tnfr 3.0.3__py3-none-any.whl → 8.5.0__py3-none-any.whl
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- tnfr/__init__.py +375 -56
- tnfr/__init__.pyi +33 -0
- tnfr/_compat.py +10 -0
- tnfr/_generated_version.py +34 -0
- tnfr/_version.py +49 -0
- tnfr/_version.pyi +7 -0
- tnfr/alias.py +723 -0
- tnfr/alias.pyi +108 -0
- tnfr/backends/__init__.py +354 -0
- tnfr/backends/jax_backend.py +173 -0
- tnfr/backends/numpy_backend.py +238 -0
- tnfr/backends/optimized_numpy.py +420 -0
- tnfr/backends/torch_backend.py +408 -0
- tnfr/cache.py +171 -0
- tnfr/cache.pyi +13 -0
- tnfr/cli/__init__.py +110 -0
- tnfr/cli/__init__.pyi +26 -0
- tnfr/cli/arguments.py +489 -0
- tnfr/cli/arguments.pyi +29 -0
- tnfr/cli/execution.py +914 -0
- tnfr/cli/execution.pyi +70 -0
- tnfr/cli/interactive_validator.py +614 -0
- tnfr/cli/utils.py +51 -0
- tnfr/cli/utils.pyi +7 -0
- tnfr/cli/validate.py +236 -0
- tnfr/compat/__init__.py +85 -0
- tnfr/compat/dataclass.py +136 -0
- tnfr/compat/jsonschema_stub.py +61 -0
- tnfr/compat/matplotlib_stub.py +73 -0
- tnfr/compat/numpy_stub.py +155 -0
- tnfr/config/__init__.py +224 -0
- tnfr/config/__init__.pyi +10 -0
- tnfr/config/constants.py +104 -0
- tnfr/config/constants.pyi +12 -0
- tnfr/config/defaults.py +54 -0
- tnfr/config/defaults_core.py +212 -0
- tnfr/config/defaults_init.py +33 -0
- tnfr/config/defaults_metric.py +104 -0
- tnfr/config/feature_flags.py +81 -0
- tnfr/config/feature_flags.pyi +16 -0
- tnfr/config/glyph_constants.py +31 -0
- tnfr/config/init.py +77 -0
- tnfr/config/init.pyi +8 -0
- tnfr/config/operator_names.py +254 -0
- tnfr/config/operator_names.pyi +36 -0
- tnfr/config/physics_derivation.py +354 -0
- tnfr/config/presets.py +83 -0
- tnfr/config/presets.pyi +7 -0
- tnfr/config/security.py +927 -0
- tnfr/config/thresholds.py +114 -0
- tnfr/config/tnfr_config.py +498 -0
- tnfr/constants/__init__.py +92 -0
- tnfr/constants/__init__.pyi +92 -0
- tnfr/constants/aliases.py +33 -0
- tnfr/constants/aliases.pyi +27 -0
- tnfr/constants/init.py +33 -0
- tnfr/constants/init.pyi +12 -0
- tnfr/constants/metric.py +104 -0
- tnfr/constants/metric.pyi +19 -0
- tnfr/core/__init__.py +33 -0
- tnfr/core/container.py +226 -0
- tnfr/core/default_implementations.py +329 -0
- tnfr/core/interfaces.py +279 -0
- tnfr/dynamics/__init__.py +238 -0
- tnfr/dynamics/__init__.pyi +83 -0
- tnfr/dynamics/adaptation.py +267 -0
- tnfr/dynamics/adaptation.pyi +7 -0
- tnfr/dynamics/adaptive_sequences.py +189 -0
- tnfr/dynamics/adaptive_sequences.pyi +14 -0
- tnfr/dynamics/aliases.py +23 -0
- tnfr/dynamics/aliases.pyi +19 -0
- tnfr/dynamics/bifurcation.py +232 -0
- tnfr/dynamics/canonical.py +229 -0
- tnfr/dynamics/canonical.pyi +48 -0
- tnfr/dynamics/coordination.py +385 -0
- tnfr/dynamics/coordination.pyi +25 -0
- tnfr/dynamics/dnfr.py +3034 -0
- tnfr/dynamics/dnfr.pyi +26 -0
- tnfr/dynamics/dynamic_limits.py +225 -0
- tnfr/dynamics/feedback.py +252 -0
- tnfr/dynamics/feedback.pyi +24 -0
- tnfr/dynamics/fused_dnfr.py +454 -0
- tnfr/dynamics/homeostasis.py +157 -0
- tnfr/dynamics/homeostasis.pyi +14 -0
- tnfr/dynamics/integrators.py +661 -0
- tnfr/dynamics/integrators.pyi +36 -0
- tnfr/dynamics/learning.py +310 -0
- tnfr/dynamics/learning.pyi +33 -0
- tnfr/dynamics/metabolism.py +254 -0
- tnfr/dynamics/nbody.py +796 -0
- tnfr/dynamics/nbody_tnfr.py +783 -0
- tnfr/dynamics/propagation.py +326 -0
- tnfr/dynamics/runtime.py +908 -0
- tnfr/dynamics/runtime.pyi +77 -0
- tnfr/dynamics/sampling.py +36 -0
- tnfr/dynamics/sampling.pyi +7 -0
- tnfr/dynamics/selectors.py +711 -0
- tnfr/dynamics/selectors.pyi +85 -0
- tnfr/dynamics/structural_clip.py +207 -0
- tnfr/errors/__init__.py +37 -0
- tnfr/errors/contextual.py +492 -0
- tnfr/execution.py +223 -0
- tnfr/execution.pyi +45 -0
- tnfr/extensions/__init__.py +205 -0
- tnfr/extensions/__init__.pyi +18 -0
- tnfr/extensions/base.py +173 -0
- tnfr/extensions/base.pyi +35 -0
- tnfr/extensions/business/__init__.py +71 -0
- tnfr/extensions/business/__init__.pyi +11 -0
- tnfr/extensions/business/cookbook.py +88 -0
- tnfr/extensions/business/cookbook.pyi +8 -0
- tnfr/extensions/business/health_analyzers.py +202 -0
- tnfr/extensions/business/health_analyzers.pyi +9 -0
- tnfr/extensions/business/patterns.py +183 -0
- tnfr/extensions/business/patterns.pyi +8 -0
- tnfr/extensions/medical/__init__.py +73 -0
- tnfr/extensions/medical/__init__.pyi +11 -0
- tnfr/extensions/medical/cookbook.py +88 -0
- tnfr/extensions/medical/cookbook.pyi +8 -0
- tnfr/extensions/medical/health_analyzers.py +181 -0
- tnfr/extensions/medical/health_analyzers.pyi +9 -0
- tnfr/extensions/medical/patterns.py +163 -0
- tnfr/extensions/medical/patterns.pyi +8 -0
- tnfr/flatten.py +262 -0
- tnfr/flatten.pyi +21 -0
- tnfr/gamma.py +354 -0
- tnfr/gamma.pyi +36 -0
- tnfr/glyph_history.py +377 -0
- tnfr/glyph_history.pyi +35 -0
- tnfr/glyph_runtime.py +19 -0
- tnfr/glyph_runtime.pyi +8 -0
- tnfr/immutable.py +218 -0
- tnfr/immutable.pyi +36 -0
- tnfr/initialization.py +203 -0
- tnfr/initialization.pyi +65 -0
- tnfr/io.py +10 -0
- tnfr/io.pyi +13 -0
- tnfr/locking.py +37 -0
- tnfr/locking.pyi +7 -0
- tnfr/mathematics/__init__.py +79 -0
- tnfr/mathematics/backend.py +453 -0
- tnfr/mathematics/backend.pyi +99 -0
- tnfr/mathematics/dynamics.py +408 -0
- tnfr/mathematics/dynamics.pyi +90 -0
- tnfr/mathematics/epi.py +391 -0
- tnfr/mathematics/epi.pyi +65 -0
- tnfr/mathematics/generators.py +242 -0
- tnfr/mathematics/generators.pyi +29 -0
- tnfr/mathematics/metrics.py +119 -0
- tnfr/mathematics/metrics.pyi +16 -0
- tnfr/mathematics/operators.py +239 -0
- tnfr/mathematics/operators.pyi +59 -0
- tnfr/mathematics/operators_factory.py +124 -0
- tnfr/mathematics/operators_factory.pyi +11 -0
- tnfr/mathematics/projection.py +87 -0
- tnfr/mathematics/projection.pyi +33 -0
- tnfr/mathematics/runtime.py +182 -0
