drbx 2.0.0.dev0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- drbx/__init__.py +20 -0
- drbx/__main__.py +5 -0
- drbx/cli.py +586 -0
- drbx/config/__init__.py +20 -0
- drbx/config/boutinp.py +556 -0
- drbx/config/model.py +34 -0
- drbx/config/normalization.py +66 -0
- drbx/data/atomic_rates/__init__.py +1 -0
- drbx/data/atomic_rates/iz_AMJUEL_H.x_2.1.5.json +213 -0
- drbx/data/atomic_rates/iz_AMJUEL_H.x_2.3.9a.json +213 -0
- drbx/data/atomic_rates/rec_AMJUEL_H.x_2.1.8.json +213 -0
- drbx/data/atomic_rates/rec_AMJUEL_H.x_2.3.13a.json +213 -0
- drbx/geometry/__init__.py +207 -0
- drbx/geometry/embedding.py +56 -0
- drbx/geometry/essos_import.py +1385 -0
- drbx/geometry/fci_geometry.py +4622 -0
- drbx/geometry/fci_maps.py +85 -0
- drbx/geometry/island_divertor.py +291 -0
- drbx/geometry/metric_tensor.py +99 -0
- drbx/geometry/open_slab.py +150 -0
- drbx/geometry/rotating_ellipse.py +253 -0
- drbx/geometry/shifted_torus.py +225 -0
- drbx/geometry/stellarator.py +287 -0
- drbx/geometry/vmec_extender_import.py +499 -0
- drbx/geometry/vmec_jax_import.py +306 -0
- drbx/linear/__init__.py +37 -0
- drbx/linear/dispersion.py +138 -0
- drbx/linear/eigen.py +91 -0
- drbx/native/__init__.py +224 -0
- drbx/native/array_backend.py +64 -0
- drbx/native/deck_runner.py +779 -0
- drbx/native/electromagnetic.py +250 -0
- drbx/native/expression.py +173 -0
- drbx/native/fci.py +295 -0
- drbx/native/fci_2_field_rhs.py +182 -0
- drbx/native/fci_4_field_rhs.py +1267 -0
- drbx/native/fci_boundaries.py +2494 -0
- drbx/native/fci_differentiable_case.py +304 -0
- drbx/native/fci_drb_EB_rhs.py +1243 -0
- drbx/native/fci_drb_rhs.py +190 -0
- drbx/native/fci_halo.py +1575 -0
- drbx/native/fci_helpers.py +350 -0
- drbx/native/fci_model.py +294 -0
- drbx/native/fci_neutral.py +139 -0
- drbx/native/fci_operators.py +4081 -0
- drbx/native/fci_sharding.py +597 -0
- drbx/native/fci_sheath_recycling.py +206 -0
- drbx/native/fci_time_integrator.py +96 -0
- drbx/native/fci_vorticity.py +198 -0
- drbx/native/fluid_1d.py +330 -0
- drbx/native/hasegawa_wakatani.py +196 -0
- drbx/native/limiters.py +57 -0
- drbx/native/mesh.py +238 -0
- drbx/native/metrics.py +234 -0
- drbx/native/neutrals/__init__.py +58 -0
- drbx/native/neutrals/atomic_rates.py +134 -0
- drbx/native/neutrals/detachment_sol_model.py +221 -0
- drbx/native/neutrals/reactions.py +164 -0
- drbx/native/neutrals/recycling_sol_model.py +197 -0
- drbx/native/sol_flux_tube.py +133 -0
- drbx/native/stellarator_turbulence.py +343 -0
- drbx/native/transport.py +134 -0
- drbx/native/units.py +32 -0
- drbx/native/vorticity.py +252 -0
- drbx/runtime/__init__.py +53 -0
- drbx/runtime/artifacts.py +161 -0
- drbx/runtime/memory.py +144 -0
- drbx/runtime/output.py +374 -0
- drbx/runtime/paths.py +9 -0
- drbx/runtime/performance.py +161 -0
- drbx/runtime/run_config.py +184 -0
- drbx/runtime/scheduler.py +99 -0
- drbx/runtime/state.py +40 -0
- drbx/validation/__init__.py +424 -0
- drbx/validation/autodiff_diffusion.py +329 -0
- drbx/validation/autodiff_diffusion_uncertainty.py +235 -0
- drbx/validation/diverted_tokamak_movie.py +558 -0
- drbx/validation/essos_fieldline_import_campaign.py +181 -0
- drbx/validation/essos_imported_artifact_audit.py +535 -0
- drbx/validation/essos_imported_drb_movie_campaign.py +2826 -0
- drbx/validation/essos_imported_fci_campaign.py +5241 -0
- drbx/validation/essos_imported_pytree_campaign.py +406 -0
- drbx/validation/essos_vmec_closed_field_campaign.py +314 -0
- drbx/validation/essos_vmec_closed_field_transient_campaign.py +629 -0
- drbx/validation/essos_vmec_fieldline_surface_campaign.py +620 -0
- drbx/validation/fluid_1d_mms_convergence.py +250 -0
- drbx/validation/geometry_lineouts.py +136 -0
- drbx/validation/geometry_slices.py +178 -0
- drbx/validation/publication_plotting.py +91 -0
- drbx/validation/stellarator_drb_pytree_campaign.py +621 -0
- drbx/validation/stellarator_fci_geometry_campaign.py +200 -0
- drbx/validation/stellarator_fci_operator_campaign.py +304 -0
- drbx/validation/stellarator_fci_suite_campaign.py +264 -0
- drbx/validation/stellarator_metric_mms_campaign.py +289 -0
- drbx/validation/stellarator_neutral_physics_campaign.py +255 -0
- drbx/validation/stellarator_sheath_recycling_campaign.py +331 -0
- drbx/validation/stellarator_sol_showcase.py +628 -0
- drbx/validation/stellarator_vorticity_campaign.py +304 -0
- drbx/validation/vmec_extender_edge_field_campaign.py +260 -0
- drbx/validation/vmec_extender_sol_smoke_campaign.py +365 -0
- drbx-2.0.0.dev0.dist-info/METADATA +380 -0
- drbx-2.0.0.dev0.dist-info/RECORD +106 -0
- drbx-2.0.0.dev0.dist-info/WHEEL +5 -0
- drbx-2.0.0.dev0.dist-info/entry_points.txt +2 -0
- drbx-2.0.0.dev0.dist-info/licenses/LICENSE +21 -0
- drbx-2.0.0.dev0.dist-info/top_level.txt +1 -0
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from __future__ import annotations
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import importlib
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import os
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import sys
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from dataclasses import dataclass
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from pathlib import Path
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from typing import Any
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import numpy as np
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import jax.numpy as jnp
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from .fci_maps import FciMaps
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from .metric_tensor import MetricTensor3D
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ESSOS_LANDREMAN_QA_RELATIVE_JSON = Path("examples/input_files/ESSOS_biot_savart_LandremanPaulQA.json")
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ESSOS_LANDREMAN_QA_RELATIVE_WOUT = Path("examples/input_files/wout_LandremanPaul2021_QA_reactorScale_lowres.nc")
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_PRIVATE_DEFAULT_ESSOS_ROOT = Path.home() / "local" / "ESSOS"
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@dataclass(frozen=True)
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class EssosFieldLineBundle:
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"""Field and field-line arrays exported from an ESSOS tracing run.
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The bundle deliberately stores arrays, not ESSOS objects. This keeps
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`drbx` independent of ESSOS at runtime after the import/export step.
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"""
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trajectories_xyz: np.ndarray
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times: np.ndarray
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initial_xyz: np.ndarray
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poincare_r: np.ndarray
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poincare_z: np.ndarray
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poincare_time: np.ndarray
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poincare_section: np.ndarray
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poincare_line_index: np.ndarray
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field_sample_xyz: np.ndarray
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field_sample_b_xyz: np.ndarray
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coil_gamma_xyz: np.ndarray
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coil_currents: np.ndarray
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metadata: dict[str, Any]
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@property
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def n_field_lines(self) -> int:
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return int(self.trajectories_xyz.shape[0])
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@property
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def n_times(self) -> int:
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return int(self.trajectories_xyz.shape[1])
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@property
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def poincare_point_count(self) -> int:
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return int(self.poincare_r.size)
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@dataclass(frozen=True)
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class EssosImportedFciGeometry:
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"""VMEC-shaped FCI geometry whose field-line maps are exported from ESSOS."""
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coordinates_x: jnp.ndarray
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coordinates_y: jnp.ndarray
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coordinates_z: jnp.ndarray
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minor_radius: jnp.ndarray
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toroidal_angle: jnp.ndarray
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poloidal_angle: jnp.ndarray
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magnetic_field_magnitude: jnp.ndarray
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connection_length: jnp.ndarray
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adjacent_step_length: jnp.ndarray | None
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target_exit_length: jnp.ndarray | None
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forward_target_exit_length: jnp.ndarray | None
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backward_target_exit_length: jnp.ndarray | None
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metric: MetricTensor3D
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maps: FciMaps
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metadata: dict[str, Any]
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@property
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def shape(self) -> tuple[int, int, int]:
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return tuple(int(value) for value in self.minor_radius.shape)
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def resolve_essos_landreman_qa_json(path: str | Path | None = None, *, essos_root: str | Path | None = None) -> Path:
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"""Resolve the Landreman-Paul QA coil JSON from an ESSOS checkout."""
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if path is not None:
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resolved = Path(path)
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else:
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root = Path(essos_root) if essos_root is not None else Path(os.environ.get("DRBX_ESSOS_ROOT", _PRIVATE_DEFAULT_ESSOS_ROOT))
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resolved = root / ESSOS_LANDREMAN_QA_RELATIVE_JSON
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if not resolved.exists():
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raise FileNotFoundError(
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"ESSOS Landreman-Paul QA coil JSON was not found. Pass coil_json_path "
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"or set DRBX_ESSOS_ROOT to an ESSOS checkout containing "
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f"{ESSOS_LANDREMAN_QA_RELATIVE_JSON}."
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)
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return resolved
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def resolve_essos_landreman_qa_wout(path: str | Path | None = None, *, essos_root: str | Path | None = None) -> Path:
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"""Resolve the matching Landreman-Paul QA VMEC wout file."""
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if path is not None:
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resolved = Path(path)
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else:
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root = Path(essos_root) if essos_root is not None else Path(os.environ.get("DRBX_ESSOS_ROOT", _PRIVATE_DEFAULT_ESSOS_ROOT))
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resolved = root / ESSOS_LANDREMAN_QA_RELATIVE_WOUT
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if not resolved.exists():
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raise FileNotFoundError(
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"ESSOS Landreman-Paul QA VMEC wout file was not found. Pass vmec_wout_path "
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"or set DRBX_ESSOS_ROOT to an ESSOS checkout containing "
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f"{ESSOS_LANDREMAN_QA_RELATIVE_WOUT}."
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)
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return resolved
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def essos_runtime_available(*, essos_root: str | Path | None = None) -> bool:
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"""Return whether ESSOS can be imported by the optional adapter."""
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try:
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_import_essos_modules(essos_root=essos_root)
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except (ImportError, ModuleNotFoundError, AttributeError):
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return False
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return True
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def trace_essos_coil_field_lines(
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*,
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coil_json_path: str | Path | None = None,
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essos_root: str | Path | None = None,
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r_min: float = 1.21,
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r_max: float = 1.40,
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n_field_lines: int = 8,
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maxtime: float = 1000.0,
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times_to_trace: int = 6000,
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trace_tolerance: float = 1.0e-8,
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poincare_shifts: tuple[float, ...] = (0.0, float(np.pi / 2.0)),
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field_sample_count: int = 256,
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) -> EssosFieldLineBundle:
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"""Trace coil-produced field lines with ESSOS and export arrays.
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ESSOS owns the magnetic-field object, adaptive field-line integration, and
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Poincare root extraction. `drbx` only normalizes the resulting arrays
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into a stable import bundle.
