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Resonant Fractal Nature Theory — a mathematical framework for coherent patterns on graph-coupled networks.

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© 2026 TNFR project — MIT licensed.DOI 10.5281/zenodo.17602860
docs
grammar
PHYSICS_VERIFICATION.md
API_CONTRACTS.mdCANONICAL_OZ_SEQUENCES.mdEMPIRICAL_CONFRONTATION_EEG.mdREADME.mdSTRUCTURAL_FIELDS_TETRAD.mdSTRUCTURAL_INTERFACE_THEORY.md
theory
APPLIED_STRUCTURAL_ANALYSIS.mdCATALOG_TYPE_HYGIENE_PROGRAMME.mdDISSIPATIVE_AND_OPEN_SYSTEMS.mdEMERGENT_ONTOLOGY.mdEXTENDED_FIELDS_AND_DERIVED_QUANTITIES.mdFUNDAMENTAL_THEORY.mdGAUGE_SYMMETRY_AND_UNIFICATION.mdGLOSSARY.mdMATHEMATICAL_DYNAMICS_BASIS.mdMINIMAL_STRUCTURAL_DEGREES.mdNUCLEUS_A_PRIME_LADDER_ATLAS.mdNUCLEUS_B_EQUIVARIANCE_OBSTRUCTIONS.mdPHYSICAL_REGIME_CORRESPONDENCES.mdREADME.mdREMESH_INFINITY_DERIVATION.mdSTRUCTURAL_CONSERVATION_THEOREM.mdSTRUCTURAL_OPERATORS.mdSTRUCTURAL_STABILITY_AND_DYNAMICS.mdTNFR_BSD_RESEARCH_NOTES.mdTNFR_HODGE_RESEARCH_NOTES.mdTNFR_NAVIER_STOKES_RESEARCH_NOTES.mdTNFR_NUMBER_THEORY.mdTNFR_P_VS_NP_RESEARCH_NOTES.mdTNFR_RIEMANN_RESEARCH_NOTES.mdTNFR_VARIATIONAL_PRINCIPLE.mdTNFR_YANG_MILLS_RESEARCH_NOTES.mdTNFR.pdfUNIFIED_GRAMMAR_RULES.md
factorization-lab
analysis
analyze_patterns.pycertificate_manifest.py
benchmarks
benchmark_analysis.pybenchmark_expansion_suite.pyfull_spectrum_factorization.pypaley_gap_extended.pypaley_gap_smoke.pytest_benchmark_suite.py
demos
experiment_contexts
exp_0b1663cd19b7.jsonexp_0bf0054b7474.jsonexp_75a4c8ca616a.jsonexp_848ee0fd1857.jsonexp_f6fe00562193.jsonexp_fdf3da424e1e.json
failure_telemetry_batch.pyfeedback_integration_demo.pyintegration_demo_snapshots.dbseed_management_integration_demo.pysnapshot_integration_demo.pytrajectory_143.jsontrajectory_77.jsontrajectory_89.jsontrajectory_91.jsontrajectory_97.json
docs
FACTORING_PLAYBOOK.mdFALSE_POSITIVE_TEST_SUITE.mdOPERATOR_CERTIFICATES.mdROADMAP.mdSPECTRAL_ROUTE.md
experiment_contexts
exp_cebe1d9e7d8e.json
notebooks
spectral_history.ipynb
scripts
run_false_positive_tests.py
tests
run_false_positive_test_suite.pytest_cli.pytest_false_positive_methodology.pytest_false_positive_verifier.pytest_feedback_integration.pytest_partitioning.pytest_seed_management.pytest_self_opt_support.pytest_snapshot_system.pytest_spectral_paley.pytest_verification_robustness.py
tnfr_factorization
__init__.pyapi.pycli.pyfailure_telemetry.pyfeedback_adapter.pyfeedback_integration.pypartitioning.pyself_opt_support.pyspectral_paley.py
demo_snapshots.dbLICENSE_SNAPSHOT.mdPACKAGE_SUMMARY.mdREADME.mdseed_management.pysnapshot_system.pytest_certificate_hashing.pytest_installation.pyverification_trajectory_77.json
benchmarks
analyze_tetrad_universality.pyb0star_alpha_canonical_product_graphs.pybenchmark_optimization_tracks.pybenchmark_utils.pyboundary_vibration.pybridge_primes_riemann.pychiral_involution.pycli_utils.pycoherence_projector_sense_index.pycommutant_bridge.pycomposition_arithmetic.pyconfinement_zones_test.pyconservation_law_validation.pydirected_paley_bridge.pyemergent_arithmetic_pulse.pyemergent_atom_dynamics.pyemergent_atomic_shells.pyemergent_base_dimension.pyemergent_dimension_dynamics.pyemergent_fractal_pulse.pyemergent_fractal_simplex_dimension.pyemergent_integers_symmetry.pyemergent_musical_nfr.pyemergent_nfr_geometry.pyemergent_nfr_where.pyemergent_rationals.pyemergent_rhythm.pyemergent_screening.pyemergent_shell_cardinals.pyemergent_shell_ordering.pyemergent_simplex_dimension.pyemergent_substrate_symmetry.pyequivariance_wall.pyexternal_phase_gate_validation.pyfield_methods_battery.pygolden_residue_remesh_bridge.pyintegrated_force_regime_study.pyinverse_spectrum_to_symmetry.pyk_phi_safety_demo.pykuramoto_farey_bridge.pymissing_piece_bridge.pymultichannel_interface_benchmark.pynavier_stokes_recipe_bridge.pynodal_propagator_residue_bridge.pyns_moment_hierarchy_cascade.pyoperational_irreducibility.pypaley_bridge.pyphase_curvature_investigation.pyphase_wall.pyphi_s_confinement_investigation.pyprimes_as_consequence.pypulse_phase_coherence_budget.pyREADME.mdremesh_infinity_riemann_baseline.pyremesh_infinity_riemann_composed.pyremesh_infinity_riemann_modified_graph.pyremesh_infinity_riemann_operator.pyremesh_infinity_riemann_spectral_basis.pyremesh_infinity_riemann_spectral_robustness.pyremesh_infinity_riemann_spectral.pyresidue_phase_vs_riemann.pystructural_interface_benchmark.pytemporal_interface_benchmark.pytetrad_results_aggregate.pyu2_destabilization_irreversibility.pyuniversality_clusters.pyxi_c_fast_experiment.py