- tnfr/mathematics/runtime.pyi +64 -0
- tnfr/mathematics/spaces.py +256 -0
- tnfr/mathematics/spaces.pyi +83 -0
- tnfr/mathematics/transforms.py +305 -0
- tnfr/mathematics/transforms.pyi +62 -0
- tnfr/metrics/__init__.py +79 -0
- tnfr/metrics/__init__.pyi +20 -0
- tnfr/metrics/buffer_cache.py +163 -0
- tnfr/metrics/buffer_cache.pyi +24 -0
- tnfr/metrics/cache_utils.py +214 -0
- tnfr/metrics/coherence.py +2009 -0
- tnfr/metrics/coherence.pyi +129 -0
- tnfr/metrics/common.py +158 -0
- tnfr/metrics/common.pyi +35 -0
- tnfr/metrics/core.py +316 -0
- tnfr/metrics/core.pyi +13 -0
- tnfr/metrics/diagnosis.py +833 -0
- tnfr/metrics/diagnosis.pyi +86 -0
- tnfr/metrics/emergence.py +245 -0
- tnfr/metrics/export.py +179 -0
- tnfr/metrics/export.pyi +7 -0
- tnfr/metrics/glyph_timing.py +379 -0
- tnfr/metrics/glyph_timing.pyi +81 -0
- tnfr/metrics/learning_metrics.py +280 -0
- tnfr/metrics/learning_metrics.pyi +21 -0
- tnfr/metrics/phase_coherence.py +351 -0
- tnfr/metrics/phase_compatibility.py +349 -0
- tnfr/metrics/reporting.py +183 -0
- tnfr/metrics/reporting.pyi +25 -0
- tnfr/metrics/sense_index.py +1203 -0
- tnfr/metrics/sense_index.pyi +9 -0
- tnfr/metrics/trig.py +373 -0
- tnfr/metrics/trig.pyi +13 -0
- tnfr/metrics/trig_cache.py +233 -0
- tnfr/metrics/trig_cache.pyi +10 -0
- tnfr/multiscale/__init__.py +32 -0
- tnfr/multiscale/hierarchical.py +517 -0
- tnfr/node.py +763 -0
- tnfr/node.pyi +139 -0
- tnfr/observers.py +255 -130
- tnfr/observers.pyi +31 -0
- tnfr/ontosim.py +144 -137
- tnfr/ontosim.pyi +28 -0
- tnfr/operators/__init__.py +1672 -0
- tnfr/operators/__init__.pyi +31 -0
- tnfr/operators/algebra.py +277 -0
- tnfr/operators/canonical_patterns.py +420 -0
- tnfr/operators/cascade.py +267 -0
- tnfr/operators/cycle_detection.py +358 -0
- tnfr/operators/definitions.py +4108 -0
- tnfr/operators/definitions.pyi +78 -0
- tnfr/operators/grammar.py +1164 -0
- tnfr/operators/grammar.pyi +140 -0
- tnfr/operators/hamiltonian.py +710 -0
- tnfr/operators/health_analyzer.py +809 -0
- tnfr/operators/jitter.py +272 -0
- tnfr/operators/jitter.pyi +11 -0
- tnfr/operators/lifecycle.py +314 -0
- tnfr/operators/metabolism.py +618 -0
- tnfr/operators/metrics.py +2138 -0
- tnfr/operators/network_analysis/__init__.py +27 -0
- tnfr/operators/network_analysis/source_detection.py +186 -0
- tnfr/operators/nodal_equation.py +395 -0
- tnfr/operators/pattern_detection.py +660 -0
- tnfr/operators/patterns.py +669 -0
- tnfr/operators/postconditions/__init__.py +38 -0
- tnfr/operators/postconditions/mutation.py +236 -0
- tnfr/operators/preconditions/__init__.py +1226 -0
- tnfr/operators/preconditions/coherence.py +305 -0
- tnfr/operators/preconditions/dissonance.py +236 -0
- tnfr/operators/preconditions/emission.py +128 -0
- tnfr/operators/preconditions/mutation.py +580 -0
- tnfr/operators/preconditions/reception.py +125 -0
- tnfr/operators/preconditions/resonance.py +364 -0
- tnfr/operators/registry.py +74 -0
- tnfr/operators/registry.pyi +9 -0
- tnfr/operators/remesh.py +1809 -0
- tnfr/operators/remesh.pyi +26 -0
- tnfr/operators/structural_units.py +268 -0
- tnfr/operators/unified_grammar.py +105 -0
- tnfr/parallel/__init__.py +54 -0
- tnfr/parallel/auto_scaler.py +234 -0
- tnfr/parallel/distributed.py +384 -0
- tnfr/parallel/engine.py +238 -0
- tnfr/parallel/gpu_engine.py +420 -0
- tnfr/parallel/monitoring.py +248 -0
- tnfr/parallel/partitioner.py +459 -0
- tnfr/py.typed +0 -0
- tnfr/recipes/__init__.py +22 -0
- tnfr/recipes/cookbook.py +743 -0
- tnfr/rng.py +178 -0
- tnfr/rng.pyi +26 -0
- tnfr/schemas/__init__.py +8 -0
- tnfr/schemas/grammar.json +94 -0
- tnfr/sdk/__init__.py +107 -0
- tnfr/sdk/__init__.pyi +19 -0
- tnfr/sdk/adaptive_system.py +173 -0
- tnfr/sdk/adaptive_system.pyi +21 -0
- tnfr/sdk/builders.py +370 -0
- tnfr/sdk/builders.pyi +51 -0
- tnfr/sdk/fluent.py +1121 -0
- tnfr/sdk/fluent.pyi +74 -0
- tnfr/sdk/templates.py +342 -0
- tnfr/sdk/templates.pyi +41 -0
- tnfr/sdk/utils.py +341 -0
- tnfr/secure_config.py +46 -0
- tnfr/security/__init__.py +70 -0
- tnfr/security/database.py +514 -0
- tnfr/security/subprocess.py +503 -0
- tnfr/security/validation.py +290 -0
- tnfr/selector.py +247 -0
- tnfr/selector.pyi +19 -0
- tnfr/sense.py +378 -0
- tnfr/sense.pyi +23 -0
- tnfr/services/__init__.py +17 -0
- tnfr/services/orchestrator.py +325 -0
- tnfr/sparse/__init__.py +39 -0
- tnfr/sparse/representations.py +492 -0
- tnfr/structural.py +705 -0
- tnfr/structural.pyi +83 -0
- tnfr/telemetry/__init__.py +35 -0
- tnfr/telemetry/cache_metrics.py +226 -0
- tnfr/telemetry/cache_metrics.pyi +64 -0
- tnfr/telemetry/nu_f.py +422 -0
- tnfr/telemetry/nu_f.pyi +108 -0
- tnfr/telemetry/verbosity.py +36 -0
- tnfr/telemetry/verbosity.pyi +15 -0
- tnfr/tokens.py +58 -0
- tnfr/tokens.pyi +36 -0
- tnfr/tools/__init__.py +20 -0
- tnfr/tools/domain_templates.py +478 -0
- tnfr/tools/sequence_generator.py +846 -0
- tnfr/topology/__init__.py +13 -0
- tnfr/topology/asymmetry.py +151 -0
- tnfr/trace.py +543 -0
- tnfr/trace.pyi +42 -0
- tnfr/tutorials/__init__.py +38 -0
- tnfr/tutorials/autonomous_evolution.py +285 -0
- tnfr/tutorials/interactive.py +1576 -0
- tnfr/tutorials/structural_metabolism.py +238 -0
- tnfr/types.py +775 -0
- tnfr/types.pyi +357 -0
- tnfr/units.py +68 -0
- tnfr/units.pyi +13 -0
- tnfr/utils/__init__.py +282 -0
- tnfr/utils/__init__.pyi +215 -0
- tnfr/utils/cache.py +4223 -0
- tnfr/utils/cache.pyi +470 -0
- tnfr/utils/callbacks.py +375 -0
- tnfr/utils/callbacks.pyi +49 -0
- tnfr/utils/chunks.py +108 -0
- tnfr/utils/chunks.pyi +22 -0
- tnfr/utils/data.py +428 -0
- tnfr/utils/data.pyi +74 -0
- tnfr/utils/graph.py +85 -0
- tnfr/utils/graph.pyi +10 -0
- tnfr/utils/init.py +821 -0
- tnfr/utils/init.pyi +80 -0
- tnfr/utils/io.py +559 -0
- tnfr/utils/io.pyi +66 -0
- tnfr/utils/numeric.py +114 -0
