CLI configuration reference

Generated from beat.cli.config by scripts/gen_cli_reference.py – do not edit. Quantities are strings with units, e.g. "0.05 ms".

[geometry]

FolderGeometry (folder)

Field	Type	Default	Description
unit	str	'mm'	Length unit of the mesh coordinates
folder	path	'geometry'	type=folder: folder to read. Generated types (slab, lv_ellipsoid, biv_ellipsoid, ukb): cache root, each mesh is cached in its own / subfolder
type	‘folder’	'folder'
fibers	FromGeometryFibers | AxisFibers | IsotropicFibers	FromGeometryFibers(type='from_geometry')

IntervalGeometry (interval)

Field	Type	Default	Description
unit	str	'mm'	Length unit of the mesh coordinates
folder	path	'geometry'	type=folder: folder to read. Generated types (slab, lv_ellipsoid, biv_ellipsoid, ukb): cache root, each mesh is cached in its own / subfolder
type	‘interval’	'interval'
length	float	10.0	Cable length (geometry.unit)
dx	float	0.1	Element size (geometry.unit)
fibers	FromGeometryFibers | AxisFibers | IsotropicFibers	IsotropicFibers(type='isotropic')

RectangleGeometry (rectangle)

Field	Type	Default	Description
unit	str	'mm'	Length unit of the mesh coordinates
folder	path	'geometry'	type=folder: folder to read. Generated types (slab, lv_ellipsoid, biv_ellipsoid, ukb): cache root, each mesh is cached in its own / subfolder
type	‘rectangle’	'rectangle'
lx	float	1.0
ly	float	1.0
dx	float	0.05
fibers	FromGeometryFibers | AxisFibers | IsotropicFibers	IsotropicFibers(type='isotropic')

BoxSlabGeometry (box_slab)

Structured tetrahedral box (beat.geometry.get_3D_slab_mesh); no gmsh needed.

Field	Type	Default	Description
unit	str	'mm'	Length unit of the mesh coordinates
folder	path	'geometry'	type=folder: folder to read. Generated types (slab, lv_ellipsoid, biv_ellipsoid, ukb): cache root, each mesh is cached in its own / subfolder
type	‘box_slab’	'box_slab'
lx	float	20.0
ly	float	7.0
lz	float	3.0
dx	float	0.5
fibers	FromGeometryFibers | AxisFibers | IsotropicFibers	AxisFibers(type='axis', direction='x')

SlabGeometry (slab)

Field	Type	Default	Description
unit	str	'mm'	Length unit of the mesh coordinates
folder	path	'geometry'	type=folder: folder to read. Generated types (slab, lv_ellipsoid, biv_ellipsoid, ukb): cache root, each mesh is cached in its own / subfolder
fiber_angle_endo	float	60.0
fiber_angle_epi	float	-60.0
fiber_space	str	'P_1'
fibers	FromGeometryFibers | AxisFibers | IsotropicFibers	FromGeometryFibers(type='from_geometry')
type	‘slab’	'slab'
lx	float	20.0
ly	float	7.0
lz	float	3.0
dx	float	1.0

LVEllipsoidGeometry (lv_ellipsoid)

Field	Type	Default	Description
unit	str	'mm'	Length unit of the mesh coordinates
folder	path	'geometry'	type=folder: folder to read. Generated types (slab, lv_ellipsoid, biv_ellipsoid, ukb): cache root, each mesh is cached in its own / subfolder
fiber_angle_endo	float	60.0
fiber_angle_epi	float	-60.0
fiber_space	str	'P_1'
fibers	FromGeometryFibers | AxisFibers | IsotropicFibers	FromGeometryFibers(type='from_geometry')
type	‘lv_ellipsoid’	'lv_ellipsoid'
r_short_endo	float	7.0
r_short_epi	float	10.0
r_long_endo	float	17.0
r_long_epi	float	20.0
psize_ref	float	3.0
mu_apex_endo	float	-3.141592653589793
mu_base_endo	float	-1.2722641256100204
mu_apex_epi	float	-3.141592653589793
mu_base_epi	float	-1.318116071652818

BiVEllipsoidGeometry (biv_ellipsoid)