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"""
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resolved_coil_json = resolve_essos_landreman_qa_json(coil_json_path, essos_root=essos_root)
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modules = _import_essos_modules(essos_root=essos_root if essos_root is not None else resolved_coil_json.parents[2])
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import jax
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import jax.numpy as jnp
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import matplotlib.pyplot as plt
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coils = modules["Coils_from_json"](str(resolved_coil_json))
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field = modules["BiotSavart"](coils)
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r0 = jnp.linspace(float(r_min), float(r_max), int(n_field_lines))
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z0 = jnp.zeros(int(n_field_lines))
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phi0 = jnp.zeros(int(n_field_lines))
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initial_xyz = jnp.array([r0 * jnp.cos(phi0), r0 * jnp.sin(phi0), z0]).T
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tracing = jax.block_until_ready(
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modules["Tracing"](
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field=field,
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model="FieldLineAdaptative",
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initial_conditions=initial_xyz,
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maxtime=float(maxtime),
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times_to_trace=int(times_to_trace),
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atol=float(trace_tolerance),
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rtol=float(trace_tolerance),
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)
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)
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trajectories_xyz = np.asarray(tracing.trajectories[:, :, :3], dtype=np.float64)
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times = np.asarray(tracing.times, dtype=np.float64)
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initial_xyz_np = np.asarray(initial_xyz, dtype=np.float64)
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fig, axis = plt.subplots(figsize=(2.0, 2.0))
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plotting_data = tracing.poincare_plot(
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shifts=[jnp.asarray(value) for value in poincare_shifts],
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ax=axis,
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show=False,
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s=0.5,
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)
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plt.close(fig)
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poincare = _flatten_essos_poincare_data(
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plotting_data,
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n_field_lines=int(n_field_lines),
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shifts=tuple(float(value) for value in poincare_shifts),
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)
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flat_trajectory = trajectories_xyz.reshape((-1, 3))
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sample_count = min(int(field_sample_count), int(flat_trajectory.shape[0]))
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sample_indices = np.linspace(0, flat_trajectory.shape[0] - 1, sample_count, dtype=int)
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field_sample_xyz = flat_trajectory[sample_indices]
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field_sample_b_xyz = _sample_essos_field(field, field_sample_xyz)
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metadata = {
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"source": "ESSOS",
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"coil_json_file": resolved_coil_json.name,
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"field_model": "essos.fields.BiotSavart",
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"tracing_model": "essos.dynamics.Tracing(FieldLineAdaptative)",
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"poincare_method": "essos.dynamics.Tracing.poincare_plot",
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"n_field_lines": int(n_field_lines),
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"times_to_trace": int(times_to_trace),
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"maxtime": float(maxtime),
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"trace_tolerance": float(trace_tolerance),
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"r_min": float(r_min),
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"r_max": float(r_max),
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"poincare_shifts": [float(value) for value in poincare_shifts],
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}
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return EssosFieldLineBundle(
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trajectories_xyz=trajectories_xyz,
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times=times,
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initial_xyz=initial_xyz_np,
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poincare_r=poincare["r"],
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poincare_z=poincare["z"],
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poincare_time=poincare["time"],
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poincare_section=poincare["section"],
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|
+
poincare_line_index=poincare["line_index"],
|
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219
|
+
field_sample_xyz=field_sample_xyz,
|
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220
|
+
field_sample_b_xyz=field_sample_b_xyz,
|
|
221
|
+
coil_gamma_xyz=np.asarray(coils.gamma, dtype=np.float64),
|
|
222
|
+
coil_currents=np.asarray(coils.currents, dtype=np.float64),
|
|
223
|
+
metadata=metadata,
|
|
224
|
+
)
|
|
225
|
+
|
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226
|
+
|
|
227
|
+
def load_essos_coil_field_axis(
|
|
228
|
+
*,
|
|
229
|
+
coil_json_path: str | Path | None = None,
|
|
230
|
+
essos_root: str | Path | None = None,
|
|
231
|
+
) -> tuple[float, float]:
|
|
232
|
+
"""Return the magnetic-axis location reported by the imported ESSOS coil field."""
|
|
233
|
+
|
|
234
|
+
resolved_coil_json = resolve_essos_landreman_qa_json(coil_json_path, essos_root=essos_root)
|
|
235
|
+
modules = _import_essos_modules(essos_root=essos_root if essos_root is not None else resolved_coil_json.parents[2])
|
|
236
|
+
coils = modules["Coils_from_json"](str(resolved_coil_json))
|
|
237
|
+
field = modules["BiotSavart"](coils)
|
|
238
|
+
return float(field.r_axis), float(field.z_axis)
|
|
239
|
+
|
|
240
|
+
|
|
241
|
+
def load_essos_vmec_field_axis(
|
|
242
|
+
*,
|
|
243
|
+
vmec_wout_path: str | Path | None = None,
|
|
244
|
+
essos_root: str | Path | None = None,
|
|
245
|
+
) -> tuple[float, float]:
|
|
246
|
+
"""Return the magnetic-axis location in an ESSOS VMEC field object."""
|
|
247
|
+
|
|
248
|
+
resolved_wout = resolve_essos_landreman_qa_wout(vmec_wout_path, essos_root=essos_root)
|
|
249
|
+
modules = _import_essos_modules(essos_root=essos_root if essos_root is not None else resolved_wout.parents[2])
|
|
250
|
+
vmec = modules["Vmec"](str(resolved_wout))
|
|
251
|
+
return float(vmec.r_axis), float(vmec.z_axis)
|
|
252
|
+
|
|
253
|
+
|
|
254
|
+
def trace_essos_coil_initial_conditions(
|
|
255
|
+
initial_xyz: np.ndarray,
|
|
256
|
+
*,
|
|
257
|
+
coil_json_path: str | Path | None = None,
|
|
258
|
+
essos_root: str | Path | None = None,
|
|
259
|
+
current_sign: float = 1.0,
|
|
260
|
+
maxtime: float = 1000.0,
|
|
261
|
+
times_to_trace: int = 6000,
|
|
262
|
+
trace_tolerance: float = 1.0e-8,
|
|
263
|
+
) -> np.ndarray:
|
|
264
|
+
"""Trace arbitrary Cartesian seed points through the optional ESSOS coil field."""
|
|
265
|
+
|
|
266
|
+
resolved_coil_json = resolve_essos_landreman_qa_json(coil_json_path, essos_root=essos_root)
|
|
267
|
+
modules = _import_essos_modules(essos_root=essos_root if essos_root is not None else resolved_coil_json.parents[2])
|
|
268
|
+
return _trace_essos_initial_conditions(
|
|
269
|
+
modules=modules,
|
|
270
|
+
resolved_coil_json=resolved_coil_json,
|
|
271
|
+
initial_xyz=np.asarray(initial_xyz, dtype=np.float64),
|
|
272
|
+
current_sign=float(current_sign),
|
|
273
|
+
maxtime=float(maxtime),
|
|
274
|
+
times_to_trace=int(times_to_trace),
|
|
275
|
+
trace_tolerance=float(trace_tolerance),
|
|
276
|
+
)
|
|
277
|
+
|
|
278
|
+
|
|
279
|
+
def trace_essos_vmec_initial_conditions(
|
|
280
|
+
initial_stp: np.ndarray,
|
|
281
|
+
*,
|
|
282
|
+
vmec_wout_path: str | Path | None = None,
|
|
283
|
+
essos_root: str | Path | None = None,
|
|
284
|
+
maxtime: float = 1000.0,
|
|
285
|
+
times_to_trace: int = 6000,
|
|
286
|
+
trace_tolerance: float = 1.0e-8,
|
|
287
|
+
) -> np.ndarray:
|
|
288
|
+
"""Trace VMEC-coordinate seed points through the optional ESSOS VMEC field."""
|
|
289
|
+
|
|
290
|
+
resolved_wout = resolve_essos_landreman_qa_wout(vmec_wout_path, essos_root=essos_root)
|
|
291
|
+
modules = _import_essos_modules(essos_root=essos_root if essos_root is not None else resolved_wout.parents[2])
|
|
292
|
+
return _trace_essos_vmec_initial_conditions(
|
|
293
|
+
modules=modules,
|
|
294
|
+
resolved_wout=resolved_wout,
|
|
295
|
+
initial_stp=np.asarray(initial_stp, dtype=np.float64),
|
|
296
|
+
maxtime=float(maxtime),
|
|
297
|
+
times_to_trace=int(times_to_trace),
|
|
298
|
+
trace_tolerance=float(trace_tolerance),
|
|
299
|
+
)
|
|
300
|
+
|
|
301
|
+
|
|
302
|
+
def build_essos_imported_fci_geometry(
|
|
303
|
+
*,
|
|
304
|
+
coil_json_path: str | Path | None = None,
|
|
305
|
+
vmec_wout_path: str | Path | None = None,
|
|
306
|
+
essos_root: str | Path | None = None,
|
|
307
|
+
map_source: str = "coil",
|
|
308
|
+
nx: int = 6,
|
|
309
|
+
ny: int = 8,
|
|
310
|
+
nz: int = 16,
|
|
311
|
+
rho_min: float = 0.10,
|
|
312
|
+
rho_max: float = 0.46,
|
|
313
|
+
maxtime: float = 140.0,
|
|
314
|
+
times_to_trace: int = 768,
|
|
315
|
+
trace_tolerance: float = 1.0e-8,
|
|
316
|
+
) -> EssosImportedFciGeometry:
|
|
317
|
+
"""Build FCI maps from ESSOS tracing on a VMEC-shaped QA seed grid.
|
|
318
|
+
|
|
319
|
+
``map_source`` selects the field-line-map semantics:
|
|
320
|
+
|
|
321
|
+
- ``"coil"`` traces the imported coil field and keeps its open-field masks;
|
|
322
|
+
- ``"vmec"`` builds surface-preserving VMEC-coordinate maps with closed
|
|
323
|
+
field-line masks;
|
|
324
|
+
- ``"hybrid"`` uses VMEC-coordinate map coordinates with coil-derived
|
|
325
|
+
boundary masks, connection lengths, and magnetic-field modulation.
|
|
326
|
+
|
|
327
|
+
The external field implementation owns the field evaluation. `drbx`
|
|
328
|
+
provides only the logical-grid conversion needed by the native FCI,
|
|
329
|
+
sheath/recycling, neutral, and PyTree RHS kernels.