- tnfr/utils/numeric.pyi +21 -0
- tnfr/validation/__init__.py +257 -0
- tnfr/validation/__init__.pyi +85 -0
- tnfr/validation/compatibility.py +460 -0
- tnfr/validation/compatibility.pyi +6 -0
- tnfr/validation/config.py +73 -0
- tnfr/validation/graph.py +139 -0
- tnfr/validation/graph.pyi +18 -0
- tnfr/validation/input_validation.py +755 -0
- tnfr/validation/invariants.py +712 -0
- tnfr/validation/rules.py +253 -0
- tnfr/validation/rules.pyi +44 -0
- tnfr/validation/runtime.py +279 -0
- tnfr/validation/runtime.pyi +28 -0
- tnfr/validation/sequence_validator.py +162 -0
- tnfr/validation/soft_filters.py +170 -0
- tnfr/validation/soft_filters.pyi +32 -0
- tnfr/validation/spectral.py +164 -0
- tnfr/validation/spectral.pyi +42 -0
- tnfr/validation/validator.py +1266 -0
- tnfr/validation/window.py +39 -0
- tnfr/validation/window.pyi +1 -0
- tnfr/visualization/__init__.py +98 -0
- tnfr/visualization/cascade_viz.py +256 -0
- tnfr/visualization/hierarchy.py +284 -0
- tnfr/visualization/sequence_plotter.py +784 -0
- tnfr/viz/__init__.py +60 -0
- tnfr/viz/matplotlib.py +278 -0
- tnfr/viz/matplotlib.pyi +35 -0
- tnfr-8.5.0.dist-info/METADATA +573 -0
- tnfr-8.5.0.dist-info/RECORD +353 -0
- tnfr-8.5.0.dist-info/entry_points.txt +3 -0
- tnfr-3.0.3.dist-info/licenses/LICENSE.txt → tnfr-8.5.0.dist-info/licenses/LICENSE.md +1 -1
- tnfr/constants.py +0 -183
- tnfr/dynamics.py +0 -543
- tnfr/helpers.py +0 -198
- tnfr/main.py +0 -37
- tnfr/operators.py +0 -296
- tnfr-3.0.3.dist-info/METADATA +0 -35
- tnfr-3.0.3.dist-info/RECORD +0 -13
- {tnfr-3.0.3.dist-info → tnfr-8.5.0.dist-info}/WHEEL +0 -0
- {tnfr-3.0.3.dist-info → tnfr-8.5.0.dist-info}/top_level.txt +0 -0
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"""Canonical ΔNFR integrators driving TNFR runtime evolution.
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This module implements numerical integration of the canonical TNFR nodal equation:
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∂EPI/∂t = νf · ΔNFR(t) + Γi(R)
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The extended equation includes:
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- Base term: νf · ΔNFR(t) - canonical structural evolution
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- Network term: Γi(R) - optional Kuramoto coupling
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Integration respects TNFR invariants:
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- Structural units (Hz_str for νf)
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- Operator closure (valid ΔNFR semantics)
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- Phase coherence (network synchronization)
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- Reproducibility (deterministic with seeds)
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The canonical base term is computed explicitly in _collect_nodal_increments()
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at line 321 and 342 as: base = vf * dnfr, implementing ∂EPI/∂t = νf·ΔNFR(t).
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"""
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from __future__ import annotations
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import math
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from abc import ABC, abstractmethod
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from collections.abc import Iterable, Mapping
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from concurrent.futures import ProcessPoolExecutor
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from multiprocessing import get_context
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from typing import Any, Literal, cast
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import networkx as nx
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from .._compat import TypeAlias
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from ..alias import collect_attr, get_attr, get_attr_str, set_attr, set_attr_str
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from ..constants import DEFAULTS
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from ..constants.aliases import (
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ALIAS_D2EPI,
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ALIAS_DEPI,
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ALIAS_DNFR,
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ALIAS_EPI,
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ALIAS_EPI_KIND,
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ALIAS_VF,
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)
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from ..gamma import _get_gamma_spec, eval_gamma
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from ..types import NodeId, TNFRGraph
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from ..utils import get_numpy, resolve_chunk_size
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from .canonical import compute_canonical_nodal_derivative
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from .structural_clip import structural_clip
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__all__ = (
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"AbstractIntegrator",
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"DefaultIntegrator",
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"prepare_integration_params",
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"update_epi_via_nodal_equation",
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)
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GammaMap: TypeAlias = dict[NodeId, float]
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"""Γ evaluation cache keyed by node identifier."""
