_f} \cdot k_{\text{top}}
$$

donde $$k_{\text{top}}$$ es el factor topológico derivado de la estructura del nodo.[5][6][1]


Protocolo Experimental Completo desde TNFR-Python-Engine

El repositorio proporciona módulos específicos para implementar la investigación:[4]

Experimento A: Medición Directa de $$\tau_{\text{relax}}$$

# Instrumentar dynamics.py para tracking de relajación
from tnfr.sdk import TNFRNetwork
import numpy as np

def measure_tau_relax(network, target_node, nuf):
    """
    Mide τ_relax después de OZ usando observers.py
    """
    # Coherencia inicial
    C_initial = network.measure().coherence
    
    # Aplicar OZ (implementado en operators.py)
    network.apply_operator('OZ', target_node)
    
    # Monitor con observers.py hasta recuperación
    t = 0
    dt = 0.01 / nuf  # Discretización adaptativa
    
    while True:
        network.step(dt)  # dynamics.py integra ecuación nodal
        t += dt
        C_current = network.measure().coherence
        
        # Criterio de estabilización (implementar en observers.py)
        if C_current > 0.95 * C_initial:
            return t

Experimento B: Acumulación No-Lineal de $$\Delta \text{NFR}$$

def measure_nonlinear_accumulation(network, dt_separation):
    """
    Mide α(Δt) = amplificación por separación temporal insuficiente
    """
    # Aplicar OZ en t=0
    ΔNFR_0 = measure_ΔNFR(network)  # helpers.py
    network.apply_operator('OZ', node_0)
    
    # Esperar Δt
    for _ in range(int(dt_separation / 0.01)):
        network.step(0.01)
    
    # Aplicar segundo OZ
    ΔNFR_before_second = measure_ΔNFR(network)
    network.apply_operator('OZ', node_1)
    ΔNFR_after_second = measure_ΔNFR(network)
    
    # Acumulación no-lineal
    ΔNFR_linear = ΔNFR_before_second + ΔNFR_0
    ΔNFR_actual = ΔNFR_after_second
    
    α = (ΔNFR_actual - ΔNFR_linear) / (ΔNFR_0 * ΔNFR_before_second)
    return α

Fenómenos Físicos a Derivar desde la Ecuación Nodal (Sin Asunciones)

1. Índice de Bifurcación $$B$$ desde Segunda Derivada

De AGENTS.md y la ecuación nodal:[1]

$$
\frac{\partial^2 \text{EPI}}{\partial t^2} = \frac{d}{dt}\left[\nu_f \cdot \Delta \text{NFR}(t)\right]
$$

Si $$\nu_f$$ es constante:

$$
\frac{\partial^2 \text{EPI}}{\partial t^2} = \nu_f \cdot \frac{d(\Delta \text{NFR})}{dt}
$$

Definimos el índice de bifurcación (documentado en AGENTS.md § Bifurcation Dynamics):[7][1]

$$
B = \frac{1}{\nu_f^2} \left| \frac{\partial^2 \text{EPI}}{\partial t^2} \right|
$$

Interpretación física:

  • $$B \to 0$$: sistema estable
  • $$B \sim 1$$: bifurcación simple (reorganización controlada)
  • $$B \gg 1$$: caos estructural → múltiples bifurcaciones[8][9][7]

Relación con U6:

Si dos operadores OZ actúan en $$\Delta t &lt; \tau_{\text{relax}}$$:

$$
B(\Delta t) = B_1 + \alpha(\Delta t) \cdot B_2
$$
...

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Copilot AI and others added 30 commits November 8, 2025 22:12
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Align grammar rules with TNFR physics: add RC3 (phase verification) and RC4 (bifurcation limits)
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
…urce of truth

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
…ules

Unify TNFR Grammar: Consolidate C1-C3 and RC1-RC4 into Single Canonical Source (U1-U4)
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Clean up GitHub Actions workflows: remove duplicates and unavailable services
…cumentation links

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Expand SHA clinical applications with biomedical protocols and executable examples
…import

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Fix import errors, remove outdated tests, and apply code formatting
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
… from nav