Field	Type	Default	Description
unit	str	'mm'	Length unit of the mesh coordinates
folder	path	'geometry'	type=folder: folder to read. Generated types (slab, lv_ellipsoid, biv_ellipsoid, ukb): cache root, each mesh is cached in its own / subfolder
fiber_angle_endo	float	60.0
fiber_angle_epi	float	-60.0
fiber_space	str	'P_1'
fibers	FromGeometryFibers | AxisFibers | IsotropicFibers	FromGeometryFibers(type='from_geometry')
type	‘biv_ellipsoid’	'biv_ellipsoid'
char_length	float	0.5

UKBGeometry (ukb)

Field	Type	Default	Description
unit	str	'mm'	Length unit of the mesh coordinates
folder	path	'geometry'	type=folder: folder to read. Generated types (slab, lv_ellipsoid, biv_ellipsoid, ukb): cache root, each mesh is cached in its own / subfolder
fiber_angle_endo	float	60.0
fiber_angle_epi	float	-60.0
fiber_space	str	'P_1'
fibers	FromGeometryFibers | AxisFibers | IsotropicFibers	FromGeometryFibers(type='from_geometry')
type	‘ukb’	'ukb'
mode	int	-1
std	float	1.5
case	‘ED’ | ‘ES’	'ED'
char_length_max	float	5.0
char_length_min	float	5.0
clipped	bool	False

[geometry.fibers]

FromGeometryFibers (from_geometry)

Field	Type	Default	Description
type	‘from_geometry’	'from_geometry'

AxisFibers (axis)

Field	Type	Default	Description
type	‘axis’	'axis'
direction	‘x’ | ‘y’ | ‘z’	'x'

IsotropicFibers (isotropic)

Field	Type	Default	Description
type	‘isotropic’	'isotropic'

[ep]

EPConfig

Field	Type	Default	Description
chi	Quantity	'1400 cm**-1'	Surface to volume ratio
C_m	Quantity	'1 uF/cm**2'	Membrane capacitance
conductivity	ConductivityConfig	ConductivityConfig(preset=None, sigma_il=None, sigma_it=None, sigma_el=None, sigma_et=None)

ConductivityConfig

Field	Type	Default	Description
preset	‘Niederer’ | ‘Bishop’ (optional)	–	Literature set from beat.conductivities.default_conductivities; explicit sigma_* override it field by field
sigma_il	Quantity (optional)	–
sigma_it	Quantity (optional)	–
sigma_el	Quantity (optional)	–
sigma_et	Quantity (optional)	–

[cell]

CellConfig

Field	Type	Default	Description
ode_file	path	required	Path to the gotranx .ode cell model
scheme	str	'generalized_rush_larsen'
v_name	str	'v'	Name of the transmembrane potential state
parameters	dict[str, float]	{}
steady_state	SteadyStateConfig (optional)	–	If set, pre-pace a single cell to steady state before the tissue run
layers	NoLayers | TransmuralLayers | CellMarkerLayers	NoLayers(method='none')
regions	dict[str, RegionConfig]	{}

SteadyStateConfig

Field	Type	Default	Description
num_beats	int	20
BCL	Quantity	'1000 ms'
dt	Quantity	'0.05 ms'
track	list[str]	[]	States to record

RegionConfig

Field	Type	Default	Description
parameters	dict[str, float]	{}

[cell.layers]

NoLayers (none)

Field	Type	Default	Description
method	‘none’	'none'

TransmuralLayers (transmural)

Field	Type	Default	Description
method	‘transmural’	'transmural'
endo_size	float	0.3
epi_size	float	0.3
endo_markers	list[str] (optional)	–	Facet markers of the endocardium. Default: [“ENDO”] if present, else [“LV”, “RV”] (BiV)
epi_marker	str	'EPI'

CellMarkerLayers (cell_markers)

Field	Type	Default	Description
method	‘cell_markers’	'cell_markers'
map	dict[str, str]	required	region name -> geometry cell marker name

[[stimulus]]

MarkerStimulus (marker)