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NodeIncrements: TypeAlias = dict[NodeId, tuple[float, ...]]
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"""Mapping of nodes to staged integration increments."""
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NodalUpdate: TypeAlias = dict[NodeId, tuple[float, float, float]]
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"""Mapping of nodes to ``(EPI, dEPI/dt, ∂²EPI/∂t²)`` tuples."""
|
|
64
|
+
|
|
65
|
+
IntegratorMethod: TypeAlias = Literal["euler", "rk4"]
|
|
66
|
+
"""Supported explicit integration schemes for nodal updates."""
|
|
67
|
+
|
|
68
|
+
_PARALLEL_GRAPH: TNFRGraph | None = None
|
|
69
|
+
|
|
70
|
+
|
|
71
|
+
def _gamma_worker_init(graph: TNFRGraph) -> None:
|
|
72
|
+
"""Initialise process-local graph reference for Γ evaluation."""
|
|
73
|
+
|
|
74
|
+
global _PARALLEL_GRAPH
|
|
75
|
+
_PARALLEL_GRAPH = graph
|
|
76
|
+
|
|
77
|
+
|
|
78
|
+
def _gamma_worker(task: tuple[list[NodeId], float]) -> list[tuple[NodeId, float]]:
|
|
79
|
+
"""Evaluate Γ for ``task`` chunk using process-local graph."""
|
|
80
|
+
|
|
81
|
+
chunk, t = task
|
|
82
|
+
if _PARALLEL_GRAPH is None:
|
|
83
|
+
raise RuntimeError("Parallel Γ worker initialised without graph reference")
|
|
84
|
+
return [(node, float(eval_gamma(_PARALLEL_GRAPH, node, t))) for node in chunk]
|
|
85
|
+
|
|
86
|
+
|
|
87
|
+
def _normalise_jobs(n_jobs: int | None, total: int) -> int | None:
|
|
88
|
+
"""Return an effective worker count respecting serial fallbacks."""
|
|
89
|
+
|
|
90
|
+
if n_jobs is None:
|
|
91
|
+
return None
|
|
92
|
+
try:
|
|
93
|
+
workers = int(n_jobs)
|
|
94
|
+
except (TypeError, ValueError):
|
|
95
|
+
return None
|
|
96
|
+
if workers <= 1 or total <= 1:
|
|
97
|
+
return None
|
|
98
|
+
return max(1, min(workers, total))
|
|
99
|
+
|
|
100
|
+
|
|
101
|
+
def _chunk_nodes(nodes: list[NodeId], chunk_size: int) -> Iterable[list[NodeId]]:
|
|
102
|
+
"""Yield deterministic chunks from ``nodes`` respecting insertion order."""
|
|
103
|
+
|
|
104
|
+
for idx in range(0, len(nodes), chunk_size):
|
|
105
|
+
yield nodes[idx : idx + chunk_size]
|
|
106
|
+
|
|
107
|
+
|
|
108
|
+
def _apply_increment_chunk(
|
|
109
|
+
chunk: list[tuple[NodeId, float, float, tuple[float, ...]]],
|
|
110
|
+
dt_step: float,
|
|
111
|
+
method: str,
|
|
112
|
+
) -> list[tuple[NodeId, tuple[float, float, float]]]:
|
|
113
|
+
"""Compute updated states for ``chunk`` using scalar arithmetic."""
|
|
114
|
+
|
|
115
|
+
results: list[tuple[NodeId, tuple[float, float, float]]] = []
|
|
116
|
+
dt_nonzero = dt_step != 0
|
|
117
|
+
|
|
118
|
+
for node, epi_i, dEPI_prev, ks in chunk:
|
|
119
|
+
if method == "rk4":
|
|
120
|
+
k1, k2, k3, k4 = ks
|
|
121
|
+
epi = epi_i + (dt_step / 6.0) * (k1 + 2 * k2 + 2 * k3 + k4)
|
|
122
|
+
dEPI_dt = k4
|
|
123
|
+
else:
|
|
124
|
+
(k1,) = ks
|
|
125
|
+
epi = epi_i + dt_step * k1
|
|
126
|
+
dEPI_dt = k1
|
|
127
|
+
d2epi = (dEPI_dt - dEPI_prev) / dt_step if dt_nonzero else 0.0
|
|
128
|
+
results.append((node, (float(epi), float(dEPI_dt), float(d2epi))))
|
|
129
|
+
|
|
130
|
+
return results
|
|
131
|
+
|
|
132
|
+
|
|
133
|
+
def _evaluate_gamma_map(
|
|
134
|
+
G: TNFRGraph,
|
|
135
|
+
nodes: list[NodeId],
|
|
136
|
+
t: float,
|
|
137
|
+
*,
|
|
138
|
+
n_jobs: int | None = None,
|
|
139
|
+
) -> GammaMap:
|
|
140
|
+
"""Return Γ evaluations for ``nodes`` at time ``t`` respecting parallelism."""
|
|
141
|
+
|
|
142
|
+
workers = _normalise_jobs(n_jobs, len(nodes))
|
|
143
|
+
if workers is None:
|
|
144
|
+
return {n: float(eval_gamma(G, n, t)) for n in nodes}
|
|
145
|
+
|
|
146
|
+
approx_chunk = math.ceil(len(nodes) / (workers * 4)) if workers > 0 else None
|
|
147
|
+
chunk_size = resolve_chunk_size(
|
|
148
|
+
approx_chunk,
|
|
149
|
+
len(nodes),
|
|
150
|
+
minimum=1,
|
|
151
|
+
)
|
|
152
|
+
mp_ctx = get_context("spawn")
|
|
153
|
+
tasks = ((chunk, t) for chunk in _chunk_nodes(nodes, chunk_size))
|
|
154
|
+
|
|
155
|
+
results: GammaMap = {}
|
|
156
|
+
with ProcessPoolExecutor(
|
|
157
|
+
max_workers=workers,
|
|
158
|
+
mp_context=mp_ctx,
|
|
159
|
+
initializer=_gamma_worker_init,
|
|
160
|
+
initargs=(G,),
|
|
161
|
+
) as executor:
|
|
162
|
+
futures = [executor.submit(_gamma_worker, task) for task in tasks]
|
|
163
|
+
for fut in futures:
|
|
164
|
+
for node, value in fut.result():
|
|
165
|
+
results[node] = value
|
|
166
|
+
return results
|
|
167
|
+
|
|
168
|
+
|
|
169
|
+
def prepare_integration_params(
|
|
170
|
+
G: TNFRGraph,
|
|
171
|
+
dt: float | None = None,
|
|
172
|
+
t: float | None = None,
|
|
173
|
+
method: Literal["euler", "rk4"] | None = None,
|
|
174
|
+
) -> tuple[float, int, float, Literal["euler", "rk4"]]:
|
|
175
|
+
"""Validate and normalise ``dt``, ``t`` and ``method`` for integration.