primality-test
benchmarks
comprehensive_benchmark.py
docs
ADVANCED_INTEGRATION.mdmathematical_foundation.mdperformance_analysis.md
examples
advanced_examples.pybasic_usage.py
tnfr_primality
__init__.py__main__.pyadvanced_cli.pyadvanced_core.pycli.pyconstants.pycore.pyoptimized.py
MANIFEST.inPACKAGE_SUMMARY.mdREADME.mdRELEASE_NOTES_v1.0.mdsetup.pytest_installation.py
tests
core_physics
__init__.pytest_conservation_laws.pytest_delta_nfr_computation_paths.pytest_delta_nfr.pytest_dispersion_coherence_sign_invariance.pytest_emergent_constants_guard.pytest_lyapunov_operators.pytest_nodal_equation.pytest_structural_triad.py
data
replay_manifests
sample_run
_manifest_summary.json_manifest.json_partition_files.txt.gz
self_opt_validation
seed_alpha
paley.json
seed_beta
integration.json
seed_gamma
unknown.json
self_optimization
test_run
partitioned
test_run
test_run_p0.jsontest_run_p1.json
_manifest_summary.json_manifest.json
engines
test_pattern_discovery_manifest.pytest_self_optimization_engine.py
mathematics
__init__.pytest_autodiff.pytest_backends.pytest_dissipative_dynamics.pytest_epi.pytest_factory_patterns.pytest_metrics.pytest_navier_stokes_refounded.pytest_number_theory_canonical.pytest_operators.pytest_residue_networks.pytest_riemann_nodal_pulse.pytest_riemann_pulse_coherence.pytest_spaces.pytest_transforms.pytest_validator.py
operators
test_canonical_operators_modern.pytest_grammar_canon.pytest_grammar_canonical_consistency.pytest_grammar_dynamics.pytest_operator_contracts.pytest_operator_strategies.py
parallel
test_fractal_partition_manifest.py
physics
test_conservation_gauge_unification.pytest_dissipative_conservation.pytest_emergent_chemistry.pytest_field_cache_invalidation.pytest_gauge.pytest_phase_transition.pytest_signatures.pytest_spectral_conservation.pytest_structural_diffusion.pytest_structural_integrity.pytest_symplectic_substrate.pytest_tetrad_bounds.pytest_variational.pytest_yang_mills_closure.pytest_yang_mills_derivability.pytest_yang_mills_scaling.pytest_yang_mills_structural_gap.pytest_yang_mills_u6_sweep.py
scripts
test_run_self_opt_validation.pytest_run_self_optimization.py
sdk
__init__.pytest_simple_advanced.py
__init__.pyconftest.pyREADME.mdtest_breast_cancer_phase_gate_demo.pytest_classical_mechanics.pytest_distributed_fft.pytest_external_phase_gate_validation.pytest_factorization_entrypoint.pytest_multichannel_interface.pytest_nodal_optimizer.pytest_phase_gate_api.pytest_replay_register_manifest.pytest_signal_confrontation.pytest_structural_interface_api.pytest_structural_interface_baselines.pytest_structural_interface_benchmark.pytest_temporal_interface.pytest_vectorized_coherence_length_regression.pytest_wine_quality_phase_gate_demo.pyutils.py
examples
01_foundations
01_hello_world.py02_musical_resonance.py03_network_formation.py04_operator_sequences.py05_coherence_evolution.py06_network_topologies.py07_phase_transitions.py08_emergent_phenomena.py09_visualization_suite.py10_simplified_sdk_showcase.py
02_physics_regimes
11_classical_limit_comparison.py115_operator_contract_audit.py12_classical_mechanics_demo.py13_quantum_mechanics_demo.py14_uncertainty_and_interference.py15_train_crossing_demo.py17_conservation_law_demo.py26_gauge_structure_demo.py27_variational_principle_demo.py28_dissipative_systems_demo.py29_lyapunov_stability_demo.py30_self_optimization_demo.py31_mathematical_constants_basis.py33_complex_field_unification.py34_conservation_protocol_suite.py35_tetrad_irreducibility.py36_grammar_violation_detector.py37_operator_tetrad_synergy.py38_grammar_energy_landscape.py39_nodal_equation_decomposition.py
03_riemann_zeta
157_nodal_pulse_phase_attack.py41_von_mangoldt_zeta_demo.py42_riemann_zeros_as_resonances.py43_prime_ladder_hamiltonian_demo.py44_weil_explicit_formula_demo.py45_li_keiper_demo.py46_weil_tnfr_positivity_demo.py47_alpha_sweep_demo.py48_admissible_family_sweep_demo.py49_nodeaware_gauge_sweep_demo.py50_uniform_coercivity_demo.py51_adaptive_coercivity_demo.py52_paley_gap_coercivity_demo.py53_lyapunov_spectral_positivity_demo.py54_hilbert_polya_demo.py55_structural_zero_density_demo.py56_spectral_emergence_demo.py57_admissible_rescaling_demo.py58_oscillatory_correction_demo.py
