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aragog.config

The aragog.config package provides the modern attrs-based configuration classes and the Config facade used by the PROTEUS wrapper. Each subclass corresponds to one TOML section; the facade composes them into a legacy Parameters object that the solver consumes internally.

Name Role
Config Top-level facade. Static constructors from_toml(path), from_dict(data), and from_file(*paths) return a legacy Parameters ready for EntropySolver.
BoundaryConfig Surface and core boundary settings: outer_boundary_condition, inner_boundary_condition, emissivity, core_bc mode (energy_balance default, quasi_steady, gradient, bower2018, core_module), the core_module_params of the core_module mode, UTBL toggle.
EnergyConfig Physics toggles (conduction, convection, gravitational separation, mixing, radionuclides, tidal), eddy-diffusivity ratio, tidal-array buffer.
InitialConditionConfig IC type (linear, user-defined, adiabatic), surface and basal temperatures, init-file path.
MeshConfig Mesh geometry, EOS method (Adams-Williamson or user-defined), surface density, gravity, bulk modulus, mass-coordinate flag, surface pressure.
MixedPhaseConfig Mushy-zone parameters: latent heat, rheological transition, smoothing widths, solidus/liquidus paths, cp_blend strategy, separation_viscosity drag source.
PhaseConfig Single-phase (solid or liquid) properties: density, heat capacity, conductivity, expansivity, viscosity, optional entropy lookup. Each property accepts a float or a path-string lookup.
RadionuclideConfig One radioisotope: name, reference time, abundance, concentration, heat production, half-life. Provides get_heating(time) (W/kg).
SolverConfig ODE driver settings: start_time, end_time, atol, rtol, surface-T step cap.

For the TOML field syntax expected on disk, see How-to: configuration. The facade returns a Parameters dataclass tree from the legacy aragog.parser module; that is the object EntropySolver actually consumes internally. The attrs Config classes documented here are the public construction surface.

Facade

Config

Top-level Aragog configuration.

Facade that constructs a Parameters object from attrs-based sub-configs or from TOML/dict input. Solver consumes the Parameters instance directly.

Parameters:

Name Type Description Default
solver dict

ODE solver parameters.

 required
boundary_conditions dict

Boundary condition parameters.

 required
mesh dict

Mesh parameters.

 required
energy dict

Energy source toggles.

 required
initial_condition dict

Initial condition parameters.

 required
phase_liquid dict

Liquid phase properties.

 required
phase_solid dict

Solid phase properties.

 required
phase_mixed dict

Mixed phase parameters.

 required
radionuclide_

Radionuclide sections (any key starting with 'radionuclide_').

 required

from_dict(data, config_dir=None) staticmethod

Construct a Parameters object from a nested dictionary.

This is the primary construction path used by the PROTEUS wrapper.

Parameters:

Name Type Description Default
data dict

Nested dictionary with section names as keys.

 required
config_dir path - like

Directory of the file data came from. Relative eos_file and init_file resolve against it first, then the working directory.

 None

Returns:

Type Description
Parameters

Legacy Parameters object, ready for Solver.
Source code in src/aragog/config/__init__.py 
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@staticmethod
def from_dict(data: dict[str, Any], config_dir=None) -> 'Parameters':
    """Construct a Parameters object from a nested dictionary.

    This is the primary construction path used by the PROTEUS wrapper.

    Parameters
    ----------
    data : dict
        Nested dictionary with section names as keys.
    config_dir : path-like, optional
        Directory of the file ``data`` came from. Relative ``eos_file``
        and ``init_file`` resolve against it first, then the working
        directory.

    Returns
    -------
    Parameters
        Legacy Parameters object, ready for Solver.
    """
    from aragog.parser import (
        Parameters,
        _BoundaryConditionsParameters,
        _EnergyParameters,
        _InitialConditionParameters,
        _MeshParameters,
        _PhaseMixedParameters,
        _PhaseParameters,
        _Radionuclide,
        _resolve_data_paths,
        _SolverParameters,
    )