|
|
330
|
+
"""
|
|
331
|
+
|
|
332
|
+
if nx < 2 or ny < 2 or nz < 4:
|
|
333
|
+
raise ValueError("ESSOS imported FCI geometry requires nx >= 2, ny >= 2, and nz >= 4")
|
|
334
|
+
map_source = _normalize_essos_map_source(map_source)
|
|
335
|
+
resolved_coil_json = resolve_essos_landreman_qa_json(coil_json_path, essos_root=essos_root)
|
|
336
|
+
modules = _import_essos_modules(essos_root=essos_root if essos_root is not None else resolved_coil_json.parents[2])
|
|
337
|
+
|
|
338
|
+
coils = modules["Coils_from_json"](str(resolved_coil_json))
|
|
339
|
+
field = modules["BiotSavart"](coils)
|
|
340
|
+
axis_major_radius = float(field.r_axis)
|
|
341
|
+
axis_vertical = float(field.z_axis)
|
|
342
|
+
|
|
343
|
+
resolved_vmec_wout = resolve_essos_landreman_qa_wout(vmec_wout_path, essos_root=essos_root)
|
|
344
|
+
coordinates = build_essos_vmec_scaled_qa_coordinates(
|
|
345
|
+
resolved_vmec_wout,
|
|
346
|
+
nx=int(nx),
|
|
347
|
+
ny=int(ny),
|
|
348
|
+
nz=int(nz),
|
|
349
|
+
rho_min=float(rho_min),
|
|
350
|
+
rho_max=float(rho_max),
|
|
351
|
+
axis_major_radius=axis_major_radius,
|
|
352
|
+
axis_vertical=axis_vertical,
|
|
353
|
+
)
|
|
354
|
+
rho_1d = coordinates["rho_1d"]
|
|
355
|
+
phi_1d = coordinates["phi_1d"]
|
|
356
|
+
theta_1d = coordinates["theta_1d"]
|
|
357
|
+
rho = coordinates["rho"]
|
|
358
|
+
phi = coordinates["phi"]
|
|
359
|
+
theta = coordinates["theta"]
|
|
360
|
+
coordinates_x = coordinates["x"]
|
|
361
|
+
coordinates_y = coordinates["y"]
|
|
362
|
+
coordinates_z = coordinates["z"]
|
|
363
|
+
initial_xyz = np.stack([coordinates_x, coordinates_y, coordinates_z], axis=-1).reshape((-1, 3))
|
|
364
|
+
start_phi = phi.reshape(-1)
|
|
365
|
+
dphi = float(2.0 * np.pi / float(ny))
|
|
366
|
+
start_y_index = np.broadcast_to(np.arange(int(ny), dtype=int)[None, :, None], (int(nx), int(ny), int(nz))).reshape(-1)
|
|
367
|
+
coil_data: dict[str, Any] | None = None
|
|
368
|
+
if map_source in {"coil", "hybrid"}:
|
|
369
|
+
coil_data = _build_essos_coil_fci_map_data(
|
|
370
|
+
modules=modules,
|
|
371
|
+
resolved_coil_json=resolved_coil_json,
|
|
372
|
+
field=field,
|
|
373
|
+
initial_xyz=initial_xyz,
|
|
374
|
+
start_phi=start_phi,
|
|
375
|
+
start_y_index=start_y_index,
|
|
376
|
+
dphi=dphi,
|
|
377
|
+
shape=(int(nx), int(ny), int(nz)),
|
|
378
|
+
coordinates_x=coordinates_x,
|
|
379
|
+
coordinates_y=coordinates_y,
|
|
380
|
+
coordinates_z=coordinates_z,
|
|
381
|
+
maxtime=float(maxtime),
|
|
382
|
+
times_to_trace=int(times_to_trace),
|
|
383
|
+
trace_tolerance=float(trace_tolerance),
|
|
384
|
+
)
|
|
385
|
+
vmec_data: dict[str, Any] | None = None
|
|
386
|
+
if map_source in {"vmec", "hybrid"}:
|
|
387
|
+
vmec_data = _build_essos_vmec_fci_map_data(
|
|
388
|
+
modules=modules,
|
|
389
|
+
resolved_wout=resolved_vmec_wout,
|
|
390
|
+
coordinates=coordinates,
|
|
391
|
+
shape=(int(nx), int(ny), int(nz)),
|
|
392
|
+
dphi=dphi,
|
|
393
|
+
)
|
|
394
|
+
|
|
395
|
+
if map_source == "coil":
|
|
396
|
+
assert coil_data is not None
|
|
397
|
+
maps = coil_data["maps"]
|
|
398
|
+
bmag = coil_data["bmag"]
|
|
399
|
+
connection_length = coil_data["connection_length"]
|
|
400
|
+
adjacent_step_length = coil_data["adjacent_step_length"]
|
|
401
|
+
target_exit_length = coil_data["target_exit_length"]
|
|
402
|
+
forward_target_exit_length = coil_data["forward_target_exit_length"]
|
|
403
|
+
backward_target_exit_length = coil_data["backward_target_exit_length"]
|
|
404
|
+
field_model = "essos.fields.BiotSavart"
|
|
405
|
+
tracing_model = "essos.dynamics.Tracing(FieldLineAdaptative)"
|
|
406
|
+
elif map_source == "vmec":
|
|
407
|
+
assert vmec_data is not None
|
|
408
|
+
maps = vmec_data["maps"]
|
|
409
|
+
bmag = vmec_data["bmag"]
|
|
410
|
+
connection_length = vmec_data["connection_length"]
|
|
411
|
+
adjacent_step_length = vmec_data["connection_length"]
|
|
412
|
+
target_exit_length = np.full_like(connection_length, np.nan, dtype=np.float64)
|
|
413
|
+
forward_target_exit_length = np.full_like(connection_length, np.nan, dtype=np.float64)
|
|
414
|
+
backward_target_exit_length = np.full_like(connection_length, np.nan, dtype=np.float64)
|
|
415
|
+
field_model = "essos.fields.Vmec"
|
|
416
|
+
tracing_model = "vmec_coordinate_rk4_map"
|
|
417
|
+
else:
|
|
418
|
+
assert coil_data is not None
|
|
419
|
+
assert vmec_data is not None
|
|
420
|
+
maps = FciMaps(
|
|
421
|
+
forward_x=vmec_data["maps"].forward_x,
|
|
422
|
+
forward_z=vmec_data["maps"].forward_z,
|
|
423
|
+
backward_x=vmec_data["maps"].backward_x,
|
|
424
|
+
backward_z=vmec_data["maps"].backward_z,
|
|
425
|
+
forward_boundary=coil_data["maps"].forward_boundary,
|
|
426
|
+
backward_boundary=coil_data["maps"].backward_boundary,
|
|
427
|
+
dphi=dphi,
|
|
428
|
+
)
|
|
429
|
+
bmag = coil_data["bmag"]
|
|
430
|
+
connection_length = coil_data["connection_length"]
|
|
431
|
+
adjacent_step_length = vmec_data["connection_length"]
|
|
432
|
+
target_exit_length = coil_data["target_exit_length"]
|
|
433
|
+
forward_target_exit_length = coil_data["forward_target_exit_length"]
|
|
434
|
+
backward_target_exit_length = coil_data["backward_target_exit_length"]
|
|
435
|
+
field_model = "hybrid: VMEC map coordinates with Biot-Savart |B| and target masks"
|
|
436
|
+
tracing_model = "vmec_coordinate_rk4_map + essos.dynamics.Tracing(FieldLineAdaptative) masks"
|
|
437
|
+
|
|
438
|
+
forward_boundary = np.asarray(maps.forward_boundary, dtype=bool)
|
|
439
|
+
backward_boundary = np.asarray(maps.backward_boundary, dtype=bool)
|
|
440
|
+
metric = _metric_from_coordinates(
|
|
441
|
+
coordinates_x,
|
|
442
|
+
coordinates_y,
|
|
443
|
+
coordinates_z,
|
|
444
|
+
s_1d=rho_1d,
|
|
445
|
+
phi_1d=phi_1d,
|
|
446
|
+
theta_1d=theta_1d,
|
|
447
|
+
Bxy=bmag,
|
|
448
|
+
)
|
|
449
|
+
forward_boundary_fraction = float(np.mean(forward_boundary))
|
|
450
|
+
backward_boundary_fraction = float(np.mean(backward_boundary))
|
|
451
|
+
return EssosImportedFciGeometry(
|
|
452
|
+
coordinates_x=jnp.asarray(coordinates_x, dtype=jnp.float64),
|
|
453
|
+
coordinates_y=jnp.asarray(coordinates_y, dtype=jnp.float64),
|
|
454
|
+
coordinates_z=jnp.asarray(coordinates_z, dtype=jnp.float64),
|
|
455
|
+
minor_radius=jnp.asarray(rho, dtype=jnp.float64),
|
|
456
|
+
toroidal_angle=jnp.asarray(phi, dtype=jnp.float64),
|
|
457
|
+
poloidal_angle=jnp.asarray(theta, dtype=jnp.float64),
|
|
458
|
+
magnetic_field_magnitude=jnp.asarray(bmag, dtype=jnp.float64),
|
|
459
|
+
connection_length=jnp.asarray(connection_length, dtype=jnp.float64),
|
|
460
|
+
adjacent_step_length=jnp.asarray(adjacent_step_length, dtype=jnp.float64),
|
|
461
|
+
target_exit_length=jnp.asarray(target_exit_length, dtype=jnp.float64),
|
|
462
|
+
forward_target_exit_length=jnp.asarray(forward_target_exit_length, dtype=jnp.float64),
|
|
463
|
+
backward_target_exit_length=jnp.asarray(backward_target_exit_length, dtype=jnp.float64),
|
|
464
|
+
metric=metric,
|
|
465
|
+
maps=maps,
|
|
466
|
+
metadata={
|
|
467
|
+
"geometry_family": "essos_imported_vmec_qa_fci",
|
|
468
|
+
"source": "ESSOS",
|
|
469
|
+
"coil_json_file": resolved_coil_json.name,
|
|
470
|
+
"vmec_wout_file": resolved_vmec_wout.name,
|
|
471
|
+
"coordinate_model": "scaled_vmec_fourier_flux_surfaces",
|
|
472
|
+
**coordinates["metadata"],
|
|
473
|
+
"map_source": map_source,
|
|
474
|
+
"field_model": field_model,
|
|
475
|
+
"tracing_model": tracing_model,
|
|
476
|
+
"nx": int(nx),
|
|
477
|
+
"ny": int(ny),
|
|
478
|
+
"nz": int(nz),
|
|
479
|
+
"rho_min": float(rho_min),
|
|
480
|
+
"rho_max": float(rho_max),
|
|
481
|
+
"axis_major_radius": float(axis_major_radius),
|
|
482
|
+
"axis_vertical": float(axis_vertical),
|
|
483
|
+
"maxtime": float(maxtime),
|
|
484
|
+
"times_to_trace": int(times_to_trace),
|
|
485
|
+
"trace_tolerance": float(trace_tolerance),
|
|
486
|
+
"coil_trace_current_sign": float(coil_data["current_sign"]) if coil_data is not None else 0.0,
|
|
487
|
+
"vmec_map_theta_step_count": int(vmec_data["theta_step_count"]) if vmec_data is not None else 0,
|
|
488
|
+
"forward_boundary_fraction": forward_boundary_fraction,
|
|
489
|
+
"backward_boundary_fraction": backward_boundary_fraction,
|
|
490
|
+
},
|
|
491
|
+
)
|
|
492
|
+
|
|
493
|
+
|
|
494
|
+
def _normalize_essos_map_source(map_source: str) -> str:
|
|
495
|
+
normalized = str(map_source).strip().lower().replace("-", "_")
|
|
496
|
+
aliases = {
|
|
497
|
+
"essos": "coil",
|
|
498
|
+
"essos_coil": "coil",
|
|
499
|
+
"coil_map": "coil",
|
|
500
|
+
"vmec_map": "vmec",
|
|
501
|
+
"hybrid_map": "hybrid",
|
|
502
|
+
}
|
|
503
|
+
normalized = aliases.get(normalized, normalized)
|
|
504
|
+
if normalized not in {"coil", "vmec", "hybrid"}:
|
|
505
|
+
raise ValueError("map_source must be one of 'coil', 'vmec', or 'hybrid'")
|
|
506
|
+
return normalized
|
|
507
|
+
|
|
508
|
+
|
|
509
|
+
def _build_essos_coil_fci_map_data(
|
|
510
|
+
*,
|
|
511
|
+
modules: dict[str, Any],
|
|
512
|
+
resolved_coil_json: Path,
|
|
513
|
+
field: Any,
|
|
514
|
+
initial_xyz: np.ndarray,
|
|
515
|
+
start_phi: np.ndarray,
|
|
516
|
+
start_y_index: np.ndarray,
|
|
517
|
+
dphi: float,
|
|
518
|
+
shape: tuple[int, int, int],
|
|
519
|
+
coordinates_x: np.ndarray,
|
|
520
|
+
coordinates_y: np.ndarray,
|
|
521
|
+
coordinates_z: np.ndarray,
|
|
522
|
+
maxtime: float,
|
|
523
|
+
times_to_trace: int,
|
|
524
|
+
trace_tolerance: float,
|
|
525
|
+
) -> dict[str, Any]:
|
|
526
|
+
import jax
|
|
527
|
+
import jax.numpy as local_jnp
|
|
528
|
+
|
|
529
|
+
nx, ny, nz = shape
|
|
530
|
+
forward_trajectories = _trace_essos_initial_conditions(
|
|
531
|
+
modules=modules,
|
|
532
|
+
resolved_coil_json=resolved_coil_json,
|
|
533
|
+
initial_xyz=initial_xyz,
|
|
534
|
+
current_sign=1.0,
|
|
535
|
+
maxtime=maxtime,
|
|
536
|
+
times_to_trace=times_to_trace,
|
|
537
|
+
trace_tolerance=trace_tolerance,
|
|
538
|
+
)
|
|
539
|
+
if _median_toroidal_advance(forward_trajectories) < 0.0:
|
|
540
|
+
forward_current_sign = -1.0
|
|
541
|
+
forward_trajectories = _trace_essos_initial_conditions(
|
|
542
|
+
modules=modules,
|
|
543
|
+
resolved_coil_json=resolved_coil_json,
|
|
544
|
+
initial_xyz=initial_xyz,
|
|
545
|
+
current_sign=forward_current_sign,
|
|
546
|
+
maxtime=maxtime,
|
|
547
|
+
times_to_trace=times_to_trace,
|
|
548
|
+
trace_tolerance=trace_tolerance,
|
|
549
|
+
)
|
|
550
|
+
else:
|
|
551
|
+
forward_current_sign = 1.0
|
|
552
|
+
backward_trajectories = _trace_essos_initial_conditions(
|
|
553
|
+
modules=modules,
|
|
554
|
+
resolved_coil_json=resolved_coil_json,
|
|
555
|
+
initial_xyz=initial_xyz,
|
|
556
|
+
current_sign=-forward_current_sign,
|
|
557
|
+
maxtime=maxtime,
|
|
558
|
+
times_to_trace=times_to_trace,
|
|
559
|
+
trace_tolerance=trace_tolerance,
|
|
560
|
+
)
|
|
561
|
+
forward_endpoint, forward_length, forward_crossed = _interpolate_trajectories_at_toroidal_plane(
|
|
562
|
+
forward_trajectories,
|
|
563
|
+
target_phi=start_phi + dphi,
|
|
564
|
+
)
|
|
565
|
+
backward_endpoint, backward_length, backward_crossed = _interpolate_trajectories_at_toroidal_plane(
|
|
566
|
+
backward_trajectories,
|
|
567
|
+
target_phi=start_phi - dphi,
|
|
568
|
+
)
|
|
569
|
+
forward_x, forward_z, forward_boundary = _cartesian_to_structured_surface_indices(
|
|
570
|
+
forward_endpoint,
|
|
571
|
+
crossed=forward_crossed,
|
|
572
|
+
target_y_index=(start_y_index + 1) % int(ny),
|
|
573
|
+
coordinates_x=coordinates_x,
|
|
574
|
+
coordinates_y=coordinates_y,
|
|
575
|
+
coordinates_z=coordinates_z,
|
|
576
|
+
)
|
|
577
|
+
backward_x, backward_z, backward_boundary = _cartesian_to_structured_surface_indices(
|
|
578
|
+
backward_endpoint,
|
|
579
|
+
crossed=backward_crossed,
|
|
580
|
+
target_y_index=(start_y_index - 1) % int(ny),
|
|
581
|
+
coordinates_x=coordinates_x,
|
|
582
|
+
coordinates_y=coordinates_y,
|
|
583
|
+
coordinates_z=coordinates_z,
|
|
584
|
+
)
|
|
585
|
+
b_xyz = np.asarray(jax.vmap(field.B)(local_jnp.asarray(initial_xyz, dtype=local_jnp.float64)), dtype=np.float64)
|
|
586
|
+
bmag = np.linalg.norm(b_xyz, axis=1).reshape(shape)
|
|
587
|
+
raw_forward_exit_length = _structured_exit_length_from_trajectories(
|
|
588
|
+
forward_trajectories,
|
|
589
|
+
coordinates_x=coordinates_x,
|
|
590
|
+
coordinates_y=coordinates_y,
|
|
591
|
+
coordinates_z=coordinates_z,
|
|
592
|
+
)
|
|
593
|
+
raw_backward_exit_length = _structured_exit_length_from_trajectories(
|
|
594
|
+
backward_trajectories,
|
|
595
|
+
coordinates_x=coordinates_x,
|
|
596
|
+
coordinates_y=coordinates_y,
|
|
597
|
+
coordinates_z=coordinates_z,
|
|
598
|
+
)
|
|
599
|
+
forward_exit_length = _mask_exit_length_to_boundary(
|
|
600
|
+
raw_forward_exit_length,
|
|
601
|
+
forward_boundary,
|
|
602
|
+
).reshape(shape)
|
|
603
|
+
backward_exit_length = _mask_exit_length_to_boundary(
|
|
604
|
+
raw_backward_exit_length,
|
|
605
|
+
backward_boundary,
|
|
606
|
+
).reshape(shape)
|
|
607
|
+
exit_length = _combine_bidirectional_exit_lengths(
|
|
608
|
+
forward_exit_length,
|
|
609
|
+
backward_exit_length,
|
|
610
|
+
)
|
|
611
|
+
adjacent_length = 0.5 * (forward_length + backward_length).reshape(shape)
|
|
612
|
+
connection_length = np.where(np.isfinite(exit_length), exit_length, adjacent_length)
|
|
613
|
+
maps = FciMaps(
|
|
614
|
+
forward_x=jnp.asarray(forward_x.reshape(shape), dtype=jnp.float64),
|
|
615
|
+
forward_z=jnp.asarray(forward_z.reshape(shape), dtype=jnp.float64),
|
|
616
|
+
backward_x=jnp.asarray(backward_x.reshape(shape), dtype=jnp.float64),
|
|
617
|
+
backward_z=jnp.asarray(backward_z.reshape(shape), dtype=jnp.float64),
|
|
618
|
+
forward_boundary=jnp.asarray(forward_boundary.reshape(shape)),
|
|
619
|
+
backward_boundary=jnp.asarray(backward_boundary.reshape(shape)),
|
|
620
|
+
dphi=dphi,
|
|
621
|
+
)
|
|
622
|
+
return {
|
|
623
|
+
"maps": maps,
|
|
624
|
+
"bmag": bmag,
|
|
625
|
+
"connection_length": connection_length,
|
|
626
|
+
"adjacent_step_length": adjacent_length,
|
|
627
|
+
"target_exit_length": exit_length,
|
|
628
|
+
"forward_target_exit_length": forward_exit_length,
|
|
629
|
+
"backward_target_exit_length": backward_exit_length,
|
|
630
|
+
"current_sign": float(forward_current_sign),
|
|
631
|
+
}
|
|
632
|
+
|
|
633
|
+
|
|
634
|
+
def _build_essos_vmec_fci_map_data(
|
|
635
|
+
*,
|
|
636
|
+
modules: dict[str, Any],
|
|
637
|
+
resolved_wout: Path,
|
|
638
|
+
coordinates: dict[str, Any],
|
|
639
|
+
shape: tuple[int, int, int],
|
|
640
|
+
dphi: float,
|
|
641
|
+
) -> dict[str, Any]:
|
|
642
|
+
import jax
|
|
643
|
+
import jax.numpy as local_jnp
|
|
644
|
+
|
|
645
|
+
nx, ny, nz = shape
|
|
646
|
+
vmec = modules["Vmec"](str(resolved_wout))
|
|
647
|
+
s = np.broadcast_to(np.asarray(coordinates["s_1d"], dtype=np.float64)[:, None, None], shape).reshape(-1)
|
|
648
|
+
theta = np.asarray(coordinates["theta"], dtype=np.float64).reshape(-1)
|
|
649
|
+
phi = np.asarray(coordinates["phi"], dtype=np.float64).reshape(-1)
|
|
650
|
+
x_index = np.broadcast_to(np.arange(nx, dtype=np.float64)[:, None, None], shape).reshape(-1)
|
|
651
|
+
step_count = max(12, min(48, int(2 * ny)))
|
|
652
|
+
forward_theta = _integrate_vmec_theta_to_toroidal_offset(
|
|
653
|
+
vmec,
|
|
654
|
+
s=s,
|
|
655
|
+
theta=theta,
|
|
656
|
+
phi=phi,
|
|
657
|
+
delta_phi=float(dphi),
|
|
658
|
+
step_count=step_count,
|
|
659
|
+
)
|
|
660
|
+
backward_theta = _integrate_vmec_theta_to_toroidal_offset(
|
|
661
|
+
vmec,
|
|
662
|
+
s=s,
|
|
663
|
+
theta=theta,
|
|
664
|
+
phi=phi,
|
|
665
|
+
delta_phi=-float(dphi),
|
|
666
|
+
step_count=step_count,
|
|
667
|
+
)
|
|
668
|
+
forward_z = np.mod(forward_theta, 2.0 * np.pi) / (2.0 * np.pi) * float(nz)
|
|
669
|
+
backward_z = np.mod(backward_theta, 2.0 * np.pi) / (2.0 * np.pi) * float(nz)
|
|
670
|
+
finite = np.isfinite(forward_z) & np.isfinite(backward_z) & (s >= 0.0) & (s <= 1.0)
|
|
671
|
+
forward_boundary = ~finite
|
|
672
|
+
backward_boundary = ~finite
|
|
673
|
+
initial_stp = np.stack([s, theta, phi], axis=-1)
|
|
674
|
+
bmag = np.asarray(jax.vmap(vmec.AbsB)(local_jnp.asarray(initial_stp, dtype=local_jnp.float64)), dtype=np.float64).reshape(shape)
|
|
675
|
+
forward_length = _vmec_map_step_length(
|
|
676
|
+
coordinates=coordinates,
|
|
677
|
+
x_index=x_index,
|
|
678
|
+
y_index=(np.broadcast_to(np.arange(ny, dtype=int)[None, :, None], shape).reshape(-1) + 1) % ny,
|
|
679
|
+
z_index=forward_z,
|
|
680
|
+
)
|
|
681
|
+
backward_length = _vmec_map_step_length(
|
|
682
|
+
coordinates=coordinates,
|
|
683
|
+
x_index=x_index,
|
|
684
|
+