04_riemann_L_twisted
59_dirichlet_l_function_demo.py60_dirichlet_l_continuation_demo.py61_dirichlet_l_hamiltonian_demo.py62_dirichlet_weil_explicit_formula_demo.py63_dirichlet_li_keiper_demo.py64_twisted_weil_positivity_demo.py65_twisted_alpha_sweep_demo.py66_twisted_admissible_family_sweep_demo.py67_twisted_nodeaware_gauge_sweep_demo.py68_twisted_hermite_family_demo.py69_twisted_coercivity_uniform_demo.py70_twisted_paley_gap_coercivity_demo.py71_twisted_lyapunov_spectral_demo.py72_twisted_hilbert_polya_demo.py73_twisted_structural_zero_density_demo.py74_twisted_spectral_emergence_demo.py75_twisted_admissible_rescaling_demo.py76_twisted_oscillatory_correction_demo.py
05_type_hygiene
77_remesh_infinity_residue_split_demo.py78_nuf_type_signature_demo.py79_epi_type_signature_demo.py80_phi_type_signature_demo.py81_dnfr_type_signature_demo.py82_remesh_window_type_signature_demo.py83_delta_phi_max_type_signature_demo.py84_coupling_weights_type_signature_demo.py85_tetrad_closure_signature_demo.py86_currents_closure_signature_demo.py87_aggregates_closure_signature_demo.py88_urules_consistency_signature_demo.py89_operator_catalog_discipline_signature_demo.py
06_navier_stokes
158_navier_stokes_two_face_refounded.py
07_number_theory
100_prime_families_orbits.py101_numbers_as_coupled_network.py102_nodal_flow_primes_equilibria.py116_nuf_emergent_prime_visibility.py146_primality_grammatical_inertness.py147_numbers_as_free_monoid_words.py148_capacity_arm_carries_von_mangoldt.py149_p14_is_the_capacity_arm_operator.py153_structural_frequency_rank_cyclotomy.py40_arithmetic_number_theory.py94_generative_number_construction.py95_primes_from_spectral_waves.py96_spectral_vibration_of_coherence.py97_goldbach_additive_multiplicative.pyemergent_chemistry_particles_demo.py
08_emergent_geometry
103_emergent_substrate_meets_riemann.py106_per_node_polarization_geometry.py107_orthogonal_structure_emergent_geometry.py108_emergent_field_generating_structure.py112_structure_predicts_coherence_flow.py113_overdamped_projection_bridge.py114_substrate_conserved_quantities.py117_emergent_geometry_residue_graph.py118_emergent_vs_classical_operator.py119_phase_sector_directed_residue.py120_symmetry_wall_substrate_vs_spectrum.py121_canonical_symmetry_break_negative.py122_factorization_phase_sector.py123_symmetry_sector_decomposition.py124_emergent_metric_fractal_consistency.py125_node_is_the_emergent_substrate.py126_two_layers_base_fiber.py127_base_is_emergent_not_imposed.py128_base_substrate_coemergence.py129_spectral_gap_base_fiber_clock.py130_operators_break_substrate_charges.py131_coemergent_loop_convergence.py132_geometric_phase_holonomy.py133_psi_topological_defects.py134_spectral_dimension_heat_kernel.py135_arrow_of_time_h_theorem.py136_heat_kernel_coefficients.py137_synchronization_transition.py138_structure_frequency_synchronization.py139_grammar_formal_language.py140_grammar_automaton.py141_grammar_rule_decomposition.py142_grammar_operator_quotient.py143_glyphic_function_sublanguage.py144_branching_combinator.py145_syntactic_monoid_starfree.py150_emergent_grammatical_pattern_parry.py151_grammar_in_emergent_geometry.py152_operator_contract_tetrahedron.py154_conductor_annotated_qr_spectrum.py155_ontological_position_of_numbers.py156_emergence_directness_law.py98_emergent_symplectic_substrate.py99_structural_diffusion.pyunified_fields_showcase.py
09_millennium
109_p_vs_np_coherence_synthesis.py110_bsd_rank_structural_pressure.py111_hodge_discrete_and_honest_gap.py
10_applications
159_empirical_confrontation_pipeline.py90_phase_gate_monitor_demo.py91_breast_cancer_phase_gate_demo.py92_wine_quality_phase_gate_demo.py93_structural_interface_demo.pypytorch_cuda_demo.py
README.md
scripts
replay
__init__.pyregister_manifest.py
__init__.pyREADME.mdrebuild_failure_manifest.pyrun_reproducible_benchmarks.pyrun_self_opt_validation.pyrun_self_optimization.pytnfr_is_prime.pyvalidate_conservation_law.pyverify_internal_references.py
src
core
__init__.pyevaluation.py
tnfr
backends
__init__.pyjax_backend.pynumpy_backend.pyoptimized_numpy.pyREADME.mdtorch_backend.py
cli