    # Case-insensitive scalings reject: keep parity with
    # parser.from_file, which lowercases the section name before
    # comparison. Keys differ in case if the dict was built from a
    # TOML by a parser that preserves case.
    if any(str(k).lower() == 'scalings' for k in data):
        raise ValueError(
            "Configuration contains a 'scalings' section, which is no "
            'longer accepted. Aragog applies its internal '
            'nondimensionalisation around the integrator only; remove '
            "the 'scalings' block from the input dict / TOML."
        )

    solver = _SolverParameters(**data['solver'])
    boundary_conditions = _BoundaryConditionsParameters(**data['boundary_conditions'])
    mesh = _MeshParameters(**data['mesh'])
    energy = _EnergyParameters(**data['energy'])
    initial_condition = _InitialConditionParameters(**data.get('initial_condition', {}))
    phase_liquid = _PhaseParameters(**data['phase_liquid'])
    phase_solid = _PhaseParameters(**data['phase_solid'])
    phase_mixed = _PhaseMixedParameters(**data['phase_mixed'])

    radionuclides: list[_Radionuclide] = []
    for key, val in data.items():
        if key.startswith('radionuclide_'):
            radionuclides.append(_Radionuclide(**val))

    if config_dir is not None:
        _resolve_data_paths(config_dir, mesh, initial_condition)
    return Parameters(
        boundary_conditions=boundary_conditions,
        energy=energy,
        initial_condition=initial_condition,
        mesh=mesh,
        phase_solid=phase_solid,
        phase_liquid=phase_liquid,
        phase_mixed=phase_mixed,
        radionuclides=radionuclides,
        solver=solver,
    )

from_file(*filenames) staticmethod

Load from a file, auto-detecting format (TOML or INI).

Parameters:

Name Type Description Default
filenames str

One or more file paths.

 ()

Returns:

Type Description
Parameters
Source code in src/aragog/config/__init__.py 
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@staticmethod
def from_file(*filenames: str) -> 'Parameters':
    """Load from a file, auto-detecting format (TOML or INI).

    Parameters
    ----------
    filenames : str
        One or more file paths.

    Returns
    -------
    Parameters
    """
    from pathlib import Path

    from aragog.parser import Parameters

    paths = [Path(f) for f in filenames]

    if any(p.suffix == '.toml' for p in paths):
        toml_path = next(p for p in paths if p.suffix == '.toml')
        return Config.from_toml(str(toml_path))

    # Fall back to legacy INI parser
    return Parameters.from_file(*filenames)

from_toml(filename) staticmethod

Load configuration from a TOML file and return a Parameters object.

Parameters:

Name Type Description Default
filename str

Path to the TOML file.

 required

Returns:

Type Description
Parameters

Legacy Parameters object, ready for Solver.
Source code in src/aragog/config/__init__.py 
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@staticmethod
def from_toml(filename: str) -> 'Parameters':
    """Load configuration from a TOML file and return a Parameters object.

    Parameters
    ----------
    filename : str
        Path to the TOML file.

    Returns
    -------
    Parameters
        Legacy Parameters object, ready for Solver.
    """
    with Path(filename).open('rb') as f:
        data = tomllib.load(f)

    return Config.from_dict(data, config_dir=Path(filename).resolve().parent)

Boundary conditions

BoundaryConfig

Boundary condition parameters.

Parameters:

Name Type Description Default
outer_boundary_condition int

1: Grey-body, 2: Zahnle, 3: Atmodeller, 4: Prescribed flux, 5: Prescribed T

 required
outer_boundary_value float

Value for outer BC (flux in W/m^2 or T in K, depending on type).

 required
inner_boundary_condition int

1: Core cooling, 2: Prescribed flux, 3: Prescribed T

 required
inner_boundary_value float

Value for inner BC.

 required
emissivity float

Surface emissivity for grey-body BC.

 required
equilibrium_temperature float

Equilibrium temperature for grey-body BC [K].

 required
core_heat_capacity float

Core heat capacity [J/(kg K)].

 required
tfac_core_avg float

Core adiabat correction factor (Bower+2018).

 required
param_utbl bool

Enable upper thermal boundary layer parameterization.

 required
param_utbl_const float

UTBL constant.