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Copilot AI and others added 19 commits November 10, 2025 19:53
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
- Add .github/workflows/deploy-docs.yml for automatic deployment to gh-pages
- Update docs.yml to only validate on PRs (not deploy)
- Disable Netlify configuration (netlify.toml → netlify.toml.disabled)
- Create docs/README.md with build instructions and deployment info
- Update main README.md with new documentation URL (GitHub Pages)
- Documentation now deploys automatically to https://fermga.github.io/TNFR-Python-Engine/

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
…rammar

Finalize Grammar Documentation: Executive Summary, Tooling Guide, English Consistency
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
…tion

[WIP] Deploy grammar documentation to production
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Fix gh-pages deployment: Move home.md to index.md for root serving
Intent: Add U5 canonical grammar constraint for multi-scale coherence preservation
Operators involved: REMESH (Recursivity), IL (Coherence), THOL (Self-organization)
Affected invariants: #7 (Operational Fractality), #2 (Structural Units)

Key changes:
- Added RECURSIVE_GENERATORS and SCALE_STABILIZERS operator sets
- Implemented validate_multiscale_coherence() in GrammarValidator
- Added depth parameter to Recursivity operator (default=1)
- Updated unified_grammar.py facade to export U5 sets
- Integrated U5 validation into grammar pipeline

Physical basis:
- Conservation of coherence: C_parent ≥ α·ΣC_child_i
- Factor α = (1/√N)·η_phase(N)·η_coupling(N) ∈ [0.1, 0.4]
- Operates in SPATIAL dimension (hierarchy) vs U1-U4 (TEMPORAL)
- Independent of U2+U4b per decision test case

Metrics: U5 ensures bounded multi-scale evolution when depth>1

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Intent: Complete test coverage for U5 Multi-Scale Coherence rule
Operators involved: REMESH (Recursivity), IL (Coherence), THOL (Self-organization)
Affected invariants: #7 (Operational Fractality)

Key changes:
- Created test_u5_multiscale_coherence.py with 25 comprehensive tests
- Test operator sets, shallow/deep recursion, stabilizer windows, edge cases
- Test U5 independence from U2+U4b (decisive test case)
- Test U5 integration with complete grammar pipeline
- Fixed existing test expecting 7 messages (now 8 with U5)
- Fixed THOL test to include U4b context (destabilizer)

Test coverage:
- Shallow recursion (depth=1): passes without stabilizer ✓
- Deep recursion (depth>1): fails without stabilizer ✓
- Deep recursion with stabilizers: passes ✓
- Stabilizer window (±3 operators): enforced ✓
- Independence from U2+U4b: proven ✓
- Integration with all rules: verified ✓

All 93 grammar tests pass (68 existing + 25 new U5 tests)

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Intent: Demonstrate U5 emerges inevitably from nodal equation, equal to other rules
Operators involved: REMESH (Recursivity), IL (Coherence), THOL (Self-organization)
Affected invariants: #7 (Fractality), #9 (Structural Metrics)

Key changes:
- Added complete 8-step derivation from ∂EPI/∂t = νf·ΔNFR(t)
- Showed chain rule inevitably leads to C_parent ≥ α·ΣC_child
- Demonstrated α = (1/√N)·η_phase·η_coupling from coupling physics
- Added detailed canonicity section equal to U1-U4 sections
- Proved independence from U2+U4b (spatial vs temporal dimensions)
- Updated all summaries to include U5 as seventh sub-rule

Physical traceability:
1. Nodal equation (axiomatic): ∂EPI/∂t = νf·ΔNFR
2. Hierarchical coupling (Inv. #7): EPI_parent = f(EPI_child_i)
3. Chain rule (calculus): ∂EPI_parent/∂t = Σ w_i·∂EPI_child_i/∂t
4. Coherence definition (Inv. #9): C ~ 1/|ΔNFR|
5. Conservation inequality: Mathematical consequence → C_parent ≥ α·ΣC_child
6. Stabilizer necessity: Only way to maintain conservation

Canonicity: STRONG (inevitable given Invariants #7 and #9)
Documentation quality: Equal to or better than U1-U4

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Implement U5: Multi-Scale Coherence grammar rule for hierarchical REMESH structures
…ation

Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Co-authored-by: fermga <203334638+fermga@users.noreply.github.com>
Document U6 Temporal Ordering as research proposal - defer canonical implementation
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