__init__.py__init__.pyiarguments.pyarguments.pyiexecution.pyexecution.pyiinteractive_validator.pyREADME.mdutils.pyutils.pyi
compat
__init__.pydataclass.pyjsonschema_stub.pymatplotlib_stub.pynumpy_stub.pyREADME.md
config
__init__.py__init__.pyiconstants.pyconstants.pyidefaults_core.pydefaults_init.pydefaults_metric.pydefaults.pyfeature_flags.pyfeature_flags.pyiglyph_constants.pyoperator_names.pyoperator_names.pyiphysics_derivation.pyprecision_modes.pypresets.pypresets.pyiREADME.mdsecurity.pythresholds.pytnfr_config.py
constants
__init__.py__init__.pyialiases.pyaliases.pyicanonical.pymetric.pymetric.pyioperational.py
core
__init__.pycontainer.pydefault_implementations.pyexceptions.pyinterfaces.pyREADME.md
dynamics
__init__.py__init__.pyiadaptation.pyadaptation.pyiadaptive_sequences.pyadaptive_sequences.pyiadelic.pyadvanced_cache_optimizer.pyadvanced_fft_arithmetic.pyaliases.pyaliases.pyibifurcation.pycache_aware_fft_engine.pycanonical.pycanonical.pyicomputational_hub.pycoordination.pycoordination.pyidistributed_fft.pydnfr.pydnfr.pyidynamic_limits.pyemergent_centralization.pyemergent_integration_engine.pyfeedback.pyfeedback.pyifft_backend.pyfft_cache_coordinator.pyfft_dispatchers.pyfft_engine.pyfft_workers.pyfused_dnfr.pyhomeostasis.pyhomeostasis.pyiintegrators.pyintegrators.pyilearning.pylearning.pyimetabolism.pymulti_modal_cache.pynbody_tnfr.pynbody.pynodal_optimizer.pyoptimization_orchestrator.pypropagation.pyREADME.mdruntime.pyruntime.pyisampling.pysampling.pyiselectors.pyselectors.pyiself_optimizing_engine.pyspectral_structural_fusion.pystructural_cache.pystructural_clip.pysymplectic.pyunified_backend.pyunified_mathematical_cache_orchestrator.py
engines
computation
__init__.pyfft_engine.pyunified_fft_engine.pyunified_gpu_system.py
constants
__init__.pycanonical.pyoperational.py
integration
__init__.pyemergent_integration.py
pattern_discovery
__init__.pymathematical_patterns.pymulti_modal_cache.py
self_optimization
__init__.pyengine.py
__init__.pyREADME.md
errors
__init__.pycontextual.py
factorization
__init__.py
flatten
README.md
gamma
README.md
glyph_history
README.md
glyph_runtime
README.md
immutable
README.md
initialization
README.md
io
README.md
math
__init__.pyfields_symbolic.pygrammar_validators.pyoptimizer.pyREADME.mdsymbolic.py
mathematics
__init__.pybackend.pybackend.pyidynamics.pydynamics.pyiepi.pyepi.pyigenerators.pygenerators.pyiliouville.pymetrics.pymetrics.pyinumber_theory.pyoperators_factory.pyoperators_factory.pyioperators.pyoperators.pyioptimized_primality.pyprojection.pyprojection.pyiREADME.mdruntime.pyruntime.pyispaces.pyspaces.pyispectral.pytransforms.pytransforms.pyiunified_cache.pyunified_numerical.pyzeta.py
metrics
__init__.py__init__.pyibuffer_cache.pybuffer_cache.pyicache_utils.pycoherence.pycoherence.pyicommon.pycommon.pyicore.pycore.pyidiagnosis.pydiagnosis.pyiemergence.pyexport.pyexport.pyiglyph_timing.pyglyph_timing.pyilearning_metrics.pylearning_metrics.pyilocal_coherence.pyphase_coherence.pyphase_compatibility.pyREADME.mdreporting.pyreporting.pyisense_index.pysense_index.pyitelemetry.pytetrad.pytrig_cache.pytrig_cache.pyitrig.pytrig.pyi
multiscale
__init__.pyhierarchical.pyREADME.md
navier_stokes
__init__.pyconservative_face.pyoperator.py
node
README.md
observers
README.md
operators
network_analysis
__init__.pysource_detection.py
postconditions
__init__.pymutation.py
preconditions
__init__.pycoherence.pydissonance.pyemission.pymutation.pyreception.pyresonance.py
strategies
__init__.pydefaults.pygpu_strategies.pystrategy.py
__init__.py__init__.pyialgebra.pycanonical_patterns.pycascade.pycoherence.pycontraction.pycoupling.pycycle_detection.pydefinitions_base.pydefinitions.pydefinitions.pyidissonance.pyemission.pyexpansion.pygrammar_application.pygrammar_canon.pygrammar_context.pygrammar_core.pygrammar_dynamics.pygrammar_error_factory.pygrammar_memoization.pygrammar_patterns.pygrammar_telemetry.pygrammar_types.pygrammar_u6.pygrammar_validate.pygrammar.pygrammar.pyihamiltonian.pyhealth_analyzer.pyintrospection.pyjitter.pyjitter.pyilifecycle.pymetabolism.pymetrics_basic.pymetrics_core.pymetrics_network.pymetrics_structural.pymetrics_u6.pymetrics.pymutation.pynodal_equation.pyoperator_contracts.pypattern_detection.pypatterns.pyREADME.mdreception.pyrecursivity.pyregistry.pyregistry.pyiremesh.pyremesh.pyiresonance.pyself_organization.pysilence.pystructural_units.pytransition.py
parallel