 required
core_bc str

Core boundary formulation for inner_boundary_condition = 1: 'quasi_steady' (alpha-factor heat-flux partition between the bottom cell and the core by heat-capacity ratio; state length N; stable but underestimates the CMB heat loss against a SPIDER-parity reference), 'energy_balance' (default, the PROTEUS production path: SPIDER-parity BC with the CMB entropy gradient as an extra state, integrated by SPIDER's bc.c:76-131 formula d/dt(dSdr_cmb) = (2/dr) ((-F_cmb area_cmb) fac_cmb - dSdt_s[0]), fac_cmb = cp_cmb / (cp_core T_cmb tfac M_core); state length N+1), 'gradient' (entropy gradient as the primary state, S rebuilt by integration from the surface; state length N+2), 'bower2018' (T_core as a state with F_cmb from conduction across the bottom half cell, orders of magnitude below the true heat loss; parity testing only) or 'core_module' (the aragog.core evolution budget with dSdr_cmb and T_core as states; state length N+2). Standalone callers that want the alpha-factor behaviour set 'quasi_steady' explicitly.

 required
top_node str

Entropy of the top basic node: 'linear' (default) extrapolates the top 2 cells; 'limited' reduces that half step smoothly near a table edge, so the node rises with the top cell and stays in the table (aragog.mesh.top_node_entropy; not on the 'gradient' core, checked also on assignment).

 required

Energy sources

EnergyConfig

Physics toggle flags, heating parameters, and solver knobs.

Defaults are aligned with the PROTEUS production path (SUNDIALS CVODE + JAX analytic Jacobian + tanh phase smoothing with the bottom-up gravitational-separation gate enabled and a phase-dependent eddy-diffusivity floor of 10 m^2/s).

Parameters:

Name Type Description Default
conduction bool
required
convection bool
required
gravitational_separation bool
required
mixing bool
required
radionuclides bool
required
tidal bool
required
eddy_diffusivity_chemical float

Ratio kappa_c / kappa_h for chemical eddy diffusivity.

 required
eddy_diffusivity_thermal float

Multiplier on the raw thermal eddy diffusivity \(\kappa_h\) before the floor is applied. The SPIDER convention also permits negative values, in which case the diffusivity is pinned to |eddy_diffusivity_thermal|. Default 1.0 passes the MLT-derived value through unchanged.

 required
kappah_floor float

Phase-dependent eddy-diffusivity floor [m^2/s]. Clamps the eddy diffusivity from below by floor * f(phi) where f falls from 1 (liquid) to 0 (solid) across the rheological transition. Default 10.0 matches PROTEUS production; set 0.0 for textbook MLT.

 required
convective_threshold float

Entropy gradient D [J/kg/K/m]. The mixing-length drive acts only where dS/dr < 0 and uses max(|dS/dr|, D) there, so an unstable node gets at least the eddy diffusivity of a gradient D. The phase-modulated kappa_h floor applies wherever dS/dr < D, so a node with 0 <= dS/dr < D gets the floor alone. Default 0.0, the dS/dr < 0 switch with no minimum drive. D = 1e-6 gives one end state in 3 replayed coupled calls that end in one of 2 states under that switch, but with D > 0 kappa_h jumps at dS/dr = 0 from the floor to the mixing-length value at D (where that is above the floor), which can stall CVODE at a node whose gradient stays near 0.

 required
bottom_up_grav_sep bool

SPIDER-analogue bottom-up gate for the gravitational mass-flux: only allow melt/solid separation across an interface when the staggered cell below is non-pure. Default True; off only for regression tests against the pre-fix CMB drain at first crystallisation.

 required
phase_smoothing str

Phase-boundary smoothing scheme for J_grav and J_mix: 'tanh' (SPIDER parity, production default) or 'cubic_hermite' (parameter-free fallback for residual EOS-mismatch cases).

 required
solver_method str

ODE backend: 'cvode' (SUNDIALS via scikits.odes, production default), 'radau' (scipy implicit Runge-Kutta), or 'bdf' (scipy BDF). When scikits.odes is not installed the solver falls back to scipy Radau and emits a warning.

 required
use_jax_jacobian bool

When True and solver_method='cvode', the integrator uses a JAX-derived analytic Jacobian (jax.jacrev) instead of CVODE's finite-difference Jacobian. Requires JAX and the aragog.jax module. Default True matches PROTEUS production; silently falls back to FD if no JAX factory was registered before solve().

