Julia¶

Pure Julia package using ccall into the native library. Distributed via a private registry.

API coverage¶

Note: Julia uses free functions dispatched on MultipleDefectModel rather than methods. The naming convention differs from C++/Python: getTimeDerivative → trapped_rates, getMobileTimeDerivative → mobile_rates, both together → rates.

C API (`Lib_Palioxis_c.h`)	Julia wrapper
Process configuration
—	`Palioxis.init(path)` / `palioxis_root(path)`
Construction
`Palioxis_ctor`	`MultipleDefectModel(xml_filename)` / `try_model(xml_filename)`
`Palioxis_delete`	`close(model)` (finaliser)
Model metadata (struct fields)
`getnGas`	`model.n_gas`
`getnTrap`	`model.n_traps`
`getnDofAfterConstraint`	`model.n_ne_species`
`getGas_name` / `gas_name_len`	`gas_names(model)`
`getTrap_name` / `trap_name_len`	`defect_names(model)`
`getDof_name` / `dof_name_len`	`trap_names(model)`
`getBoltzmannConst`	`model.kb` (cached)
`self_consistent`	`self_consistent(model)`
`getMaxOccupancy`	`get_max_trap_occupancy(model, trap_index)`
Diffusion
`getDiffusionConstant`	`diffusion_constants(model, T)`
`effectiveDiffusionCoefficientPrefactor`	`effective_diffusion_prefactor(model, mobile, defects, T)`
`getDiffusionConstantStress`	`diffusion_constants_stress(model, T, stress)`
`effectiveDiffusionCoefficientPrefactorStress`	`effective_diffusion_prefactor_stress(model, mobile, defects, T, stress)`
`getRelaxationVolume`	`get_relaxation_volume(model)`
`getHeatOfTransport`	—
Time integration
`getTimeDerivative`	`trapped_rates(model, mobile, trapped, T)` / `trapped_rates!(out, ...)`
`getMobileTimeDerivative`	`mobile_rates(model, mobile, defects, trapped, T)` / `mobile_rates!(out, ...)`
—	`rates(model, mobile, defects, trapped, T)` (both) / `rates!(...)`
`getTimeDerivativesJacobian`	`time_derivatives_jacobian(model, defects, mobile, trapped, T)` → `TimeDerivativesJacobian`
`getMobileTimeDerivativeJacobianFromTrapped`	`mobile_time_derivative_jacobian_from_trapped(model, defects, trapped, T, dyc, ddyc_dx, ddyc_dyc)` → `MobileTimeDerivativeJacobian`
`getTimeDerivativeskBTJacobian`	`time_derivatives_temperature_sensitivity(model, defects, mobile, trapped, T)` → `TimeDerivativesTemperatureSensitivity`
Initialisation
`defect_density`	`get_defect_concentrations(model, z1, z2)`
`gas_fluence`	`set_fluence_source_rate(model, z1, z2)`
`setInitial_condition`	`set_initial_conditions(model, mobile, T)`
`gas_flux`	`gas_flux(model, z1, z2)`
—	`get_ic_from_xml(model, location, z1, z2, T)` (composite)
Bounds / validation
`ensureBounds`	`ensure_bounds!(model, mobile, defects, trapped)`
`inBounds`	`in_bounds(model, mobile, defects, trapped)`
Surface
`surfaceRate`	`surface_rates(model, location, mobile, T)` / `surface_rates!(out, ...)`
`surfaceVoxSetDirichlet`	`set_surface_dirichlet!(model, location, mobile, T)`
Retention
`retention`	`retention(model, mobile, defects, trapped, T, location, thickness)`
`retention_noneq`	`noneq_retention(model, defects, trapped, T)`
`retention_trapped_by_occupation`	`trapped_retention_by_occupation(model, trap_index, mobile, defects, trapped, T)`
`retention_trapped_by_trap`	`trapped_retention_by_trap(model, mobile, defects, trapped, T)`
`probability_of_occupation`	`probability_of_occupation(model, trap_index, mobile, trapped, T)`
`calculate_mobile_steady_state`	`calculate_mobile_steady_state(model, mobile, defects, T, trapped)`
`calculate_steady_state`	`calculate_steady_state!(model, mobile, defects, trapped, T)` (in-place)
Diagnostics
`report`	`report(model; verbose=false)`
`Lib_Palioxis_init_MPI`	—
`echo_message`	—

Usage¶

Install from the private registry:

using Pkg
Pkg.activate(temp=true)

Pkg.Registry.add("General")
Pkg.Registry.add(url="https://github.com/stephen-dixon/julia-registry.git")

Pkg.add("Palioxis")

Example:

using Palioxis

# Set the Palioxis data root once per process.
Palioxis.init("/path/to/palioxis")

# Construct a model — try_model returns nothing on failure rather than throwing.
m = Palioxis.try_model("input.xml")

# Cached metadata available as struct fields.
println(m.n_gas, " ", m.gas_names, " ", m.defect_names)

# State vectors — sizes follow the cached dimensions.
mobile  = zeros(m.n_gas)
defects = zeros(m.n_traps)
trapped = zeros(m.n_ne_species)
T = 800.0  # Kelvin

# Effective diffusion coefficient prefactor (ShapedDoubleData with .shape and .data).
D_eff = effective_diffusion_prefactor(m, mobile, defects, T)

# Both mobile and trapped time derivatives in a single call.
dy = rates(m, mobile, defects, trapped, T)
# dy.mobile  — mobile rates  [n_gas]
# dy.trapped — trapped rates [n_ne_species]