y_index=(np.broadcast_to(np.arange(ny, dtype=int)[None, :, None], shape).reshape(-1) - 1) % ny,
|
|
685
|
+
z_index=backward_z,
|
|
686
|
+
)
|
|
687
|
+
connection_length = 0.5 * (forward_length + backward_length).reshape(shape)
|
|
688
|
+
maps = FciMaps(
|
|
689
|
+
forward_x=jnp.asarray(x_index.reshape(shape), dtype=jnp.float64),
|
|
690
|
+
forward_z=jnp.asarray(forward_z.reshape(shape), dtype=jnp.float64),
|
|
691
|
+
backward_x=jnp.asarray(x_index.reshape(shape), dtype=jnp.float64),
|
|
692
|
+
backward_z=jnp.asarray(backward_z.reshape(shape), dtype=jnp.float64),
|
|
693
|
+
forward_boundary=jnp.asarray(forward_boundary.reshape(shape)),
|
|
694
|
+
backward_boundary=jnp.asarray(backward_boundary.reshape(shape)),
|
|
695
|
+
dphi=float(dphi),
|
|
696
|
+
)
|
|
697
|
+
return {
|
|
698
|
+
"maps": maps,
|
|
699
|
+
"bmag": bmag,
|
|
700
|
+
"connection_length": connection_length,
|
|
701
|
+
"theta_step_count": int(step_count),
|
|
702
|
+
}
|
|
703
|
+
|
|
704
|
+
|
|
705
|
+
def _integrate_vmec_theta_to_toroidal_offset(
|
|
706
|
+
vmec: Any,
|
|
707
|
+
*,
|
|
708
|
+
s: np.ndarray,
|
|
709
|
+
theta: np.ndarray,
|
|
710
|
+
phi: np.ndarray,
|
|
711
|
+
delta_phi: float,
|
|
712
|
+
step_count: int,
|
|
713
|
+
) -> np.ndarray:
|
|
714
|
+
import jax
|
|
715
|
+
import jax.numpy as local_jnp
|
|
716
|
+
|
|
717
|
+
s_jax = local_jnp.asarray(s, dtype=local_jnp.float64)
|
|
718
|
+
theta_jax = local_jnp.asarray(theta, dtype=local_jnp.float64)
|
|
719
|
+
phi_jax = local_jnp.asarray(phi, dtype=local_jnp.float64)
|
|
720
|
+
h = float(delta_phi) / float(step_count)
|
|
721
|
+
|
|
722
|
+
def rhs(theta_value: jax.Array, phi_value: jax.Array) -> jax.Array:
|
|
723
|
+
points = local_jnp.stack([s_jax, theta_value, phi_value], axis=-1)
|
|
724
|
+
b_contra = jax.vmap(vmec.B_contravariant)(points)
|
|
725
|
+
b_phi = local_jnp.where(local_jnp.abs(b_contra[:, 2]) > 1.0e-30, b_contra[:, 2], 1.0e-30)
|
|
726
|
+
return b_contra[:, 1] / b_phi
|
|
727
|
+
|
|
728
|
+
def body(_: int, carry: tuple[jax.Array, jax.Array]) -> tuple[jax.Array, jax.Array]:
|
|
729
|
+
theta_value, phi_value = carry
|
|
730
|
+
k1 = rhs(theta_value, phi_value)
|
|
731
|
+
k2 = rhs(theta_value + 0.5 * h * k1, phi_value + 0.5 * h)
|
|
732
|
+
k3 = rhs(theta_value + 0.5 * h * k2, phi_value + 0.5 * h)
|
|
733
|
+
k4 = rhs(theta_value + h * k3, phi_value + h)
|
|
734
|
+
next_theta = theta_value + (h / 6.0) * (k1 + 2.0 * k2 + 2.0 * k3 + k4)
|
|
735
|
+
return next_theta, phi_value + h
|
|
736
|
+
|
|
737
|
+
integrate = jax.jit(lambda theta0, phi0: jax.lax.fori_loop(0, int(step_count), body, (theta0, phi0))[0])
|
|
738
|
+
return np.asarray(integrate(theta_jax, phi_jax), dtype=np.float64)
|
|
739
|
+
|
|
740
|
+
|
|
741
|
+
def _vmec_map_step_length(
|
|
742
|
+
*,
|
|
743
|
+
coordinates: dict[str, Any],
|
|
744
|
+
x_index: np.ndarray,
|
|
745
|
+
y_index: np.ndarray,
|
|
746
|
+
z_index: np.ndarray,
|
|
747
|
+
) -> np.ndarray:
|
|
748
|
+
current = np.stack(
|
|
749
|
+
[
|
|
750
|
+
np.asarray(coordinates["x"], dtype=np.float64).reshape(-1),
|
|
751
|
+
np.asarray(coordinates["y"], dtype=np.float64).reshape(-1),
|
|
752
|
+
np.asarray(coordinates["z"], dtype=np.float64).reshape(-1),
|
|
753
|
+
],
|
|
754
|
+
axis=-1,
|
|
755
|
+
)
|
|
756
|
+
endpoint = _sample_structured_coordinates(
|
|
757
|
+
np.asarray(coordinates["x"], dtype=np.float64),
|
|
758
|
+
np.asarray(coordinates["y"], dtype=np.float64),
|
|
759
|
+
np.asarray(coordinates["z"], dtype=np.float64),
|
|
760
|
+
x_index=x_index,
|
|
761
|
+
y_index=y_index,
|
|
762
|
+
z_index=z_index,
|
|
763
|
+
)
|
|
764
|
+
length = np.linalg.norm(endpoint - current, axis=1)
|
|
765
|
+
return np.where(np.isfinite(length), length, 0.0)
|
|
766
|
+
|
|
767
|
+
|
|
768
|
+
def _sample_structured_coordinates(
|
|
769
|
+
coordinates_x: np.ndarray,
|
|
770
|
+
coordinates_y: np.ndarray,
|
|
771
|
+
coordinates_z: np.ndarray,
|
|
772
|
+
*,
|
|
773
|
+
x_index: np.ndarray,
|
|
774
|
+
y_index: np.ndarray,
|
|
775
|
+
z_index: np.ndarray,
|
|
776
|
+
) -> np.ndarray:
|
|
777
|
+
nx, ny, nz = coordinates_x.shape
|
|
778
|
+
x0 = np.clip(np.floor(x_index).astype(int), 0, nx - 1)
|
|
779
|
+
x1 = np.clip(x0 + 1, 0, nx - 1)
|
|
780
|
+
y = np.mod(y_index.astype(int), ny)
|
|
781
|
+
z = np.mod(z_index, float(nz))
|
|
782
|
+
z0 = np.floor(z).astype(int) % nz
|
|
783
|
+
z1 = (z0 + 1) % nz
|
|
784
|
+
wx = np.clip(x_index - x0.astype(np.float64), 0.0, 1.0)
|
|
785
|
+
wz = z - np.floor(z)
|
|
786
|
+
result = []
|
|
787
|
+
for values in (coordinates_x, coordinates_y, coordinates_z):
|
|
788
|
+
f00 = values[x0, y, z0]
|
|
789
|
+
f10 = values[x1, y, z0]
|
|
790
|
+
f01 = values[x0, y, z1]
|
|
791
|
+
f11 = values[x1, y, z1]
|
|
792
|
+
result.append((1.0 - wx) * (1.0 - wz) * f00 + wx * (1.0 - wz) * f10 + (1.0 - wx) * wz * f01 + wx * wz * f11)
|
|
793
|
+
return np.stack(result, axis=-1)
|
|
794
|
+
|
|
795
|
+
|
|
796
|
+
def save_essos_field_line_bundle_npz(bundle: EssosFieldLineBundle, path: str | Path) -> Path:
|
|
797
|
+
"""Write a portable ESSOS field-line import bundle."""
|
|
798
|
+
|
|
799
|
+
resolved = Path(path)
|
|
800
|
+
resolved.parent.mkdir(parents=True, exist_ok=True)
|
|
801
|
+
np.savez_compressed(
|
|
802
|
+
resolved,
|
|
803
|
+
trajectories_xyz=bundle.trajectories_xyz.astype(np.float32),
|
|
804
|
+
times=bundle.times.astype(np.float64),
|
|
805
|
+
initial_xyz=bundle.initial_xyz.astype(np.float32),
|
|
806
|
+
poincare_r=bundle.poincare_r.astype(np.float32),
|
|
807
|
+
poincare_z=bundle.poincare_z.astype(np.float32),
|
|
808
|
+
poincare_time=bundle.poincare_time.astype(np.float32),
|
|
809
|
+
poincare_section=bundle.poincare_section.astype(np.float32),
|
|
810
|
+
poincare_line_index=bundle.poincare_line_index.astype(np.int32),
|
|
811
|
+
field_sample_xyz=bundle.field_sample_xyz.astype(np.float32),
|
|
812
|
+
field_sample_b_xyz=bundle.field_sample_b_xyz.astype(np.float32),
|
|
813
|
+
coil_gamma_xyz=bundle.coil_gamma_xyz.astype(np.float32),
|
|
814
|
+
coil_currents=bundle.coil_currents.astype(np.float64),
|
|
815
|
+
)
|
|
816
|
+
return resolved
|
|
817
|
+
|
|
818
|
+
|
|
819
|
+
def load_essos_field_line_bundle_npz(path: str | Path, *, metadata: dict[str, Any] | None = None) -> EssosFieldLineBundle:
|
|
820
|
+
"""Load an ESSOS field-line import bundle produced by `drbx`."""
|
|
821
|
+
|
|
822
|
+
with np.load(Path(path)) as data:
|
|
823
|
+
return EssosFieldLineBundle(
|
|
824
|
+
trajectories_xyz=np.asarray(data["trajectories_xyz"], dtype=np.float64),
|
|
825
|
+
times=np.asarray(data["times"], dtype=np.float64),
|
|
826
|
+
initial_xyz=np.asarray(data["initial_xyz"], dtype=np.float64),
|
|
827
|
+
poincare_r=np.asarray(data["poincare_r"], dtype=np.float64),
|
|
828
|
+
poincare_z=np.asarray(data["poincare_z"], dtype=np.float64),
|
|
829
|
+
poincare_time=np.asarray(data["poincare_time"], dtype=np.float64),
|
|
830
|
+
poincare_section=np.asarray(data["poincare_section"], dtype=np.float64),
|
|
831
|
+
poincare_line_index=np.asarray(data["poincare_line_index"], dtype=np.int32),
|
|
832
|
+
field_sample_xyz=np.asarray(data["field_sample_xyz"], dtype=np.float64),
|
|
833
|
+
field_sample_b_xyz=np.asarray(data["field_sample_b_xyz"], dtype=np.float64),
|
|
834
|
+
coil_gamma_xyz=np.asarray(data["coil_gamma_xyz"], dtype=np.float64),
|
|
835
|
+
coil_currents=np.asarray(data["coil_currents"], dtype=np.float64),
|
|
836
|
+
metadata={} if metadata is None else dict(metadata),
|
|
837
|
+
)
|
|
838
|
+
|
|
839
|
+
|
|
840
|
+
def _import_essos_modules(*, essos_root: str | Path | None = None) -> dict[str, Any]:
|
|
841
|
+
import jax
|
|
842
|
+
|
|
843
|
+
jax.config.update("jax_enable_x64", True)
|
|
844
|
+
if essos_root is not None:
|
|
845
|
+
root = Path(essos_root)
|
|
846
|
+
else:
|
|
847
|
+
root = Path(os.environ.get("DRBX_ESSOS_ROOT", _PRIVATE_DEFAULT_ESSOS_ROOT))
|
|
848
|
+
if root.exists():
|
|
849
|
+
root_text = str(root)
|
|
850
|
+
if root_text not in sys.path:
|
|
851
|
+
sys.path.insert(0, root_text)
|
|
852
|
+
coils_module = importlib.import_module("essos.coils")
|
|
853
|
+
fields_module = importlib.import_module("essos.fields")
|
|
854
|
+
dynamics_module = importlib.import_module("essos.dynamics")
|
|
855
|
+
if os.environ.get("DRBX_ESSOS_PROGRESS") != "1" and hasattr(dynamics_module, "NoProgressMeter"):
