pyextal.jaxGeo.settings

Every option of a refinement, in one place.

RefineSettings is what jaxGeo.refine.refine runs and what the command line (jaxGeo.cli) fills in; the command line takes its defaults from an instance, so a script sets dataset defaults by building one. resolved checks the options against each other and returns a copy with every field in canonical form, so the Python API and the command line accept the same spellings.

Attributes

GEOMETRY
PROBE_RANGE
SF_MASKS

Exceptions

SetupError

A dataset, file or option problem found before anything is refined.

Classes

RefineSettings

Options for jaxGeo.refine.refine.

Functions

_tuple(value, kind)	A comma-separated string or a sequence, as a tuple of kind.
_hkl(value)	'1,0,0', (1, 0, 0) -> (1, 0, 0).

Module Contents

exception pyextal.jaxGeo.settings.SetupError

Bases: ValueError

A dataset, file or option problem found before anything is refined.

pyextal.jaxGeo.settings.GEOMETRY = ('gl', 'rotation', 'tiltx', 'tilty')

pyextal.jaxGeo.settings.PROBE_RANGE = (0.05, 3.0)

pyextal.jaxGeo.settings.SF_MASKS

pyextal.jaxGeo.settings._tuple(value, kind)

A comma-separated string or a sequence, as a tuple of kind.

pyextal.jaxGeo.settings._hkl(value)

'1,0,0', (1, 0, 0) -> (1, 0, 0).

class pyextal.jaxGeo.settings.RefineSettings

Options for jaxGeo.refine.refine.

Field names match the command-line options (geo_max_block is --geo-max-block); the command line’s --help describes each.

h5: pathlib.Path | None = None

dat: pathlib.Path | None = None

subsample: int = 2

reflections: str | int | tuple = 'review'

review_dir: pathlib.Path | None = None

symmetry: str | None = None

imag: str = 'none'

layers: int = 1

layer_fractions: Tuple[float, ...] | None = None

refine_layers: Tuple[int, ...] | None = None

diagonalise_measured: bool = True

steps: int = 800

warmup: int = 5

lr: float = 0.0001

tile: int = 32

thickness_window: float = 0.2

scale_window: float = 0.05

background_window: float = 0.05

kernel_radius: int = 4

voigt: bool = True

probe_sigma_start: float = 0.5

probe_gamma_start: float = 0.5

tilt_batch: int | None = None

sim_batch: int | None = None

sim_memory: float = 1.5

memory_warn: float = 8.0

figure: pathlib.Path | str | None = 'auto'

history: bool = True

logy: bool = False

notes: str = ''

dry_run: bool = False

cpu: bool = False

precision: str = 'highest'

geometry: bool = True

geo_start: int = 100

geo_every: int = 100

geo_params: Tuple[str, ...] = ('gl', 'rotation', 'tiltx', 'tilty')

geo_iters: int = 8

geo_hessian: str = 'auto'

geo_max_block: float | None = None

geo_tile: int | None = None

geo_step_gl: float = 0.01

geo_step_rotation: float = 0.2

geo_step_tilt: float = 0.02

geo_trust: float = 1.0

geo_refresh: float = 2.0

geo_lambda: float = 0.001

geo_tol: float = 1e-05

geo_check: bool = False

oversub: Tuple[Tuple[int, int, int], ...] = ()

oversub_start: int | None = None

oversub_leak: bool = True

resolved()

Checks the options and returns a canonical copy.

Returns:

reflections as ‘exported’/’review’/int/tuple of triples, symmetry decided, layer_fractions normalised to sum to one, refine_layers and geo_params as tuples, oversub as triples and oversub_start filled in.

Return type:

RefineSettings

Raises:

SetupError – On any inconsistent or unknown option.

property frozen_layers

0-based layers whose structure factors are held (OptConfig.frozen_layers).

classmethod field_names()