__init__.pyauto_scaler.pydistributed.pyengine.pymonitoring.pypartitioner.pyREADME.md
performance
guardrails.py
physics
__init__.py_helpers.pycalibration.pycanonical.pycell.pyclassical_mechanics.pyconservation_gauge_unification.pyconservation.pydissipative_conservation.pyemergent_chemistry.pyemergent_particles.pyextended.pyfields.pygauge.pyintegrity.pyinteractions.pylife.pylyapunov.pypatterns.pyphase_transition.pyquantum_mechanics.pyREADME.mdsignatures.pyspectral_conservation.pyspectral_metrics.pystructural_diffusion.pysymplectic_substrate.pytelemetry.pyunified.pyvariational.pyvectorized_ops.py
primality
__init__.py
recipes
__init__.pycookbook.pyREADME.md
riemann
__init__.pyadmissible_family_sweep.pyadmissible_rescaling.pyaggregates_closure_signature.pyalpha_sweep.pyanalytic_continuation_dirichlet.pyanalytic_continuation.pycoercivity_uniform.pycoupling_weights_type_signature.pycurrents_closure_signature.pydelta_phi_max_type_signature.pydirichlet_l.pydnfr_type_signature.pyepi_type_signature.pyhilbert_polya.pyli_keiper.pylyapunov_spectral_positivity.pynodal_pulse.pynodeaware_gauge_sweep.pynuf_type_signature.pyoperator_catalog_discipline_signature.pyoperator.pyoscillatory_correction.pypaley_gap_coercivity.pyphi_type_signature.pyprime_ladder_hamiltonian.pypulse_coherence.pyremesh_infinity_residue_split.pyremesh_window_type_signature.pyspectral_emergence.pystructural_zero_density.pytelemetry.pytetrad_closure_signature.pytwisted_admissible_family_sweep.pytwisted_admissible_rescaling.pytwisted_alpha_sweep.pytwisted_coercivity_uniform.pytwisted_hermite_family.pytwisted_hilbert_polya.pytwisted_li_keiper.pytwisted_lyapunov_spectral_positivity.pytwisted_nodeaware_gauge_sweep.pytwisted_oscillatory_correction.pytwisted_paley_gap_coercivity.pytwisted_prime_ladder_hamiltonian.pytwisted_spectral_emergence.pytwisted_structural_zero_density.pytwisted_weil_explicit_formula.pytwisted_weil_positivity.pyurules_consistency_signature.pyvon_mangoldt.pyweil_explicit_formula.pyweil_positivity.py
schemas
__init__.pygrammar.jsonREADME.md
sdk
__init__.py__init__.pyiadaptive_system.pyadaptive_system.pyibuilders.pybuilders.pyifluent.pyfluent.pyiREADME.mdself_opt.pysimple.pytemplates.pytemplates.pyiutils.py
security
__init__.pycrypto.pydatabase.pyREADME.mdsubprocess.pyvalidation.py
sequencing
__init__.pypatterns.pyREADME.md
services
__init__.pyorchestrator.pyREADME.md
sparse
__init__.pyREADME.mdrepresentations.py
structural
README.md
telemetry
__init__.pycache_metrics.pycache_metrics.pyiconstants.pynu_f.pynu_f.pyiREADME.mdunified_telemetry_system.pyverbosity.pyverbosity.pyi
tools
__init__.pydomain_templates.pyREADME.mdsequence_generator.pytnfr_is_prime_cli_optimized.pytnfr_is_prime_cli.py
topology
__init__.pyasymmetry.pyREADME.md
utils
cache_layers.pycache.pycache.pyicallbacks.pycallbacks.pyichunks.pychunks.pyidata.pydata.pyifast_diameter.pygraph.pygraph.pyiinit.pyinit.pyiio.pyio.pyinumeric.pynumeric.pyiREADME.mdtopology.pyunified_cache.py
validation
__init__.py__init__.pyiaggregator.pybase.pycompatibility.pycompatibility.pyiconfig.pygraph.pygraph.pyihealth.pyinput_validation.pyinterface_baselines.pyinvariants.pymultichannel_interface.pyphase_gate.pyREADME.mdrules.pyrules.pyiruntime.pyruntime.pyisequence_validator.pysignal_confrontation.pysoft_filters.pysoft_filters.pyispectral.pyspectral.pyistructural_interface.pytemporal_interface.pyunified_validation_system.pyvalidator.pywindow.pywindow.pyi
visualization
__init__.pycascade_viz.pyhierarchy.pyREADME.mdsequence_plotter.py
yang_mills
__init__.pyclosure.pyderivability.pyscaling.pystructural_gap.pyu6_sweep.py
__init__.py__init__.pyi_compat.py_version.py_version.pyialias.pyalias.pyibackend_config.pycache.pycache.pyiexecution.pyexecution.pyiflatten.pyflatten.pyigamma.pygamma.pyiglyph_history.pyglyph_history.pyiglyph_runtime.pyglyph_runtime.pyiimmutable.pyimmutable.pyiinitialization.pyinitialization.pyiio.pyio.pyilocking.pylocking.pyinode.pynode.pyiobservers.pyobservers.pyiontosim.pyontosim.pyipy.typedrng.pyrng.pyisecure_config.pyselector.pyselector.pyisense.pysense.pyistructural.pystructural.pyitokens.pytokens.pyitrace.pytrace.pyitypes.pytypes.pyiunits.pyunits.pyi
tetrad_evaluator.py
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FILE: src/tnfr/mathematics/dynamics.py