|
|
856
|
+
dynamics_module.TqdmProgressMeter = dynamics_module.NoProgressMeter
|
|
857
|
+
return {
|
|
858
|
+
# Newer ESSOS branches replace the module-level loader with a
|
|
859
|
+
# classmethod; accept either.
|
|
860
|
+
"Coils_from_json": getattr(coils_module, "Coils_from_json", None)
|
|
861
|
+
or coils_module.Coils.from_json,
|
|
862
|
+
"BiotSavart": fields_module.BiotSavart,
|
|
863
|
+
"Vmec": fields_module.Vmec,
|
|
864
|
+
"Tracing": dynamics_module.Tracing,
|
|
865
|
+
}
|
|
866
|
+
|
|
867
|
+
|
|
868
|
+
def _trace_essos_initial_conditions(
|
|
869
|
+
*,
|
|
870
|
+
modules: dict[str, Any],
|
|
871
|
+
resolved_coil_json: Path,
|
|
872
|
+
initial_xyz: np.ndarray,
|
|
873
|
+
current_sign: float,
|
|
874
|
+
maxtime: float,
|
|
875
|
+
times_to_trace: int,
|
|
876
|
+
trace_tolerance: float,
|
|
877
|
+
) -> np.ndarray:
|
|
878
|
+
import jax
|
|
879
|
+
import jax.numpy as local_jnp
|
|
880
|
+
|
|
881
|
+
coils = modules["Coils_from_json"](str(resolved_coil_json))
|
|
882
|
+
if current_sign < 0.0:
|
|
883
|
+
coils.dofs_currents = -coils.dofs_currents
|
|
884
|
+
field = modules["BiotSavart"](coils)
|
|
885
|
+
tracing = jax.block_until_ready(
|
|
886
|
+
modules["Tracing"](
|
|
887
|
+
field=field,
|
|
888
|
+
model="FieldLineAdaptative",
|
|
889
|
+
initial_conditions=local_jnp.asarray(initial_xyz, dtype=local_jnp.float64),
|
|
890
|
+
maxtime=float(maxtime),
|
|
891
|
+
times_to_trace=int(times_to_trace),
|
|
892
|
+
atol=float(trace_tolerance),
|
|
893
|
+
rtol=float(trace_tolerance),
|
|
894
|
+
)
|
|
895
|
+
)
|
|
896
|
+
return np.asarray(tracing.trajectories[:, :, :3], dtype=np.float64)
|
|
897
|
+
|
|
898
|
+
|
|
899
|
+
def _trace_essos_vmec_initial_conditions(
|
|
900
|
+
*,
|
|
901
|
+
modules: dict[str, Any],
|
|
902
|
+
resolved_wout: Path,
|
|
903
|
+
initial_stp: np.ndarray,
|
|
904
|
+
maxtime: float,
|
|
905
|
+
times_to_trace: int,
|
|
906
|
+
trace_tolerance: float,
|
|
907
|
+
) -> np.ndarray:
|
|
908
|
+
import jax
|
|
909
|
+
import jax.numpy as local_jnp
|
|
910
|
+
|
|
911
|
+
vmec = modules["Vmec"](str(resolved_wout))
|
|
912
|
+
tracing = jax.block_until_ready(
|
|
913
|
+
modules["Tracing"](
|
|
914
|
+
field=vmec,
|
|
915
|
+
model="FieldLineAdaptative",
|
|
916
|
+
initial_conditions=local_jnp.asarray(initial_stp, dtype=local_jnp.float64),
|
|
917
|
+
maxtime=float(maxtime),
|
|
918
|
+
times_to_trace=int(times_to_trace),
|
|
919
|
+
atol=float(trace_tolerance),
|
|
920
|
+
rtol=float(trace_tolerance),
|
|
921
|
+
)
|
|
922
|
+
)
|
|
923
|
+
return np.asarray(tracing.trajectories[:, :, :3], dtype=np.float64)
|
|
924
|
+
|
|
925
|
+
|
|
926
|
+
def _median_toroidal_advance(trajectories_xyz: np.ndarray) -> float:
|
|
927
|
+
phi = np.unwrap(np.arctan2(trajectories_xyz[:, :, 1], trajectories_xyz[:, :, 0]), axis=1)
|
|
928
|
+
return float(np.nanmedian(phi[:, -1] - phi[:, 0]))
|
|
929
|
+
|
|
930
|
+
|
|
931
|
+
def _interpolate_trajectories_at_toroidal_plane(
|
|
932
|
+
trajectories_xyz: np.ndarray,
|
|
933
|
+
*,
|
|
934
|
+
target_phi: np.ndarray,
|
|
935
|
+
) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
|
|
936
|
+
endpoints = np.full((trajectories_xyz.shape[0], 3), np.nan, dtype=np.float64)
|
|
937
|
+
lengths = np.full(trajectories_xyz.shape[0], np.nan, dtype=np.float64)
|
|
938
|
+
crossed = np.zeros(trajectories_xyz.shape[0], dtype=bool)
|
|
939
|
+
for index, trajectory in enumerate(trajectories_xyz):
|
|
940
|
+
phi = np.unwrap(np.arctan2(trajectory[:, 1], trajectory[:, 0]))
|
|
941
|
+
arc_length = np.concatenate(
|
|
942
|
+
[
|
|
943
|
+
np.zeros(1, dtype=np.float64),
|
|
944
|
+
np.cumsum(np.linalg.norm(np.diff(trajectory, axis=0), axis=1)),
|
|
945
|
+
]
|
|
946
|
+
)
|
|
947
|
+
if phi[-1] < phi[0]:
|
|
948
|
+
phi = phi[::-1]
|
|
949
|
+
trajectory = trajectory[::-1]
|
|
950
|
+
arc_length = arc_length[-1] - arc_length[::-1]
|
|
951
|
+
target = float(target_phi[index])
|
|
952
|
+
if target < phi[0] or target > phi[-1] or not np.all(np.isfinite(phi)):
|
|
953
|
+
continue
|
|
954
|
+
endpoints[index, 0] = np.interp(target, phi, trajectory[:, 0])
|
|
955
|
+
endpoints[index, 1] = np.interp(target, phi, trajectory[:, 1])
|
|
956
|
+
endpoints[index, 2] = np.interp(target, phi, trajectory[:, 2])
|
|
957
|
+
lengths[index] = np.interp(target, phi, arc_length)
|
|
958
|
+
crossed[index] = True
|
|
959
|
+
return endpoints, lengths, crossed
|
|
960
|
+
|
|
961
|
+
|
|
962
|
+
def _cartesian_to_annular_indices(
|
|
963
|
+
points_xyz: np.ndarray,
|
|
964
|
+
*,
|
|
965
|
+
crossed: np.ndarray,
|
|
966
|
+
axis_major_radius: float,
|
|
967
|
+
axis_vertical: float,
|
|
968
|
+
rho_min: float,
|
|
969
|
+
rho_max: float,
|
|
970
|
+
nx: int,
|
|
971
|
+
nz: int,
|
|
972
|
+
) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
|
|
973
|
+
major = np.sqrt(points_xyz[:, 0] ** 2 + points_xyz[:, 1] ** 2)
|
|
974
|
+
vertical = points_xyz[:, 2]
|
|
975
|
+
radial_offset = major - float(axis_major_radius)
|
|
976
|
+
vertical_offset = vertical - float(axis_vertical)
|
|
977
|
+
rho = np.sqrt(radial_offset * radial_offset + vertical_offset * vertical_offset)
|
|
978
|
+
theta = np.mod(np.arctan2(vertical_offset, radial_offset), 2.0 * np.pi)
|
|
979
|
+
x_index = (rho - float(rho_min)) / max(float(rho_max - rho_min), 1.0e-30) * float(nx - 1)
|
|
980
|
+
z_index = theta / (2.0 * np.pi) * float(nz)
|
|
981
|
+
boundary = (~crossed) | (~np.isfinite(x_index)) | (x_index < 0.0) | (x_index > float(nx - 1))
|
|
982
|
+
x_index = np.where(boundary, 0.0, x_index)
|
|
983
|
+
z_index = np.where(boundary | (~np.isfinite(z_index)), 0.0, z_index)
|
|
984
|
+
return x_index, z_index, boundary
|
|
985
|
+
|
|
986
|
+
|
|
987
|
+
def build_essos_vmec_scaled_qa_coordinates(
|
|
988
|
+
wout_path: Path,
|
|
989
|
+
*,
|
|
990
|
+
nx: int,
|
|
991
|
+
ny: int,
|
|
992
|
+
nz: int,
|
|
993
|
+
rho_min: float,
|
|
994
|
+
rho_max: float,
|
|
995
|
+
axis_major_radius: float,
|
|
996
|
+
axis_vertical: float,
|
|
997
|
+
) -> dict[str, Any]:
|
|
998
|
+
"""Evaluate scaled Landreman-Paul QA VMEC Fourier surfaces on a logical grid."""
|
|
999
|
+
|
|
1000
|
+
from netCDF4 import Dataset
|
|
1001
|
+
|
|
1002
|
+
with Dataset(wout_path) as dataset:
|
|
1003
|
+
xm = np.asarray(dataset.variables["xm"][:], dtype=np.float64)
|
|
1004
|
+
xn = np.asarray(dataset.variables["xn"][:], dtype=np.float64)
|
|
1005
|
+
rmnc = np.asarray(dataset.variables["rmnc"][:], dtype=np.float64)
|
|
1006
|
+
zmns = np.asarray(dataset.variables["zmns"][:], dtype=np.float64)
|
|
1007
|
+
nfp = int(np.asarray(dataset.variables["nfp"][:]).reshape(()))
|
|
1008
|
+
|
|
1009
|
+
if rmnc.ndim != 2 or zmns.shape != rmnc.shape:
|
|
1010
|
+
raise ValueError("VMEC wout Fourier arrays must have shape (ns, mnmax)")
|
|
1011
|
+
|
|
1012
|
+
rho_1d = np.linspace(float(rho_min), float(rho_max), int(nx))
|
|
1013
|
+
phi_1d = np.linspace(0.0, 2.0 * np.pi, int(ny), endpoint=False)
|
|
1014
|
+
theta_1d = np.linspace(0.0, 2.0 * np.pi, int(nz), endpoint=False)
|
|
1015
|
+
rho, phi, theta = np.meshgrid(rho_1d, phi_1d, theta_1d, indexing="ij")
|
|
1016
|
+
|
|
1017
|
+
ns = int(rmnc.shape[0])
|
|
1018
|
+
s_full = np.linspace(0.0, 1.0, ns)
|
|
1019
|
+
normalized_radius = (rho_1d - float(rho_min)) / max(float(rho_max - rho_min), 1.0e-30)
|
|
1020
|
+
normalized_radius = (float(rho_min) / max(float(rho_max), 1.0e-30)) + (
|
|
1021
|
+
1.0 - float(rho_min) / max(float(rho_max), 1.0e-30)
|
|
1022
|
+
) * normalized_radius
|
|
1023
|
+
s_requested = np.clip(normalized_radius * normalized_radius, 0.0, 1.0)
|
|
1024
|
+
|
|
1025
|
+
rmnc_shells = np.empty((int(nx), rmnc.shape[1]), dtype=np.float64)
|
|
1026
|
+
zmns_shells = np.empty_like(rmnc_shells)
|
|
1027
|
+
for mode_index in range(rmnc.shape[1]):
|
|
1028
|
+
rmnc_shells[:, mode_index] = np.interp(s_requested, s_full, rmnc[:, mode_index])
|
|
1029
|
+
zmns_shells[:, mode_index] = np.interp(s_requested, s_full, zmns[:, mode_index])
|
|
1030
|
+
|
|
1031
|
+
raw_axis_major = float(rmnc[0, 0])
|
|
1032
|
+
raw_axis_vertical = float(zmns[0, 0])
|
|
1033
|
+
scale = float(axis_major_radius) / max(abs(raw_axis_major), 1.0e-30)
|
|
1034
|
+
phase = xm[None, None, None, :] * theta[..., None] - xn[None, None, None, :] * phi[..., None]
|
|
1035
|
+
raw_major = np.sum(rmnc_shells[:, None, None, :] * np.cos(phase), axis=-1)
|
|
1036
|
+
raw_vertical = np.sum(zmns_shells[:, None, None, :] * np.sin(phase), axis=-1)
|
|
1037
|
+
major = float(axis_major_radius) + scale * (raw_major - raw_axis_major)
|
|
1038
|
+
vertical = float(axis_vertical) + scale * (raw_vertical - raw_axis_vertical)
|
|
1039
|
+
x = major * np.cos(phi)
|
|
1040
|
+
y = major * np.sin(phi)
|
|
1041
|
+
z = vertical
|
|
1042
|
+
|
|
1043
|
+
edge_major = major[-1]
|
|
1044
|
+
edge_vertical = vertical[-1]
|
|
1045
|
+
mean_edge_major_by_phi = np.mean(edge_major, axis=1)
|
|
1046
|
+
nonaxisymmetric_major_rms = float(np.std(mean_edge_major_by_phi) / max(abs(float(np.mean(mean_edge_major_by_phi))), 1.0e-30))
|
|
1047
|
+
edge_extent = np.sqrt((edge_major - np.mean(edge_major, axis=1, keepdims=True)) ** 2 + edge_vertical**2)
|
|
1048
|
+