|
|
176
|
+
|
|
177
|
+
The function raises :class:`TypeError` when ``dt`` cannot be coerced to a
|
|
178
|
+
number, :class:`ValueError` if ``dt`` is negative, and another
|
|
179
|
+
:class:`ValueError` when an unsupported method is requested. When ``dt``
|
|
180
|
+
exceeds a positive ``DT_MIN`` stored on ``G`` the span is deterministically
|
|
181
|
+
subdivided into integer steps so that the resulting ``dt_step`` never falls
|
|
182
|
+
below that minimum threshold.
|
|
183
|
+
|
|
184
|
+
Returns ``(dt_step, steps, t0, method)`` where ``dt_step`` is the effective
|
|
185
|
+
step, ``steps`` the number of substeps and ``t0`` the prepared initial
|
|
186
|
+
time.
|
|
187
|
+
"""
|
|
188
|
+
if dt is None:
|
|
189
|
+
dt = float(G.graph.get("DT", DEFAULTS["DT"]))
|
|
190
|
+
else:
|
|
191
|
+
if not isinstance(dt, (int, float)):
|
|
192
|
+
raise TypeError("dt must be a number")
|
|
193
|
+
if dt < 0:
|
|
194
|
+
raise ValueError("dt must be non-negative")
|
|
195
|
+
dt = float(dt)
|
|
196
|
+
|
|
197
|
+
if t is None:
|
|
198
|
+
t = float(G.graph.get("_t", 0.0))
|
|
199
|
+
else:
|
|
200
|
+
t = float(t)
|
|
201
|
+
|
|
202
|
+
method_value = (
|
|
203
|
+
method
|
|
204
|
+
or G.graph.get("INTEGRATOR_METHOD", DEFAULTS.get("INTEGRATOR_METHOD", "euler"))
|
|
205
|
+
).lower()
|
|
206
|
+
if method_value not in ("euler", "rk4"):
|
|
207
|
+
raise ValueError("method must be 'euler' or 'rk4'")
|
|
208
|
+
|
|
209
|
+
dt_min = float(G.graph.get("DT_MIN", DEFAULTS.get("DT_MIN", 0.0)))
|
|
210
|
+
steps = 1
|
|
211
|
+
if dt_min > 0 and dt > dt_min:
|
|
212
|
+
ratio = dt / dt_min
|
|
213
|
+
steps = max(1, int(math.floor(ratio + 1e-12)))
|
|
214
|
+
if dt / steps < dt_min:
|
|
215
|
+
steps = int(math.ceil(ratio))
|
|
216
|
+
dt_step = dt / steps if steps else 0.0
|
|
217
|
+
|
|
218
|
+
return dt_step, steps, t, cast(Literal["euler", "rk4"], method_value)
|
|
219
|
+
|
|
220
|
+
|
|
221
|
+
def _apply_increments(
|
|
222
|
+
G: TNFRGraph,
|
|
223
|
+
dt_step: float,
|
|
224
|
+
increments: NodeIncrements,
|
|
225
|
+
*,
|
|
226
|
+
method: str,
|
|
227
|
+
n_jobs: int | None = None,
|
|
228
|
+
) -> NodalUpdate:
|
|
229
|
+
"""Combine precomputed increments to update node states."""
|
|
230
|
+
|
|
231
|
+
nodes: list[NodeId] = list(G.nodes)
|
|
232
|
+
if not nodes:
|
|
233
|
+
return {}
|
|
234
|
+
|
|
235
|
+
np = get_numpy()
|
|
236
|
+
|
|
237
|
+
epi_initial: list[float] = []
|
|
238
|
+
dEPI_prev: list[float] = []
|
|
239
|
+
ordered_increments: list[tuple[float, ...]] = []
|
|
240
|
+
|
|
241
|
+
for node in nodes:
|
|
242
|
+
nd = G.nodes[node]
|
|
243
|
+
_, _, dEPI_dt_prev, epi_i = _node_state(nd)
|
|
244
|
+
epi_initial.append(float(epi_i))
|
|
245
|
+
dEPI_prev.append(float(dEPI_dt_prev))
|
|
246
|
+
ordered_increments.append(increments[node])
|
|
247
|
+
|
|
248
|
+
if np is not None:
|
|
249
|
+
epi_arr = np.asarray(epi_initial, dtype=float)
|
|
250
|
+
dEPI_prev_arr = np.asarray(dEPI_prev, dtype=float)
|
|
251
|
+
k_arr = np.asarray(ordered_increments, dtype=float)
|
|
252
|
+
|
|
253
|
+
if method == "rk4":
|
|
254
|
+
if k_arr.ndim != 2 or k_arr.shape[1] != 4:
|
|
255
|
+
raise ValueError("rk4 increments require four staged values")
|
|
256
|
+
dt_factor = dt_step / 6.0
|
|
257
|
+
k1 = k_arr[:, 0]
|
|
258
|
+
k2 = k_arr[:, 1]
|
|
259
|
+
k3 = k_arr[:, 2]
|
|
260
|
+
k4 = k_arr[:, 3]
|
|
261
|
+
epi = epi_arr + dt_factor * (k1 + 2 * k2 + 2 * k3 + k4)
|
|
262
|
+
dEPI_dt = k4
|
|
263
|
+
else:
|
|
264
|
+
if k_arr.ndim == 1:
|
|
265
|
+
k1 = k_arr
|
|
266
|
+
else:
|
|
267
|
+
k1 = k_arr[:, 0]
|
|
268
|
+
epi = epi_arr + dt_step * k1
|
|
269
|
+
dEPI_dt = k1
|
|
270
|
+
|
|
271
|
+
if dt_step != 0:
|
|
272
|
+
d2epi = (dEPI_dt - dEPI_prev_arr) / dt_step
|
|
273
|
+
else:
|
|
274
|
+
d2epi = np.zeros_like(dEPI_dt)
|
|
275
|
+
|
|
276
|
+
results: NodalUpdate = {}
|
|
277
|
+
for idx, node in enumerate(nodes):
|
|
278
|
+
results[node] = (
|
|
279
|
+
float(epi[idx]),
|
|
280
|
+
float(dEPI_dt[idx]),
|
|
281
|
+
float(d2epi[idx]),
|
|
282
|
+
)
|
|
283
|
+
return results
|
|
284
|
+
|
|
285
|
+
payload: list[tuple[NodeId, float, float, tuple[float, ...]]] = list(
|
|
286
|
+
zip(nodes, epi_initial, dEPI_prev, ordered_increments)
|
|
287
|
+
)
|
|
288
|
+
|
|
289
|
+
workers = _normalise_jobs(n_jobs, len(nodes))
|
|
290
|
+
if workers is None:
|
|
291
|
+
return dict(_apply_increment_chunk(payload, dt_step, method))
|
|
292
|
+
|
|
293
|
+
approx_chunk = math.ceil(len(nodes) / (workers * 4)) if workers > 0 else None
|
|
294
|
+
chunk_size = resolve_chunk_size(
|
|
295
|
+
approx_chunk,
|
|
296
|
+
len(nodes),
|
|
297
|
+
minimum=1,
|
|
298
|
+
)
|
|
299
|
+
mp_ctx = get_context("spawn")
|
|
300
|
+
|
|
301
|
+
results: NodalUpdate = {}
|
|
302
|
+
with ProcessPoolExecutor(max_workers=workers, mp_context=mp_ctx) as executor:
|
|
303
|
+
futures = [
|
|
304
|
+
executor.submit(
|
|
305
|
+
_apply_increment_chunk,
|
|
306
|
+
chunk,
|
|
307
|
+
dt_step,
|
|
308
|
+
method,
|
|
309
|
+
)
|
|
310
|
+
for chunk in _chunk_nodes(payload, chunk_size)
|
|
311
|
+
]
|
|
312
|
+
for fut in futures:
|
|
313
|
+
for node, value in fut.result():
|
|
314
|
+
results[node] = value
|
|
315
|
+
|
|
316
|
+
return {node: results[node] for node in nodes}
|
|
317
|
+
|
|
318
|
+
|
|
319
|
+
def _collect_nodal_increments(
|
|
320
|
+
G: TNFRGraph,
|
|
321
|
+
gamma_maps: tuple[GammaMap, ...],
|
|
322
|
+
*,
|
|
323
|
+
method: str,
|
|
324
|
+
) -> NodeIncrements:
|
|
325
|
+
"""Combine node base state with staged Γ contributions.