 required
phi_step_cap float or None

Per-call mass-weighted |ΔΦ_global| cap (SUNDIALS root function). When positive and at least one staggered cell sits in or near the mushy band at solve() entry, CVODE returns at the exact time where the change first reaches this value. None (the default) disables the cap; any non-positive value disables it too. 0.05 is typical for production evolution of 1 M_E PALEOS-2phase mantles.

 required
temperature_step_cap float or None

Per-call per-cell |ΔT| cap [K] (SUNDIALS root function), firing on the maximum single-cell temperature change since solve() entry. Bounds the core-temperature drop on the solid adiabat below the solidus, which the melt-fraction cap cannot see. None (the default) disables the cap.

 required
entropy_step_cap float or None

Per-call per-cell |ΔS| cap [J/kg/K] in the native solver variable; same role as the temperature cap without an EOS lookup in the root function. None (the default) disables the cap.

 required
eos_floor_margin float or None

Margin m [J/kg/K] above the minimum entropy S_min of the EOS tables. A CVODE root (scipy: a terminal event) ends the call when the smaller of the top basic-node entropy, which sets the surface temperature, and the smallest cell entropy reaches S_min + m, or S_min + m/2 when the call starts below S_min + m; the call then returns a shorter step. A call that starts at or below S_min + m/2 arms a level at half its distance to S_min, and does not advance (status 1) when that entropy falls fast enough to reach the level before the call ends; a caller that retries with a shorter span can then advance closer to S_min; there the top node counts as falling only when the top cell falls too. At or below S_min + 2e-6 m the call does not advance on any fall, the top node at its own rate, at every span, and a start at or below S_min, also of the extrapolated top node alone, or with no level between it and S_min, does not advance at all. A call whose stop lands below S_min through the root location error, which grows with the call time, is discarded as a refusal. A call with no span skips the floor. Default 0: the floor is off, so a drain past S_min continues at the clamped table-edge temperature and the EOS lookup logs its out-of-range WARNING (it raises only for an EOS built with strict_range=True). A positive margin turns it on (100 is the tested value) and must stay below the entropy span of the tables; None (not in TOML) or a non-positive value disables it, and a bool, NaN, infinity or a value that is not a numbers.Real is refused.

 required
phase_boundary_entropy_margin float

Proximity band [J/kg/K] within which a staggered cell counts as "near" a phase boundary, tightening the integrator max_step so CVODE resolves the stiff RHS across the solidus/liquidus (reduced to 1 yr under phase_boundary_cap = 'fixed', or adaptive segments under 'rate'; on CVODE a 'rate' call also arms its segments within the stiff-zone half-width when that exceeds the margin, while the step caps keep the margin). This is a solver-accuracy control, not a physics threshold. Lowering it can under-resolve a real phase crossing and shift the converged state by more than the nominal tolerance, because CVODE's local error control can accept an over-large step across the near-discontinuous two-phase RHS. Default 200.0, a fraction of a typical silicate fusion entropy (S_liquidus - S_solidus), wide enough to arm the tighter stepping before a cell reaches the boundary yet narrow enough to leave the deep-solid thermal history on unrestricted steps. A non-finite or non-positive value falls back to the default.

 required
phase_boundary_cap str or None

How max_step is set while a cell is near or inside the two-phase band. None (default) means 'rate'. 'fixed' uses 1 yr. 'rate' uses event-driven CVODE segments with max_step set to 0.1 of the shortest time to reach a phase boundary, clipped to [1, 100] yr. Inside the stiff zone or below the rate floor, the estimate uses the distance to the nearer boundary. The gradient core and the scipy integrators keep 1 yr, with one log line per solver (INFO when the mode is the default, WARNING when 'rate' is set). An rtol above 1e-7 logs one rate-cap warning per solver. The accuracy of 'rate' against 'fixed' is tabulated in the energy-equation docs and computed by tools/verification/run_phase_boundary_cap_accuracy.py.

 required
tidal_array ndarray

Tidal heating per unit mass [W/kg] at each layer.

 required

Initial condition

InitialConditionConfig

Initial condition parameters.

Parameters:

Name Type Description Default
initial_condition int

1: Linear profile, 2: User-defined from file, 3: Adiabatic profile.

 required
surface_temperature float

Surface temperature [K].

 required
basal_temperature float

Basal temperature [K].

 required
init_file str

Path to user-defined temperature file (for IC type 2).

 required

Mesh

MeshConfig

Mesh and static pressure profile parameters.