poloidal_extent_rms = float(np.sqrt(np.mean(edge_extent * edge_extent)))
|
|
1049
|
+
|
|
1050
|
+
return {
|
|
1051
|
+
"rho_1d": rho_1d,
|
|
1052
|
+
"s_1d": s_requested,
|
|
1053
|
+
"phi_1d": phi_1d,
|
|
1054
|
+
"theta_1d": theta_1d,
|
|
1055
|
+
"rho": rho,
|
|
1056
|
+
"phi": phi,
|
|
1057
|
+
"theta": theta,
|
|
1058
|
+
"major": major,
|
|
1059
|
+
"vertical": vertical,
|
|
1060
|
+
"x": x,
|
|
1061
|
+
"y": y,
|
|
1062
|
+
"z": z,
|
|
1063
|
+
"metadata": {
|
|
1064
|
+
"vmec_nfp": int(nfp),
|
|
1065
|
+
"vmec_ns": ns,
|
|
1066
|
+
"vmec_mnmax": int(rmnc.shape[1]),
|
|
1067
|
+
"vmec_raw_axis_major_radius": raw_axis_major,
|
|
1068
|
+
"vmec_raw_axis_vertical": raw_axis_vertical,
|
|
1069
|
+
"vmec_to_essos_length_scale": scale,
|
|
1070
|
+
"vmec_s_min": float(np.min(s_requested)),
|
|
1071
|
+
"vmec_s_max": float(np.max(s_requested)),
|
|
1072
|
+
"surface_nonaxisymmetric_major_rms": nonaxisymmetric_major_rms,
|
|
1073
|
+
"surface_poloidal_extent_rms": poloidal_extent_rms,
|
|
1074
|
+
},
|
|
1075
|
+
}
|
|
1076
|
+
|
|
1077
|
+
|
|
1078
|
+
def _cartesian_to_structured_surface_indices(
|
|
1079
|
+
points_xyz: np.ndarray,
|
|
1080
|
+
*,
|
|
1081
|
+
crossed: np.ndarray,
|
|
1082
|
+
target_y_index: np.ndarray,
|
|
1083
|
+
coordinates_x: np.ndarray,
|
|
1084
|
+
coordinates_y: np.ndarray,
|
|
1085
|
+
coordinates_z: np.ndarray,
|
|
1086
|
+
) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
|
|
1087
|
+
nx, ny, nz = coordinates_x.shape
|
|
1088
|
+
x_index = np.zeros(points_xyz.shape[0], dtype=np.float64)
|
|
1089
|
+
z_index = np.zeros(points_xyz.shape[0], dtype=np.float64)
|
|
1090
|
+
boundary = np.ones(points_xyz.shape[0], dtype=bool)
|
|
1091
|
+
|
|
1092
|
+
plane_spacing = _structured_plane_spacing(coordinates_x, coordinates_y, coordinates_z)
|
|
1093
|
+
for index, point in enumerate(points_xyz):
|
|
1094
|
+
if not bool(crossed[index]) or not np.all(np.isfinite(point)):
|
|
1095
|
+
continue
|
|
1096
|
+
y_index = int(target_y_index[index]) % ny
|
|
1097
|
+
plane = np.column_stack(
|
|
1098
|
+
[
|
|
1099
|
+
coordinates_x[:, y_index, :].reshape(-1),
|
|
1100
|
+
coordinates_y[:, y_index, :].reshape(-1),
|
|
1101
|
+
coordinates_z[:, y_index, :].reshape(-1),
|
|
1102
|
+
]
|
|
1103
|
+
)
|
|
1104
|
+
distance_squared = np.sum((plane - point[None, :]) ** 2, axis=1)
|
|
1105
|
+
nearest = int(np.argmin(distance_squared))
|
|
1106
|
+
nearest_distance = float(np.sqrt(distance_squared[nearest]))
|
|
1107
|
+
radial_index = nearest // nz
|
|
1108
|
+
poloidal_index = nearest % nz
|
|
1109
|
+
x_index[index] = float(radial_index)
|
|
1110
|
+
z_index[index] = float(poloidal_index)
|
|
1111
|
+
max_distance = 2.75 * float(plane_spacing[y_index])
|
|
1112
|
+
boundary[index] = (
|
|
1113
|
+
nearest_distance > max_distance
|
|
1114
|
+
or radial_index <= 0
|
|
1115
|
+
or radial_index >= nx - 1
|
|
1116
|
+
)
|
|
1117
|
+
if boundary[index]:
|
|
1118
|
+
x_index[index] = 0.0
|
|
1119
|
+
z_index[index] = 0.0
|
|
1120
|
+
return x_index, z_index, boundary
|
|
1121
|
+
|
|
1122
|
+
|
|
1123
|
+
def _structured_plane_spacing(coordinates_x: np.ndarray, coordinates_y: np.ndarray, coordinates_z: np.ndarray) -> np.ndarray:
|
|
1124
|
+
coords = np.stack([coordinates_x, coordinates_y, coordinates_z], axis=-1)
|
|
1125
|
+
radial_spacing = np.linalg.norm(np.diff(coords, axis=0), axis=-1)
|
|
1126
|
+
poloidal_spacing = np.linalg.norm(np.diff(np.concatenate([coords, coords[:, :, :1, :]], axis=2), axis=2), axis=-1)
|
|
1127
|
+
spacing = []
|
|
1128
|
+
for y_index in range(coords.shape[1]):
|
|
1129
|
+
values = np.concatenate([radial_spacing[:, y_index, :].reshape(-1), poloidal_spacing[:, y_index, :].reshape(-1)])
|
|
1130
|
+
finite = values[np.isfinite(values) & (values > 0.0)]
|
|
1131
|
+
spacing.append(float(np.median(finite)) if finite.size else 1.0)
|
|
1132
|
+
return np.asarray(spacing, dtype=np.float64)
|
|
1133
|
+
|
|
1134
|
+
|
|
1135
|
+
def _annular_exit_length_from_trajectories(
|
|
1136
|
+
trajectories_xyz: np.ndarray,
|
|
1137
|
+
*,
|
|
1138
|
+
axis_major_radius: float,
|
|
1139
|
+
axis_vertical: float,
|
|
1140
|
+
rho_min: float,
|
|
1141
|
+
rho_max: float,
|
|
1142
|
+
) -> np.ndarray:
|
|
1143
|
+
major = np.sqrt(trajectories_xyz[:, :, 0] ** 2 + trajectories_xyz[:, :, 1] ** 2)
|
|
1144
|
+
vertical = trajectories_xyz[:, :, 2]
|
|
1145
|
+
rho = np.sqrt((major - float(axis_major_radius)) ** 2 + (vertical - float(axis_vertical)) ** 2)
|
|
1146
|
+
tolerance = 1.0e-10 * max(float(rho_max - rho_min), 1.0)
|
|
1147
|
+
outside = (rho < float(rho_min) - tolerance) | (rho > float(rho_max) + tolerance) | (~np.isfinite(rho))
|
|
1148
|
+
arc_length = np.concatenate(
|
|
1149
|
+
[
|
|
1150
|
+
np.zeros((trajectories_xyz.shape[0], 1), dtype=np.float64),
|
|
1151
|
+
np.cumsum(np.linalg.norm(np.diff(trajectories_xyz, axis=1), axis=2), axis=1),
|
|
1152
|
+
],
|
|
1153
|
+
axis=1,
|
|
1154
|
+
)
|
|
1155
|
+
first_exit = np.argmax(outside, axis=1)
|
|
1156
|
+
has_exit = np.any(outside, axis=1)
|
|
1157
|
+
return np.where(has_exit, arc_length[np.arange(trajectories_xyz.shape[0]), first_exit], arc_length[:, -1])
|
|
1158
|
+
|
|
1159
|
+
|
|
1160
|
+
def _structured_exit_length_from_trajectories(
|
|
1161
|
+
trajectories_xyz: np.ndarray,
|
|
1162
|
+
*,
|
|
1163
|
+
coordinates_x: np.ndarray,
|
|
1164
|
+
coordinates_y: np.ndarray,
|
|
1165
|
+
coordinates_z: np.ndarray,
|
|
1166
|
+
) -> np.ndarray:
|
|
1167
|
+
nx, ny, nz = coordinates_x.shape
|
|
1168
|
+
coords = np.stack([coordinates_x, coordinates_y, coordinates_z], axis=-1)
|
|
1169
|
+
radial_min = np.nanmin(np.sqrt(coordinates_x[0] * coordinates_x[0] + coordinates_y[0] * coordinates_y[0]))
|
|
1170
|
+
radial_max = np.nanmax(np.sqrt(coordinates_x[-1] * coordinates_x[-1] + coordinates_y[-1] * coordinates_y[-1]))
|
|
1171
|
+
vertical_min = np.nanmin(coordinates_z[-1])
|
|
1172
|
+
vertical_max = np.nanmax(coordinates_z[-1])
|
|
1173
|
+
padding = max(float(np.nanmedian(_structured_plane_spacing(coordinates_x, coordinates_y, coordinates_z))), 1.0e-6)
|
|
1174
|
+
arc_length = np.concatenate(
|
|
1175
|
+
[
|
|
1176
|
+
np.zeros((trajectories_xyz.shape[0], 1), dtype=np.float64),
|
|
1177
|
+
np.cumsum(np.linalg.norm(np.diff(trajectories_xyz, axis=1), axis=2), axis=1),
|
|
1178
|
+
],
|
|
1179
|
+
axis=1,
|
|
1180
|
+
)
|
|
1181
|
+
major = np.sqrt(trajectories_xyz[:, :, 0] ** 2 + trajectories_xyz[:, :, 1] ** 2)
|
|
1182
|
+
vertical = trajectories_xyz[:, :, 2]
|
|
1183
|
+
broad_exit = (
|
|
1184
|
+
(major < radial_min - padding)
|
|
1185
|
+
| (major > radial_max + padding)
|
|
1186
|
+
| (vertical < vertical_min - padding)
|
|
1187
|
+
| (vertical > vertical_max + padding)
|
|
1188
|
+
| (~np.isfinite(major))
|
|
1189
|
+
| (~np.isfinite(vertical))
|
|
1190
|
+
)
|
|
1191
|
+
first_exit = np.argmax(broad_exit, axis=1)
|
|
1192
|
+
has_exit = np.any(broad_exit, axis=1)
|
|
1193
|
+
if nx * ny * nz <= 4096:
|
|
1194
|
+
flat_coords = coords.reshape((-1, 3))
|
|
1195
|
+
max_distance = 3.0 * padding
|
|
1196
|
+
for line_index, trajectory in enumerate(trajectories_xyz):
|
|
1197
|
+
if has_exit[line_index]:
|
|
1198
|
+
continue
|
|
1199
|
+
stride = max(int(trajectory.shape[0] // 48), 1)
|
|
1200
|
+
sampled = trajectory[::stride]
|
|
1201
|
+
distances = np.sqrt(np.min(np.sum((sampled[:, None, :] - flat_coords[None, :, :]) ** 2, axis=-1), axis=1))
|
|
1202
|
+
exit_candidates = np.flatnonzero(distances > max_distance)
|
|
1203
|
+
if exit_candidates.size:
|
|
1204
|
+
first_exit[line_index] = min(int(exit_candidates[0]) * stride, trajectory.shape[0] - 1)
|
|
1205
|
+
has_exit[line_index] = True
|
|
1206
|
+
return np.where(has_exit, arc_length[np.arange(trajectories_xyz.shape[0]), first_exit], np.nan)
|
|
1207
|
+
|
|
1208
|
+
|
|
1209
|
+
def _combine_bidirectional_exit_lengths(
|
|
1210
|
+
forward_exit_length: np.ndarray,
|
|
1211
|
+
backward_exit_length: np.ndarray,
|
|
1212
|
+
) -> np.ndarray:
|
|
1213
|
+
"""Return the shortest finite target-exit length from either traced direction."""
|
|
1214
|
+
|
|
1215
|
+
forward = np.asarray(forward_exit_length, dtype=np.float64)
|
|
1216
|
+
backward = np.asarray(backward_exit_length, dtype=np.float64)
|
|
1217
|
+
if forward.shape != backward.shape:
|
|
1218
|
+
raise ValueError(
|
|
1219
|
+
"Forward and backward target-exit length arrays must have the same shape."
|
|
1220
|
+
)
|
|
1221
|
+
combined = np.full(forward.shape, np.nan, dtype=np.float64)
|
|
1222
|
+
forward_finite = np.isfinite(forward)
|
|
1223
|
+
backward_finite = np.isfinite(backward)
|
|
1224
|
+
both = forward_finite & backward_finite
|
|
1225
|
+
combined[both] = np.minimum(forward[both], backward[both])
|
|
1226
|
+
only_forward = forward_finite & ~backward_finite
|
|
1227
|
+
only_backward = backward_finite & ~forward_finite
|
|
1228
|
+
combined[only_forward] = forward[only_forward]
|
|
1229
|
+
combined[only_backward] = backward[only_backward]
|
|
1230
|
+
return combined
|
|
1231
|
+
|
|
1232
|
+
|
|
1233
|
+
def _mask_exit_length_to_boundary(exit_length: np.ndarray, boundary: np.ndarray) -> np.ndarray:
|
|
1234
|
+
"""Keep target-exit lengths only where an FCI direction reaches a boundary."""