|
|
326
|
+
|
|
327
|
+
Implements the canonical TNFR nodal equation in two parts:
|
|
328
|
+
|
|
329
|
+
1. **Base term** (canonical equation):
|
|
330
|
+
base = vf * dnfr → ∂EPI/∂t = νf · ΔNFR(t)
|
|
331
|
+
|
|
332
|
+
This is the fundamental TNFR equation where:
|
|
333
|
+
- vf (νf): structural frequency in Hz_str
|
|
334
|
+
- dnfr (ΔNFR): nodal gradient (reorganization operator)
|
|
335
|
+
- base: instantaneous rate of EPI evolution
|
|
336
|
+
|
|
337
|
+
2. **Network coupling term**:
|
|
338
|
+
Γi(R) from gamma_maps - optional Kuramoto order parameter
|
|
339
|
+
|
|
340
|
+
The full extended equation is: ∂EPI/∂t = νf·ΔNFR(t) + Γi(R)
|
|
341
|
+
|
|
342
|
+
Args:
|
|
343
|
+
G: TNFR graph with node attributes vf and dnfr
|
|
344
|
+
gamma_maps: Staged Γ evaluations (1 for Euler, 4 for RK4)
|
|
345
|
+
method: Integration method ('euler' or 'rk4')
|
|
346
|
+
|
|
347
|
+
Returns:
|
|
348
|
+
Mapping of nodes to staged integration increments
|
|
349
|
+
|
|
350
|
+
Notes:
|
|
351
|
+
- Line 321 implements the canonical nodal equation explicitly
|
|
352
|
+
- Units: vf in Hz_str, dnfr dimensionless, base in Hz_str
|
|
353
|
+
- Preserves TNFR operator closure and structural semantics
|
|
354
|
+
"""
|
|
355
|
+
|
|
356
|
+
nodes: list[NodeId] = list(G.nodes())
|
|
357
|
+
if not nodes:
|
|
358
|
+
return {}
|
|
359
|
+
|
|
360
|
+
if method == "rk4":
|
|
361
|
+
expected_maps = 4
|
|
362
|
+
elif method == "euler":
|
|
363
|
+
expected_maps = 1
|
|
364
|
+
else:
|
|
365
|
+
raise ValueError("method must be 'euler' or 'rk4'")
|
|
366
|
+
|
|
367
|
+
if len(gamma_maps) != expected_maps:
|
|
368
|
+
raise ValueError(f"{method} integration requires {expected_maps} gamma maps")
|
|
369
|
+
|
|
370
|
+
np = get_numpy()
|
|
371
|
+
if np is not None:
|
|
372
|
+
vf = collect_attr(G, nodes, ALIAS_VF, 0.0, np=np)
|
|
373
|
+
dnfr = collect_attr(G, nodes, ALIAS_DNFR, 0.0, np=np)
|
|
374
|
+
# CANONICAL TNFR EQUATION: ∂EPI/∂t = νf · ΔNFR(t)
|
|
375
|
+
# This implements the fundamental nodal equation explicitly
|
|
376
|
+
base = vf * dnfr
|
|
377
|
+
|
|
378
|
+
gamma_arrays = [
|
|
379
|
+
np.fromiter((gm.get(n, 0.0) for n in nodes), float, count=len(nodes))
|
|
380
|
+
for gm in gamma_maps
|
|
381
|
+
]
|
|
382
|
+
if gamma_arrays:
|
|
383
|
+
gamma_stack = np.stack(gamma_arrays, axis=1)
|
|
384
|
+
combined = base[:, None] + gamma_stack
|
|
385
|
+
else:
|
|
386
|
+
combined = base[:, None]
|
|
387
|
+
|
|
388
|
+
return {
|
|
389
|
+
node: tuple(float(value) for value in combined[idx])
|
|
390
|
+
for idx, node in enumerate(nodes)
|
|
391
|
+
}
|
|
392
|
+
|
|
393
|
+
increments: NodeIncrements = {}
|
|
394
|
+
for node in nodes:
|
|
395
|
+
nd = G.nodes[node]
|
|
396
|
+
vf, dnfr, *_ = _node_state(nd)
|
|
397
|
+
# CANONICAL TNFR EQUATION: ∂EPI/∂t = νf · ΔNFR(t)
|
|
398
|
+
# Scalar implementation of the fundamental nodal equation
|
|
399
|
+
base = vf * dnfr
|
|
400
|
+
gammas = [gm.get(node, 0.0) for gm in gamma_maps]
|
|
401
|
+
|
|
402
|
+
if method == "rk4":
|
|
403
|
+
k1, k2, k3, k4 = gammas
|
|
404
|
+
increments[node] = (
|
|
405
|
+
base + k1,
|
|
406
|
+
base + k2,
|
|
407
|
+
base + k3,
|
|
408
|
+
base + k4,
|
|
409
|
+
)
|
|
410
|
+
else:
|
|
411
|
+
(k1,) = gammas
|
|
412
|
+
increments[node] = (base + k1,)
|
|
413
|
+
|
|
414
|
+
return increments
|
|
415
|
+
|
|
416
|
+
|
|
417
|
+
def _build_gamma_increments(
|
|
418
|
+
G: TNFRGraph,
|
|
419
|
+
dt_step: float,
|
|
420
|
+
t_local: float,
|
|
421
|
+
*,
|
|
422
|
+
method: str,
|
|
423
|
+
n_jobs: int | None = None,
|
|
424
|
+
) -> NodeIncrements:
|
|
425
|
+
"""Evaluate Γ contributions and merge them with ``νf·ΔNFR`` base terms."""