Parameters:

Name Type Description Default
outer_radius float

Outer radius of the mantle shell (planet radius minus atmosphere depth, in practice the same as planet.radius) [m].

 required
inner_radius float

Inner radius of the mantle shell, i.e. the core-mantle boundary (CMB) radius [m].

 required
number_of_nodes int

Number of basic mesh nodes.

 required
mixing_length_profile str

'constant' or 'nearest_boundary'.

 required
mixing_length_constant_fraction float

Fraction of the mantle thickness to use as the mixing length when mixing_length_profile = 'constant'. Default 0.25. Ignored for 'nearest_boundary'.

 required
core_density float

Core density [kg/m^3].

 required
eos_method int

1: Adams-Williamson, 2: User-defined.

 required
surface_density float

Surface-mantle density anchor [kg/m^3]. Used only by the analytic Adams-Williamson EOS (eos_method = 1) as the constant rho_top in rho(P) = rho_top * exp(P/K_S). NOT the runtime material density (which is pressure-entropy dependent and comes from the P-S property tables). Default 4078.95095544 matches the SPIDER -adams_williamson_rhos value used in PROTEUS production runs. Ignored when eos_method = 2.

 required
gravitational_acceleration float

Gravitational acceleration [m/s^2].

 required
adiabatic_bulk_modulus float

Adiabatic bulk modulus [Pa].

 required
surface_pressure float

Surface pressure [Pa].

 required
mass_coordinates bool

Use uniform spacing in mass-coordinate space instead of radius. Gives larger cells at the surface (lower density) and matches SPIDER's mesh. Default True matches the PROTEUS production path.

 required
eos_file str

Path to user-defined EOS file.

 required

Phases (single and mixed)

PhaseConfig(density, heat_capacity, melt_fraction, thermal_conductivity, thermal_expansivity, viscosity, entropy='', rheology=None, **flat_rheo)

Single-phase (solid or liquid) material properties.

Each property can be a float (constant value) or a str (path to a lookup table file). Rheology parameters are owned by SolidRheologyParams.

Parameters:

Name Type Description Default
density float or str

Reference density [kg/m^3] or path to lookup table.

 required
heat_capacity float or str

Specific heat capacity [J/kg/K] or path to lookup table.

 required
melt_fraction float

Melt fraction (0 for solid, 1 for liquid).

 required
thermal_conductivity float or str

Thermal conductivity [W/m/K] or path to lookup table.

 required
thermal_expansivity float or str

Thermal expansivity [1/K] or path to lookup table.

 required
viscosity float or str

Dynamic viscosity [Pa s] or path to lookup table.

 required
entropy float or str

Reference entropy [J/kg/K] or path to lookup table. Empty string means unused.

 ''
rheology SolidRheologyParams

Solid-state rheology parameters container. Each SolidRheologyParams field is also exposed as a read-only property on PhaseConfig via delegate_rheology.

 None
**flat_rheo Any

Flat rheology attributes forwarded to rheology container.

 {}
Source code in src/aragog/config/phases.py 
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def __init__(
    self,
    density: float | str,
    heat_capacity: float | str,
    melt_fraction: float,
    thermal_conductivity: float | str,
    thermal_expansivity: float | str,
    viscosity: float | str,
    entropy: float | str = '',
    rheology: SolidRheologyParams | None = None,
    **flat_rheo: Any,
):
    if viscosity is None:
        raise ValueError('viscosity must not be None')
    self.density = density
    self.heat_capacity = heat_capacity
    self.melt_fraction = melt_fraction
    self.thermal_conductivity = thermal_conductivity
    self.thermal_expansivity = thermal_expansivity
    self.viscosity = viscosity
    self.entropy = entropy
    self.rheology = merge_rheology(rheology, flat_rheo)

MixedPhaseConfig

Mixed-phase (mushy zone) parameters.