dynamics.py

Spectral dynamics helpers driven by ΔNFR generators.

Source Code

python
"""Spectral dynamics helpers driven by ΔNFR generators."""

from __future__ import annotations

from dataclasses import field
from typing import Any, NamedTuple, Sequence

from ..compat.dataclass import dataclass
from .backend import MathematicsBackend, ensure_array, ensure_numpy, get_backend
from .spaces import HilbertSpace
from .unified_numerical import TNFRValueError, np

try:  # pragma: no cover - optional SciPy dependency
    from scipy.linalg import expm as _scipy_expm  # type: ignore
except Exception:  # pragma: no cover - SciPy not installed
    _scipy_expm = None

__all__ = ["MathematicalDynamicsEngine", "ContractiveDynamicsEngine"]


def _has_backend_matrix_exp(backend: MathematicsBackend) -> bool:
    """Return ``True`` when ``backend`` exposes a usable ``matrix_exp``."""

    matrix_exp = getattr(backend, "matrix_exp", None)
    if not callable(matrix_exp):
        return False

    try:
        probe = ensure_array([[0.0]], dtype=np.complex128, backend=backend)
        matrix_exp(probe)
    except (AttributeError, NotImplementedError):
        return False
    except Exception:
        # Older backends may surface missing implementations as runtime errors;
        # treat them as signals to fall back to SciPy when available.
        return False
    return True


def _as_matrix(
    matrix: Sequence[Sequence[complex]] | np.ndarray | Any,
    *,
    backend: MathematicsBackend,
) -> Any:
    arr = ensure_array(matrix, dtype=np.complex128, backend=backend)
    shape = getattr(arr, "shape", None)
    if shape is None or len(shape) != 2 or shape[0] != shape[1]:
        raise TNFRValueError(
            "Generator matrix must be square.",
            context={"shape": shape},
            suggestion="Provide a square matrix.",
        )
    return arr


def _is_hermitian(
    matrix: Any, *, atol: float = 1e-9, backend: MathematicsBackend
) -> bool:
    matrix_np = ensure_numpy(matrix, backend=backend)
    return bool(np.allclose(matrix_np, matrix_np.conj().T, atol=atol))


def _vectorize_density(matrix: Any, *, backend: MathematicsBackend) -> Any:
    arr = ensure_array(matrix, dtype=np.complex128, backend=backend)
    return arr.transpose(1, 0).reshape((-1,))


def _devectorize_density(vector: Any, dim: int, *, backend: MathematicsBackend) -> Any:
    arr = ensure_array(vector, dtype=np.complex128, backend=backend)
    return arr.reshape((dim, dim)).transpose(1, 0)


class TraceValue(NamedTuple):
    """Container for trace evaluations in both backend and NumPy space."""

    backend: Any
    numpy: complex | None


def _trace(matrix: Any, *, backend: MathematicsBackend) -> TraceValue:
    traced_backend = backend.einsum("ii->", matrix)
    try:
        traced_numpy = complex(
            np.asarray(ensure_numpy(traced_backend, backend=backend))
        )
    except (ValueError, TypeError, Exception):
        # Fallback for backends where conversion fails (e.g. JAX tracing)
        traced_numpy = None
    return TraceValue(traced_backend, traced_numpy)


@dataclass(slots=True)
class MathematicalDynamicsEngine:
    """Unitary evolution generated by Hermitian ΔNFR operators.

    The engine accepts inputs expressed as backend-native tensors (NumPy,
    :mod:`jax`, :mod:`torch`).  When the configured backend supports automatic
    differentiation the evolution map ``exp(-i·Δ·dt)`` remains differentiable
    because native propagators are now preferred.  Passing ``use_scipy=True``
    explicitly opts into SciPy's exponential; we only fall back automatically
    when the backend lacks a ``matrix_exp`` implementation.
    """

    generator: np.ndarray
    hilbert_space: HilbertSpace
    atol: float = 1e-9
    _use_scipy: bool = False
    backend: MathematicsBackend = field(init=False, repr=False)
    _generator_backend: Any = field(init=False, repr=False)
    _numpy_generator: np.ndarray = field(init=False, repr=False)

    def __init__(
        self,
        generator: Sequence[Sequence[complex]] | np.ndarray | Any,
        hilbert_space: HilbertSpace,
        *,
        atol: float = 1e-9,
        use_scipy: bool | None = None,
        backend: MathematicsBackend | None = None,
    ) -> None:
        resolved_backend = backend or get_backend()
        matrix = _as_matrix(generator, backend=resolved_backend)
        matrix_np = ensure_numpy(matrix, backend=resolved_backend)
        if matrix_np.shape != (hilbert_space.dimension, hilbert_space.dimension):
            raise TNFRValueError(
                "Generator dimension must match the Hilbert space.",
                context={
                    "generator_shape": matrix_np.shape,
                    "hilbert_dimension": hilbert_space.dimension,
                },
                suggestion="Ensure generator matches Hilbert space dimension.",
            )
        if not _is_hermitian(matrix, atol=atol, backend=resolved_backend):
            raise TNFRValueError(
                "Dynamics generator must be Hermitian.",
                context={"atol": atol},
                suggestion="Ensure generator is Hermitian.",
            )
        self.backend = resolved_backend
        self._generator_backend = matrix
        self._numpy_generator = matrix_np
        self.generator = matrix_np
        self.hilbert_space = hilbert_space
        self.atol = float(atol)
        if use_scipy is None:
            has_matrix_exp = _has_backend_matrix_exp(self.backend)
            if has_matrix_exp:
                self._use_scipy = False
            elif _scipy_expm is not None:
                self._use_scipy = True
            else:
                raise RuntimeError(
                    "Backend lacks matrix_exp and SciPy is unavailable for fallback."
                )
        else:
            if use_scipy and _scipy_expm is None:
                raise RuntimeError("SciPy expm requested but SciPy is not available.")
            self._use_scipy = bool(use_scipy and _scipy_expm is not None)

    def _unitary_backend(self, dt: float) -> Any:
        if self._use_scipy and _scipy_expm is not None:
            return ensure_array(
                _scipy_expm(-1j * dt * self._numpy_generator),
                backend=self.backend,
            )
        return self.backend.matrix_exp(-1j * dt * self._generator_backend)

    def step(
        self,
        state: Sequence[complex] | np.ndarray | Any,
        *,
        dt: float = 1.0,
        normalize: bool = True,
    ) -> Any:
        """Evolve ``state`` by ``dt`` using the unitary ``exp(-i·Δ·dt)``."""