|
|
1235
|
+
|
|
1236
|
+
length = np.asarray(exit_length, dtype=np.float64)
|
|
1237
|
+
mask = np.asarray(boundary, dtype=bool)
|
|
1238
|
+
if length.shape != mask.shape:
|
|
1239
|
+
raise ValueError(
|
|
1240
|
+
"Target-exit length and boundary mask shapes must match: "
|
|
1241
|
+
f"length={length.shape}, boundary={mask.shape}."
|
|
1242
|
+
)
|
|
1243
|
+
return np.where(mask & np.isfinite(length), length, np.nan)
|
|
1244
|
+
|
|
1245
|
+
|
|
1246
|
+
def _metric_from_coordinates(
|
|
1247
|
+
x_cart: np.ndarray,
|
|
1248
|
+
y_cart: np.ndarray,
|
|
1249
|
+
z_cart: np.ndarray,
|
|
1250
|
+
*,
|
|
1251
|
+
s_1d: np.ndarray,
|
|
1252
|
+
phi_1d: np.ndarray,
|
|
1253
|
+
theta_1d: np.ndarray,
|
|
1254
|
+
Bxy: np.ndarray,
|
|
1255
|
+
) -> MetricTensor3D:
|
|
1256
|
+
ds = float(s_1d[1] - s_1d[0]) if s_1d.size > 1 else 1.0
|
|
1257
|
+
dphi = float(phi_1d[1] - phi_1d[0]) if phi_1d.size > 1 else 2.0 * np.pi
|
|
1258
|
+
dtheta = float(theta_1d[1] - theta_1d[0]) if theta_1d.size > 1 else 2.0 * np.pi
|
|
1259
|
+
edge_order = 2 if min(x_cart.shape) > 2 else 1
|
|
1260
|
+
|
|
1261
|
+
derivs = []
|
|
1262
|
+
for coords in (x_cart, y_cart, z_cart):
|
|
1263
|
+
derivs.append(np.gradient(coords, ds, dphi, dtheta, edge_order=edge_order))
|
|
1264
|
+
|
|
1265
|
+
r_s = np.stack([derivs[0][0], derivs[1][0], derivs[2][0]], axis=-1)
|
|
1266
|
+
r_phi = np.stack([derivs[0][1], derivs[1][1], derivs[2][1]], axis=-1)
|
|
1267
|
+
r_theta = np.stack([derivs[0][2], derivs[1][2], derivs[2][2]], axis=-1)
|
|
1268
|
+
cov = np.empty(x_cart.shape + (3, 3), dtype=np.float64)
|
|
1269
|
+
basis = (r_s, r_phi, r_theta)
|
|
1270
|
+
for i, left in enumerate(basis):
|
|
1271
|
+
for j, right in enumerate(basis):
|
|
1272
|
+
cov[..., i, j] = np.sum(left * right, axis=-1)
|
|
1273
|
+
determinant = np.linalg.det(cov)
|
|
1274
|
+
regularization = np.maximum(1.0e-12, 1.0e-11 * np.nanmax(np.abs(determinant)))
|
|
1275
|
+
bad = determinant <= regularization
|
|
1276
|
+
if np.any(bad):
|
|
1277
|
+
cov[bad] = cov[bad] + np.eye(3) * regularization
|
|
1278
|
+
contrav = np.linalg.inv(cov)
|
|
1279
|
+
jacobian = np.sqrt(np.maximum(np.linalg.det(cov), regularization))
|
|
1280
|
+
return MetricTensor3D(
|
|
1281
|
+
dx=jnp.asarray(np.full_like(x_cart, ds), dtype=jnp.float64),
|
|
1282
|
+
dy=jnp.asarray(np.full_like(x_cart, dphi), dtype=jnp.float64),
|
|
1283
|
+
dz=jnp.asarray(np.full_like(x_cart, dtheta), dtype=jnp.float64),
|
|
1284
|
+
J=jnp.asarray(jacobian, dtype=jnp.float64),
|
|
1285
|
+
Bxy=jnp.asarray(Bxy, dtype=jnp.float64),
|
|
1286
|
+
g11=jnp.asarray(contrav[..., 0, 0], dtype=jnp.float64),
|
|
1287
|
+
g22=jnp.asarray(contrav[..., 1, 1], dtype=jnp.float64),
|
|
1288
|
+
g33=jnp.asarray(contrav[..., 2, 2], dtype=jnp.float64),
|
|
1289
|
+
g12=jnp.asarray(contrav[..., 0, 1], dtype=jnp.float64),
|
|
1290
|
+
g13=jnp.asarray(contrav[..., 0, 2], dtype=jnp.float64),
|
|
1291
|
+
g23=jnp.asarray(contrav[..., 1, 2], dtype=jnp.float64),
|
|
1292
|
+
g_11=jnp.asarray(cov[..., 0, 0], dtype=jnp.float64),
|
|
1293
|
+
g_22=jnp.asarray(cov[..., 1, 1], dtype=jnp.float64),
|
|
1294
|
+
g_33=jnp.asarray(cov[..., 2, 2], dtype=jnp.float64),
|
|
1295
|
+
g_12=jnp.asarray(cov[..., 0, 1], dtype=jnp.float64),
|
|
1296
|
+
g_13=jnp.asarray(cov[..., 0, 2], dtype=jnp.float64),
|
|
1297
|
+
g_23=jnp.asarray(cov[..., 1, 2], dtype=jnp.float64),
|
|
1298
|
+
)
|
|
1299
|
+
|
|
1300
|
+
|
|
1301
|
+
def _annular_metric_tensor(
|
|
1302
|
+
*,
|
|
1303
|
+
rho: np.ndarray,
|
|
1304
|
+
major: np.ndarray,
|
|
1305
|
+
bmag: np.ndarray,
|
|
1306
|
+
drho: float,
|
|
1307
|
+
dphi: float,
|
|
1308
|
+
dtheta: float,
|
|
1309
|
+
) -> MetricTensor3D:
|
|
1310
|
+
zeros = np.zeros_like(rho)
|
|
1311
|
+
safe_rho = np.maximum(rho, 1.0e-8)
|
|
1312
|
+
safe_major = np.maximum(major, 1.0e-8)
|
|
1313
|
+
jacobian = safe_major * safe_rho
|
|
1314
|
+
return MetricTensor3D(
|
|
1315
|
+
dx=jnp.asarray(np.full_like(rho, float(drho)), dtype=jnp.float64),
|
|
1316
|
+
dy=jnp.asarray(np.full_like(rho, float(dphi)), dtype=jnp.float64),
|
|
1317
|
+
dz=jnp.asarray(np.full_like(rho, float(dtheta)), dtype=jnp.float64),
|
|
1318
|
+
J=jnp.asarray(jacobian, dtype=jnp.float64),
|
|
1319
|
+
Bxy=jnp.asarray(bmag, dtype=jnp.float64),
|
|
1320
|
+
g11=jnp.asarray(np.ones_like(rho), dtype=jnp.float64),
|
|
1321
|
+
g22=jnp.asarray(1.0 / (safe_major * safe_major), dtype=jnp.float64),
|
|
1322
|
+
g33=jnp.asarray(1.0 / (safe_rho * safe_rho), dtype=jnp.float64),
|
|
1323
|
+
g12=jnp.asarray(zeros, dtype=jnp.float64),
|
|
1324
|
+
g13=jnp.asarray(zeros, dtype=jnp.float64),
|
|
1325
|
+
g23=jnp.asarray(zeros, dtype=jnp.float64),
|
|
1326
|
+
g_11=jnp.asarray(np.ones_like(rho), dtype=jnp.float64),
|
|
1327
|
+
g_22=jnp.asarray(safe_major * safe_major, dtype=jnp.float64),
|
|
1328
|
+
g_33=jnp.asarray(safe_rho * safe_rho, dtype=jnp.float64),
|
|
1329
|
+
g_12=jnp.asarray(zeros, dtype=jnp.float64),
|
|
1330
|
+
g_13=jnp.asarray(zeros, dtype=jnp.float64),
|
|
1331
|
+
g_23=jnp.asarray(zeros, dtype=jnp.float64),
|
|
1332
|
+
)
|
|
1333
|
+
|
|
1334
|
+
|
|
1335
|
+
def _flatten_essos_poincare_data(
|
|
1336
|
+
plotting_data: list[tuple[Any, Any, Any]],
|
|
1337
|
+
*,
|
|
1338
|
+
n_field_lines: int,
|
|
1339
|
+
shifts: tuple[float, ...],
|
|
1340
|
+
) -> dict[str, np.ndarray]:
|
|
1341
|
+
r_values: list[np.ndarray] = []
|
|
1342
|
+
z_values: list[np.ndarray] = []
|
|
1343
|
+
time_values: list[np.ndarray] = []
|
|
1344
|
+
section_values: list[np.ndarray] = []
|
|
1345
|
+
line_values: list[np.ndarray] = []
|
|
1346
|
+
for index, (r_slice, z_slice, time_slice) in enumerate(plotting_data):
|
|
1347
|
+
r_array = np.asarray(r_slice, dtype=np.float64).reshape(-1)
|
|
1348
|
+
z_array = np.asarray(z_slice, dtype=np.float64).reshape(-1)
|
|
1349
|
+
time_array = np.asarray(time_slice, dtype=np.float64).reshape(-1)
|
|
1350
|
+
finite = np.isfinite(r_array) & np.isfinite(z_array) & np.isfinite(time_array)
|
|
1351
|
+
r_array = r_array[finite]
|
|
1352
|
+
z_array = z_array[finite]
|
|
1353
|
+
time_array = time_array[finite]
|
|
1354
|
+
if r_array.size == 0:
|
|
1355
|
+
continue
|
|
1356
|
+
shift_index = min(index // max(int(n_field_lines), 1), max(len(shifts) - 1, 0))
|
|
1357
|
+
line_index = index % max(int(n_field_lines), 1)
|
|
1358
|
+
r_values.append(r_array)
|
|
1359
|
+
z_values.append(z_array)
|
|
1360
|
+
time_values.append(time_array)
|
|
1361
|
+
section_values.append(np.full(r_array.shape, shifts[shift_index], dtype=np.float64))
|
|
1362
|
+
line_values.append(np.full(r_array.shape, line_index, dtype=np.int32))
|
|
1363
|
+
if not r_values:
|
|
1364
|
+
return {
|
|
1365
|
+
"r": np.empty(0, dtype=np.float64),
|
|
1366
|
+
"z": np.empty(0, dtype=np.float64),
|
|
1367
|
+
"time": np.empty(0, dtype=np.float64),
|
|
1368
|
+
"section": np.empty(0, dtype=np.float64),
|
|
1369
|
+
"line_index": np.empty(0, dtype=np.int32),
|
|
1370
|
+
}
|
|
1371
|
+
return {
|
|
1372
|
+
"r": np.concatenate(r_values),
|
|
1373
|
+
"z": np.concatenate(z_values),
|
|
1374
|
+
"time": np.concatenate(time_values),
|
|
1375
|
+
"section": np.concatenate(section_values),
|
|
1376
|
+
"line_index": np.concatenate(line_values),
|
|
1377
|
+
}
|
|
1378
|
+
|
|
1379
|
+
|
|
1380
|
+
def _sample_essos_field(field: Any, points_xyz: np.ndarray) -> np.ndarray:
|
|
1381
|
+
import jax
|
|
1382
|
+
import jax.numpy as jnp
|
|
1383
|
+
|
|
1384
|
+
points = jnp.asarray(points_xyz, dtype=jnp.float64)
|
|
1385
|
+
return np.asarray(jax.vmap(field.B)(points), dtype=np.float64)
|