Parameters:

Name Type Description Default
latent_heat_of_fusion float

Latent heat [J/kg].

 required
rheological_transition_melt_fraction float

Melt fraction at rheological transition.

 required
rheological_transition_width float

Width of the tanh smoothing around the transition.

 required
solidus str

Path to solidus lookup file.

 required
liquidus str

Path to liquidus lookup file.

 required
phase str

Active phase mode: 'solid', 'liquid', 'mixed', or 'composite'.

 required
phase_transition_width float

Width of smoothing at phase boundaries.

 required
grain_size float

Grain size [m] for permeability calculations.

 required
separation_viscosity str

Drag viscosity source for gravitational separation: 'melt' (single-phase liquid viscosity, matches SPIDER's GetGravitationalHeatFlux) or 'mixture' (the rheological-transition-blended bulk viscosity). Default 'melt'.

 required
cp_blend str

Mushy-zone Cp blending mode: 'latent' (SPIDER-parity, latent-heat-augmented) or 'linear' (linear blend of pure-phase Cp without the latent term). Default 'latent'.

 required
matprop_smooth_width float

Half-width of the tanh used to smooth phase-dependent material properties around the rheological transition. Default 0.0 reproduces SPIDER's convention of no smoothing on the property side; 0.01 is the typical JAX setting.

 required
const_properties bool

Replace the EOS-tabulated \((\rho, c_p, \alpha, k)\) and \(\log_{10}\eta\) with the seven constant-property values below. Mirrors SPIDER's -use_const_properties. Default False (use the EOS tables).

 required
const_rho float

Constant density [kg/m^3] when const_properties is True.

 required
const_Cp float

Constant heat capacity [J/(kg K)] when const_properties is True.

 required
const_alpha float

Constant thermal expansivity [1/K] when const_properties is True.

 required
const_cond float

Constant thermal conductivity [W/(m K)] when const_properties is True.

 required
const_log10visc float

Constant \(\log_{10}\) dynamic viscosity [log10(Pa s)] when const_properties is True.

 required
const_T_ref float

Reference temperature [K] for the constant-properties EOS, used to anchor \(T(P, S)\) on the analytic isentrope.

 required
const_S_ref float

Reference entropy [J/(kg K)] for the constant-properties EOS, paired with const_T_ref.

 required

Radionuclides

RadionuclideConfig

Single radionuclide heating source.

Parameters:

Name Type Description Default
name str

Isotope name (e.g., 'K40', 'U238').

 required
t0_years float

Reference time for initial abundance [years].

 required
abundance float

Isotopic abundance ratio (e.g., 40K/K).

 required
concentration float

Elemental concentration [ppm].

 required
heat_production float

Specific heat production [W/kg].

 required
half_life_years float

Half-life [years].

 required

get_heating(time)

Compute radiogenic heating at a given time.

Parameters:

Name Type Description Default
time float or ndarray

Time [years].

 required

Returns:

Type Description
float or ndarray

Heat production [W/kg].
Source code in src/aragog/config/radionuclides.py 
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def get_heating(self, time: npt.NDArray | float) -> npt.NDArray | float:
    """Compute radiogenic heating at a given time.

    Parameters
    ----------
    time : float or ndarray
        Time [years].

    Returns
    -------
    float or ndarray
        Heat production [W/kg].
    """
    arg = np.log(2) * (self.t0_years - time) / self.half_life_years
    amplitude = self.heat_production * self.abundance * self.concentration
    return amplitude * np.exp(np.where(amplitude, arg, 0.0))

Solver driver

SolverConfig

ODE solver parameters.

Parameters:

Name Type Description Default
start_time float

Start time [years].

 required
end_time float

End time [years].

 required
atol float

Absolute tolerance, floored at 1e-8. Default 1e-8.

 required
rtol float

Relative tolerance. Default 1e-8, the value at which phase_boundary_cap = 'rate' is verified. Above 1e-8 a CVODE run logs one warning: a loose rtol can lock CVODE at the convective switch (the convective mask and the kappa_h floor).

 required
tsurf_poststep_change float

Maximum surface temperature change per step [K].

 required
cvode_output_points int

Number of points on the CVODE dense output grid.

 required
max_steps int

Maximum number of internal CVODE steps per output interval (SUNDIALS mxstep).

 required
tcore_change_limit float or None

Optional per-solve core-temperature change limit [K]. The flag is also set, independent of this limit, when any sampled core temperature is non-finite.

 required