        vector = ensure_array(state, dtype=np.complex128, backend=self.backend)
        if vector.shape != (self.hilbert_space.dimension,):
            raise TNFRValueError(
                "State vector dimension mismatch.",
                context={
                    "vector_shape": vector.shape,
                    "expected_dimension": self.hilbert_space.dimension,
                },
                suggestion="Ensure state vector matches Hilbert space dimension.",
            )
        unitary = self._unitary_backend(dt)
        evolved = self.backend.matmul(unitary, vector)
        if normalize:
            norm_backend = self.backend.norm(evolved)
            norm_numpy = float(
                np.asarray(ensure_numpy(norm_backend, backend=self.backend))
            )
            if np.isclose(norm_numpy, 0.0, atol=self.atol):
                raise TNFRValueError(
                    "Cannot normalise a null state vector.",
                    context={"norm": norm_numpy, "atol": self.atol},
                    suggestion="Provide a non-zero state vector.",
                )
            evolved = evolved / norm_backend
        return evolved

    def evolve(
        self,
        state: Sequence[complex] | np.ndarray | Any,
        *,
        steps: int,
        dt: float = 1.0,
        normalize: bool = True,
    ) -> Any:
        """Return trajectory of length ``steps + 1`` starting from ``state``."""

        if steps < 0:
            raise TNFRValueError(
                "steps must be non-negative.",
                context={"steps": steps},
                suggestion="Provide a non-negative integer for steps.",
            )
        current = ensure_array(state, dtype=np.complex128, backend=self.backend)
        if current.shape != (self.hilbert_space.dimension,):
            raise TNFRValueError(
                "State dimension mismatch.",
                context={
                    "expected_dimension": self.hilbert_space.dimension,
                    "received_shape": current.shape,
                },
                suggestion="Ensure state vector matches Hilbert space dimension.",
            )
        trajectory: list[Any] = [current]
        for _ in range(steps):
            current = self.step(current, dt=dt, normalize=normalize)
            trajectory.append(current)
        return self.backend.stack(trajectory, axis=0)


@dataclass(slots=True)
class ContractiveDynamicsEngine:
    """Contractive semigroup evolution driven by Lindblad ΔNFR generators.

    Backend-native tensors are accepted for all density operators.  When the
    chosen backend supports automatic differentiation we keep gradients intact
    by default because native semigroup propagators are preferred.  Requesting
    ``use_scipy=True`` still falls back to SciPy's :func:`scipy.linalg.expm`,
    primarily for generators missing backend support.
    """

    generator: np.ndarray
    hilbert_space: HilbertSpace
    atol: float = 1e-9
    _use_scipy: bool = False
    backend: MathematicsBackend = field(init=False, repr=False)
    _generator_backend: Any = field(init=False, repr=False)
    _numpy_generator: np.ndarray = field(init=False, repr=False)
    _identity_backend: Any = field(init=False, repr=False)
    _last_contractivity_gap: float = field(init=False, repr=False)

    def __init__(
        self,
        generator: Sequence[Sequence[complex]] | np.ndarray | Any,
        hilbert_space: HilbertSpace,
        *,
        atol: float = 1e-9,
        ensure_contractive: bool = True,
        use_scipy: bool | None = None,
        backend: MathematicsBackend | None = None,
    ) -> None:
        resolved_backend = backend or get_backend()
        matrix = _as_matrix(generator, backend=resolved_backend)
        matrix_np = ensure_numpy(matrix, backend=resolved_backend)
        expected = hilbert_space.dimension * hilbert_space.dimension
        if matrix_np.shape != (expected, expected):
            raise TNFRValueError(
                "Generator must act on vectorised density operators.",
                context={
                    "expected_dimension": (expected, expected),
                    "received_shape": matrix_np.shape,
                },
                suggestion="Ensure generator dimension matches vectorized Hilbert space.",
            )
        self.backend = resolved_backend
        self._generator_backend = matrix
        self._numpy_generator = matrix_np.astype(np.complex128, copy=False)
        self.generator = self._numpy_generator
        self.hilbert_space = hilbert_space
        self.atol = float(atol)
        if use_scipy is None:
            has_matrix_exp = _has_backend_matrix_exp(self.backend)
            if has_matrix_exp:
                self._use_scipy = False
            elif _scipy_expm is not None:
                self._use_scipy = True
            else:
                raise RuntimeError(
                    "Backend lacks matrix_exp and SciPy is unavailable for fallback."
                )
        else:
            if use_scipy and _scipy_expm is None:
                raise RuntimeError("SciPy expm requested but SciPy is not available.")
            self._use_scipy = bool(use_scipy and _scipy_expm is not None)

        self._identity_backend = ensure_array(
            np.eye(hilbert_space.dimension, dtype=np.complex128),
            backend=self.backend,
        )
        self._last_contractivity_gap = float("nan")
        if ensure_contractive:
            eigenvalues_backend, _ = self.backend.eig(self._generator_backend)
            eigenvalues = ensure_numpy(eigenvalues_backend, backend=self.backend)
            if np.max(eigenvalues.real) > self.atol:
                raise TNFRValueError(
                    "ΔNFR generator is not contractive: positive real eigenvalues detected.",
                    context={"max_real_eigenvalue": np.max(eigenvalues.real)},
                    suggestion="Ensure generator is dissipative.",
                )

    def _propagator_backend(self, dt: float) -> Any:
        if self._use_scipy and _scipy_expm is not None:
            return ensure_array(
                _scipy_expm(dt * self._numpy_generator),
                backend=self.backend,
            )
        return self.backend.matrix_exp(dt * self._generator_backend)

    def frobenius_norm(
        self,
        density: Sequence[Sequence[complex]] | np.ndarray | Any,
        *,
        center: bool = False,
    ) -> float:
        """Return the Frobenius norm associated with the Hilbert space."""