|
|
426
|
+
|
|
427
|
+
if method == "rk4":
|
|
428
|
+
gamma_count = 4
|
|
429
|
+
elif method == "euler":
|
|
430
|
+
gamma_count = 1
|
|
431
|
+
else:
|
|
432
|
+
raise ValueError("method must be 'euler' or 'rk4'")
|
|
433
|
+
|
|
434
|
+
gamma_spec = G.graph.get("_gamma_spec")
|
|
435
|
+
if gamma_spec is None:
|
|
436
|
+
gamma_spec = _get_gamma_spec(G)
|
|
437
|
+
|
|
438
|
+
gamma_type = ""
|
|
439
|
+
if isinstance(gamma_spec, Mapping):
|
|
440
|
+
gamma_type = str(gamma_spec.get("type", "")).lower()
|
|
441
|
+
|
|
442
|
+
if gamma_type == "none":
|
|
443
|
+
gamma_maps: tuple[GammaMap, ...] = tuple(
|
|
444
|
+
cast(GammaMap, {}) for _ in range(gamma_count)
|
|
445
|
+
)
|
|
446
|
+
return _collect_nodal_increments(G, gamma_maps, method=method)
|
|
447
|
+
|
|
448
|
+
nodes: list[NodeId] = list(G.nodes)
|
|
449
|
+
if not nodes:
|
|
450
|
+
gamma_maps = tuple(cast(GammaMap, {}) for _ in range(gamma_count))
|
|
451
|
+
return _collect_nodal_increments(G, gamma_maps, method=method)
|
|
452
|
+
|
|
453
|
+
if method == "rk4":
|
|
454
|
+
t_mid = t_local + dt_step / 2.0
|
|
455
|
+
t_end = t_local + dt_step
|
|
456
|
+
g1_map = _evaluate_gamma_map(G, nodes, t_local, n_jobs=n_jobs)
|
|
457
|
+
g_mid_map = _evaluate_gamma_map(G, nodes, t_mid, n_jobs=n_jobs)
|
|
458
|
+
g4_map = _evaluate_gamma_map(G, nodes, t_end, n_jobs=n_jobs)
|
|
459
|
+
gamma_maps = (g1_map, g_mid_map, g_mid_map, g4_map)
|
|
460
|
+
else: # method == "euler"
|
|
461
|
+
gamma_maps = (_evaluate_gamma_map(G, nodes, t_local, n_jobs=n_jobs),)
|
|
462
|
+
|
|
463
|
+
return _collect_nodal_increments(G, gamma_maps, method=method)
|
|
464
|
+
|
|
465
|
+
|
|
466
|
+
def _integrate_euler(
|
|
467
|
+
G: TNFRGraph,
|
|
468
|
+
dt_step: float,
|
|
469
|
+
t_local: float,
|
|
470
|
+
*,
|
|
471
|
+
n_jobs: int | None = None,
|
|
472
|
+
) -> NodalUpdate:
|
|
473
|
+
"""One explicit Euler integration step."""
|
|
474
|
+
increments = _build_gamma_increments(
|
|
475
|
+
G,
|
|
476
|
+
dt_step,
|
|
477
|
+
t_local,
|
|
478
|
+
method="euler",
|
|
479
|
+
n_jobs=n_jobs,
|
|
480
|
+
)
|
|
481
|
+
return _apply_increments(
|
|
482
|
+
G,
|
|
483
|
+
dt_step,
|
|
484
|
+
increments,
|
|
485
|
+
method="euler",
|
|
486
|
+
n_jobs=n_jobs,
|
|
487
|
+
)
|
|
488
|
+
|
|
489
|
+
|
|
490
|
+
def _integrate_rk4(
|
|
491
|
+
G: TNFRGraph,
|
|
492
|
+
dt_step: float,
|
|
493
|
+
t_local: float,
|
|
494
|
+
*,
|
|
495
|
+
n_jobs: int | None = None,
|
|
496
|
+
) -> NodalUpdate:
|
|
497
|
+
"""One Runge–Kutta order-4 integration step."""
|
|
498
|
+
increments = _build_gamma_increments(
|
|
499
|
+
G,
|
|
500
|
+
dt_step,
|
|
501
|
+
t_local,
|
|
502
|
+
method="rk4",
|
|
503
|
+
n_jobs=n_jobs,
|
|
504
|
+
)
|
|
505
|
+
return _apply_increments(
|
|
506
|
+
G,
|
|
507
|
+
dt_step,
|
|
508
|
+
increments,
|
|
509
|
+
method="rk4",
|
|
510
|
+
n_jobs=n_jobs,
|
|
511
|
+
)
|
|
512
|
+
|
|
513
|
+
|
|
514
|
+
class AbstractIntegrator(ABC):
|
|
515
|
+
"""Abstract base class encapsulating nodal equation integration."""
|
|
516
|
+
|
|
517
|
+
@abstractmethod
|
|
518
|
+
def integrate(
|
|
519
|
+
self,
|
|
520
|
+
graph: TNFRGraph,
|
|
521
|
+
*,
|
|
522
|
+
dt: float | None,
|
|
523
|
+
t: float | None,
|
|
524
|
+
method: str | None,
|
|
525
|
+
n_jobs: int | None,
|
|
526
|
+
) -> None:
|
|
527
|
+
"""Advance ``graph`` coherence states according to the nodal equation."""
|
|
528
|
+
|
|
529
|
+
|
|
530
|
+
class DefaultIntegrator(AbstractIntegrator):
|
|
531
|
+
"""Explicit integrator combining Euler and RK4 step implementations."""
|
|
532
|
+
|
|
533
|
+
def integrate(
|
|
534
|
+
self,
|
|
535
|
+
graph: TNFRGraph,
|
|
536
|
+
*,
|
|
537
|
+
dt: float | None,
|
|
538
|
+
t: float | None,
|
|
539
|
+
method: str | None,
|
|
540
|
+
n_jobs: int | None,
|
|
541
|
+
) -> None:
|
|
542
|
+
"""Integrate the nodal equation updating EPI, ΔEPI and Δ²EPI."""