Field	Type	Default	Description
amplitude	str	required	Current density: uA/cm2 for a marker stimulus on a facet marker, uA/cm3 for a marker stimulus on a cell marker and for box/random_endocardial stimuli (any mesh dimension); see beat.stimulation.define_stimulus
duration	Quantity	'2 ms'
start	Quantity	'0 ms'
period	Quantity (optional)	–	If set, repeat the pulse every period
num_pulses	int (optional)	–	Number of pulses (requires period). Default: until the end time
type	‘marker’	'marker'
marker	str	required	Facet or cell marker name from the geometry

BoxStimulus (box)

Field	Type	Default	Description
amplitude	str	required	Current density: uA/cm2 for a marker stimulus on a facet marker, uA/cm3 for a marker stimulus on a cell marker and for box/random_endocardial stimuli (any mesh dimension); see beat.stimulation.define_stimulus
duration	Quantity	'2 ms'
start	Quantity	'0 ms'
period	Quantity (optional)	–	If set, repeat the pulse every period
num_pulses	int (optional)	–	Number of pulses (requires period). Default: until the end time
type	‘box’	'box'
min	list[float]	required
max	list[float]	required

RandomEndocardialStimulus (random_endocardial)

Field	Type	Default	Description
amplitude	str	required	Current density: uA/cm2 for a marker stimulus on a facet marker, uA/cm3 for a marker stimulus on a cell marker and for box/random_endocardial stimuli (any mesh dimension); see beat.stimulation.define_stimulus
duration	Quantity	'2 ms'
start	Quantity	'0 ms'
period	Quantity (optional)	–	If set, repeat the pulse every period
num_pulses	int (optional)	–	Number of pulses (requires period). Default: until the end time
type	‘random_endocardial’	'random_endocardial'
markers	list[str]	['LV', 'RV']
num_points	int	200
delay_range	tuple[Quantity, Quantity]	('0 ms', '4 ms')
seed	int	0
tol	float	1.0	Radius around each point (geometry.unit)

[solver]

SolverConfig

Field	Type	Default	Description
dt	Quantity	'0.05 ms'
theta	float	1.0	Splitting: 1.0 Godunov, 0.5 Strang
end_time	Quantity (optional)	–	Simulated end time. Give either this or num_beats and BCL
num_beats	int (optional)	–	Run length in beats: end time = num_beats x BCL
BCL	Quantity (optional)	–	Basic cycle length, only used for the run length (num_beats x BCL). It does not pace anything: set a [[stimulus]] period for that
pde	ThetaPDE | IrksomePDE	ThetaPDE(type='theta', theta=0.5, linear_solver='direct')
ode	DolfinODE | IrksomeODE | ExternalOperatorODE	DolfinODE(type='dolfin')
petsc_options	dict[str, str | int | float | bool]	{}

[solver.pde]

ThetaPDE (theta)

Field	Type	Default	Description
type	‘theta’	'theta'
theta	float	0.5	PDE theta-scheme parameter
linear_solver	‘direct’ | ‘iterative’	'direct'

IrksomePDE (irksome)

Field	Type	Default	Description
type	‘irksome’	'irksome'
tableau	str	'RadauIIA'	Irksome Butcher tableau class name
stages	int	1
linear_solver	‘direct’ | ‘iterative’	'direct'

[solver.ode]

DolfinODE (dolfin)

Field	Type	Default	Description
type	‘dolfin’	'dolfin'

IrksomeODE (irksome)

Field	Type	Default	Description
type	‘irksome’	'irksome'
tableau	str	'RadauIIA'
stages	int	1

ExternalOperatorODE (external_operator)

Field	Type	Default	Description
type	‘external_operator’	'external_operator'

[output]

OutputConfig

Field	Type	Default	Description
folder	path	'output'
save_every	Quantity	'1 ms'
fields	list[str]	[]	Extra ODE states to save
checkpoint_every	Quantity	'0 ms'	Restart checkpoint interval; 0 = end only
performance	bool	False
log_every	int	100

[postprocess]

PostprocessConfig

Field	Type	Default	Description
points	dict[str, list[float]]	{}
activation_threshold	float	0.0
sigma_b	float	1.0
vtx	bool	True
make_gif	bool	False