        matrix = ensure_array(density, dtype=np.complex128, backend=self.backend)
        if matrix.shape != (self.hilbert_space.dimension, self.hilbert_space.dimension):
            raise TNFRValueError(
                "Density operator dimension mismatch.",
                context={
                    "expected_dimension": (
                        self.hilbert_space.dimension,
                        self.hilbert_space.dimension,
                    ),
                    "received_shape": matrix.shape,
                },
                suggestion="Ensure density operator matches Hilbert space dimension.",
            )
        if center:
            trace_value = _trace(matrix, backend=self.backend)
            trace_backend = trace_value.backend / self.hilbert_space.dimension
            matrix = matrix - trace_backend * self._identity_backend
        norm_backend = self.backend.norm(matrix, ord="fro")
        return float(np.asarray(ensure_numpy(norm_backend, backend=self.backend)))

    @property
    def last_contractivity_gap(self) -> float:
        """Return the latest monitored contractivity gap (NaN if unavailable)."""

        return float(self._last_contractivity_gap)

    def step(
        self,
        density: Sequence[Sequence[complex]] | np.ndarray | Any,
        *,
        dt: float = 1.0,
        normalize_trace: bool = True,
        enforce_contractivity: bool = True,
        raise_on_violation: bool = False,
        symmetrize: bool = True,
    ) -> Any:
        """Advance ``density`` by ``dt`` enforcing trace and contractivity control."""

        matrix = ensure_array(density, dtype=np.complex128, backend=self.backend)
        dim = self.hilbert_space.dimension
        if matrix.shape != (dim, dim):
            raise TNFRValueError(
                "Density operator dimension mismatch.",
                context={
                    "expected_dimension": (dim, dim),
                    "received_shape": matrix.shape,
                },
                suggestion="Ensure density operator matches Hilbert space dimension.",
            )

        initial_norm = None
        if enforce_contractivity:
            trace_value = _trace(matrix, backend=self.backend)
            trace_backend = trace_value.backend / dim
            centered = matrix - trace_backend * self._identity_backend
            initial_norm_backend = self.backend.norm(centered, ord="fro")
            try:
                initial_norm = float(
                    np.asarray(ensure_numpy(initial_norm_backend, backend=self.backend))
                )
            except (ValueError, TypeError, Exception):
                initial_norm = None

        vector = _vectorize_density(matrix, backend=self.backend)
        propagator = self._propagator_backend(dt)
        evolved_vec = self.backend.matmul(propagator, vector)
        evolved = _devectorize_density(evolved_vec, dim, backend=self.backend)

        if symmetrize:
            evolved = 0.5 * (evolved + self.backend.conjugate_transpose(evolved))

        if normalize_trace:
            trace_value = _trace(evolved, backend=self.backend)
            if trace_value.numpy is not None:
                if np.isclose(trace_value.numpy, 0.0, atol=self.atol):
                    raise TNFRValueError(
                        "Trace collapsed below tolerance during evolution.",
                        context={"trace": trace_value.numpy, "atol": self.atol},
                        suggestion="Check generator properties or initial state.",
                    )
                if not np.isclose(trace_value.numpy, 1.0, atol=10 * self.atol):
                    evolved = evolved / trace_value.backend
            else:
                # Tracing fallback: always normalize
                evolved = evolved / trace_value.backend

        if enforce_contractivity and initial_norm is not None:
            trace_value = _trace(evolved, backend=self.backend)
            trace_backend = trace_value.backend / dim
            centered = evolved - trace_backend * self._identity_backend
            evolved_norm_backend = self.backend.norm(centered, ord="fro")
            try:
                evolved_norm = float(
                    np.asarray(ensure_numpy(evolved_norm_backend, backend=self.backend))
                )
                self._last_contractivity_gap = initial_norm - evolved_norm
                if raise_on_violation and self._last_contractivity_gap < -5 * self.atol:
                    raise TNFRValueError(
                        "Contractivity violated: Frobenius norm increased beyond tolerance.",
                        context={
                            "initial_norm": initial_norm,
                            "evolved_norm": evolved_norm,
                            "gap": self._last_contractivity_gap,
                            "atol": self.atol,
                        },
                        suggestion="Ensure generator is contractive.",
                    )
            except (ValueError, TypeError, Exception):
                self._last_contractivity_gap = float("nan")
        else:
            self._last_contractivity_gap = float("nan")

        return evolved

    def evolve(
        self,
        density: Sequence[Sequence[complex]] | np.ndarray | Any,
        *,
        steps: int,
        dt: float = 1.0,
        normalize_trace: bool = True,
        enforce_contractivity: bool = True,
        raise_on_violation: bool = False,
        symmetrize: bool = True,
    ) -> Any:
        """Return trajectory of density operators for the contractive semigroup."""

        if steps < 0:
            raise TNFRValueError(
                "steps must be non-negative.",
                context={"steps": steps},
                suggestion="Provide a non-negative number of steps.",
            )

        current = ensure_array(density, dtype=np.complex128, backend=self.backend)
        dim = self.hilbert_space.dimension
        if current.shape != (dim, dim):
            raise TNFRValueError(
                "Density operator dimension mismatch.",
                context={"expected_shape": (dim, dim), "actual_shape": current.shape},
                suggestion="Ensure density operator matches Hilbert space dimension.",
            )

        trajectory: list[Any] = [current]
        for _ in range(steps):
            current = self.step(
                current,
                dt=dt,
                normalize_trace=normalize_trace,
                enforce_contractivity=enforce_contractivity,
                raise_on_violation=raise_on_violation,
                symmetrize=symmetrize,
            )
            trajectory.append(current)
        return self.backend.stack(trajectory, axis=0)