|
|
543
|
+
|
|
544
|
+
if not isinstance(
|
|
545
|
+
graph, (nx.Graph, nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph)
|
|
546
|
+
):
|
|
547
|
+
raise TypeError("G must be a networkx graph instance")
|
|
548
|
+
|
|
549
|
+
dt_step, steps, t0, resolved_method = prepare_integration_params(
|
|
550
|
+
graph, dt, t, cast(IntegratorMethod | None, method)
|
|
551
|
+
)
|
|
552
|
+
|
|
553
|
+
t_local = t0
|
|
554
|
+
for _ in range(steps):
|
|
555
|
+
if resolved_method == "rk4":
|
|
556
|
+
updates: NodalUpdate = _integrate_rk4(
|
|
557
|
+
graph, dt_step, t_local, n_jobs=n_jobs
|
|
558
|
+
)
|
|
559
|
+
else:
|
|
560
|
+
updates = _integrate_euler(graph, dt_step, t_local, n_jobs=n_jobs)
|
|
561
|
+
|
|
562
|
+
for n, (epi, dEPI_dt, d2epi) in updates.items():
|
|
563
|
+
nd = graph.nodes[n]
|
|
564
|
+
epi_kind = get_attr_str(nd, ALIAS_EPI_KIND, "")
|
|
565
|
+
|
|
566
|
+
# Apply structural boundary preservation
|
|
567
|
+
epi_min = float(
|
|
568
|
+
graph.graph.get("EPI_MIN", DEFAULTS.get("EPI_MIN", -1.0))
|
|
569
|
+
)
|
|
570
|
+
epi_max = float(
|
|
571
|
+
graph.graph.get("EPI_MAX", DEFAULTS.get("EPI_MAX", 1.0))
|
|
572
|
+
)
|
|
573
|
+
clip_mode_str = str(graph.graph.get("CLIP_MODE", "hard"))
|
|
574
|
+
# Validate clip mode and cast to proper type
|
|
575
|
+
if clip_mode_str not in ("hard", "soft"):
|
|
576
|
+
clip_mode_str = "hard"
|
|
577
|
+
clip_mode: Literal["hard", "soft"] = clip_mode_str # type: ignore[assignment]
|
|
578
|
+
clip_k = float(graph.graph.get("CLIP_SOFT_K", 3.0))
|
|
579
|
+
|
|
580
|
+
epi_clipped = structural_clip(
|
|
581
|
+
epi,
|
|
582
|
+
lo=epi_min,
|
|
583
|
+
hi=epi_max,
|
|
584
|
+
mode=clip_mode,
|
|
585
|
+
k=clip_k,
|
|
586
|
+
record_stats=False,
|
|
587
|
+
)
|
|
588
|
+
|
|
589
|
+
set_attr(nd, ALIAS_EPI, epi_clipped)
|
|
590
|
+
if epi_kind:
|
|
591
|
+
set_attr_str(nd, ALIAS_EPI_KIND, epi_kind)
|
|
592
|
+
set_attr(nd, ALIAS_DEPI, dEPI_dt)
|
|
593
|
+
set_attr(nd, ALIAS_D2EPI, d2epi)
|
|
594
|
+
|
|
595
|
+
t_local += dt_step
|
|
596
|
+
|
|
597
|
+
graph.graph["_t"] = t_local
|
|
598
|
+
|
|
599
|
+
|
|
600
|
+
def update_epi_via_nodal_equation(
|
|
601
|
+
G: TNFRGraph,
|
|
602
|
+
*,
|
|
603
|
+
dt: float | None = None,
|
|
604
|
+
t: float | None = None,
|
|
605
|
+
method: Literal["euler", "rk4"] | None = None,
|
|
606
|
+
n_jobs: int | None = None,
|
|
607
|
+
) -> None:
|
|
608
|
+
"""TNFR nodal equation.
|
|
609
|
+
|
|
610
|
+
Implements the extended nodal equation:
|
|
611
|
+
∂EPI/∂t = νf · ΔNFR(t) + Γi(R)
|
|
612
|
+
|
|
613
|
+
Where:
|
|
614
|
+
- EPI is the node's Primary Information Structure.
|
|
615
|
+
- νf is the node's structural frequency (Hz_str).
|
|
616
|
+
- ΔNFR(t) is the nodal gradient (reorganisation need), typically a mix
|
|
617
|
+
of components (e.g. phase θ, EPI, νf).
|
|
618
|
+
- Γi(R) is the optional network coupling as a function of Kuramoto order
|
|
619
|
+
``R`` (see :mod:`gamma`), used to modulate network integration.
|
|
620
|
+
|
|
621
|
+
TNFR references: nodal equation (manual), νf/ΔNFR/EPI glossary, Γ operator.
|
|
622
|
+
Side effects: caches dEPI and updates EPI via explicit integration.
|
|
623
|
+
"""
|
|
624
|
+
DefaultIntegrator().integrate(
|
|
625
|
+
G,
|
|
626
|
+
dt=dt,
|
|
627
|
+
t=t,
|
|
628
|
+
method=method,
|
|
629
|
+
n_jobs=n_jobs,
|
|
630
|
+
)
|
|
631
|
+
|
|
632
|
+
|
|
633
|
+
def _node_state(nd: dict[str, Any]) -> tuple[float, float, float, float]:
|
|
634
|
+
"""Return common node state attributes for canonical equation evaluation.
|
|
635
|
+
|
|
636
|
+
Extracts the fundamental TNFR variables from node data:
|
|
637
|
+
- νf (vf): Structural frequency in Hz_str
|
|
638
|
+
- ΔNFR (dnfr): Nodal gradient (reorganization operator)
|
|
639
|
+
- dEPI/dt (previous): Last computed EPI derivative
|
|
640
|
+
- EPI (current): Current Primary Information Structure
|
|
641
|
+
|
|
642
|
+
These variables are used in the canonical nodal equation:
|
|
643
|
+
∂EPI/∂t = νf · ΔNFR(t)
|
|
644
|
+
|
|
645
|
+
Args:
|
|
646
|
+
nd: Node data dictionary containing TNFR attributes
|
|
647
|
+
|
|
648
|
+
Returns:
|
|
649
|
+
Tuple of (vf, dnfr, dEPI_dt_prev, epi_i) with 0.0 defaults
|
|
650
|
+
|
|
651
|
+
Notes:
|
|
652
|
+
- vf alias maps to VF, frequency, or structural_frequency
|
|
653
|
+
- dnfr alias maps to DNFR, delta_nfr, or reorganization_gradient
|
|
654
|
+
- All values are coerced to float for numerical stability
|
|
655
|
+
"""
|
|
656
|
+
|
|
657
|
+
vf = get_attr(nd, ALIAS_VF, 0.0)
|
|
658
|
+
dnfr = get_attr(nd, ALIAS_DNFR, 0.0)
|
|
659
|
+
dEPI_dt_prev = get_attr(nd, ALIAS_DEPI, 0.0)
|
|
660
|
+
epi_i = get_attr(nd, ALIAS_EPI, 0.0)
|
|
661
|
+
return vf, dnfr, dEPI_dt_prev, epi_i
|
|
@@ -0,0 +1,36 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
|
|
3
|
+
from typing import Literal
|
|
4
|
+
|
|
5
|
+
from tnfr.types import TNFRGraph
|
|
6
|
+
|
|
7
|
+
__all__: tuple[str, ...]
|
|
8
|
+
|
|
9
|
+
class AbstractIntegrator:
|
|
10
|
+
def integrate(
|
|
11
|
+
self,
|
|
12
|
+
graph: TNFRGraph,
|
|
13
|
+
*,
|
|
14
|
+
dt: float | None = ...,
|
|
15
|
+
t: float | None = ...,
|
|
16
|
+
method: str | None = ...,
|
|
17
|
+
n_jobs: int | None = ...,
|
|
18
|
+
) -> None: ...
|
|
19
|
+
|
|
20
|
+
class DefaultIntegrator(AbstractIntegrator):
|
|
21
|
+
def __init__(self) -> None: ...
|
|
22
|
+
|
|
23
|
+
def prepare_integration_params(
|
|
24
|
+
G: TNFRGraph,
|
|
25
|
+
dt: float | None = ...,
|
|
26
|
+
t: float | None = ...,
|
|
27
|
+
method: Literal["euler", "rk4"] | None = ...,
|
|
28
|
+
) -> tuple[float, int, float, Literal["euler", "rk4"]]: ...
|
|
29
|
+
def update_epi_via_nodal_equation(
|
|
30
|
+
G: TNFRGraph,
|
|
31
|
+
*,
|
|
32
|
+
dt: float | None = ...,
|
|
33
|
+
t: float | None = ...,
|
|
34
|
+
method: Literal["euler", "rk4"] | None = ...,
|
|
35
|
+
n_jobs: int | None = ...,
|
|
36
|
+
) -> None: ...
|