MATLAB / Octave

MEX extension built with Octave’s mkoctfile, compatible with both Octave and MATLAB. Platform ZIPs (Linux x86_64, macOS Intel, macOS ARM) are attached to each GitHub release.

API coverage

C API (Lib_Palioxis_c.h)

MATLAB wrapper

Process configuration

—

palioxis.set_root(path)

—

palioxis.root()

Construction / destruction

Palioxis_ctor

palioxis.MultipleDefectModel(xml_filename)

Palioxis_delete

destructor

Model metadata (read-only properties)

getnGas

model.n_gas

getnTrap

model.n_trap_types

getnDofAfterConstraint

model.n_ne_traps

getGas_name / gas_name_len

model.gas_names

getTrap_name / trap_name_len

model.defect_names

getDof_name / dof_name_len

model.trap_names

getBoltzmannConst

palioxis.MultipleDefectModel.get_boltzmann_const()

getMinMobileConc

palioxis.MultipleDefectModel.get_min_mobile_conc()

self_consistent

—

getMaxOccupancy

used internally by retention_trapped_by_occupation

Diffusion

getDiffusionConstant

model.get_diffusion_constant(T)

effectiveDiffusionCoefficientPrefactor

model.effective_diffusion_prefactor(mobile, defects, T)

getDiffusionConstantStress

—

effectiveDiffusionCoefficientPrefactorStress

—

getRelaxationVolume

—

getHeatOfTransport

—

Time integration

getTimeDerivative

model.get_time_derivative(mobile, trapped, T)

getMobileTimeDerivative

model.get_mobile_time_derivative(mobile, defects, trapped, T)

—

[trapped_dy, mobile_dy] = model.get_time_derivatives(mobile, defects, trapped, T)

getTimeDerivativesJacobian

model.get_time_derivatives_jacobian(defects, mobile, trapped, T)

getMobileTimeDerivativeJacobianFromTrapped

model.get_mobile_jacobian_from_trapped(defects, trapped, T, dyc, ddyc_dx, ddyc_dyc)

getTimeDerivativeskBTJacobian

model.get_time_derivatives_temperature_sensitivity(defects, mobile, trapped, T)

Initialisation

defect_density

model.get_defect_concentrations(z1, z2)

gas_fluence

model.get_fluence_source_rate(z1, z2)

setInitial_condition

model.set_initial_conditions(mobile, T)

gas_flux

model.get_gas_flux(z1, z2)

—

model.get_ic_from_xml(z1, z2, T) (composite)

Bounds / validation

ensureBounds

[mobile, defects, trapped] = model.ensure_bounds(mobile, defects, trapped)

inBounds

model.in_bounds(mobile, defects, trapped)

Surface

surfaceRate

model.get_surface_rate(location, mobile, T)

surfaceVoxSetDirichlet

—

Retention

retention

model.retention(mobile, defects, trapped, T, location, thickness)

retention_noneq

model.non_equilibrium_retention(defects, trapped, T)

retention_trapped_by_occupation

model.retention_trapped_by_occupation(trap_index, mobile, defects, trapped, T)

retention_trapped_by_trap

model.retention_trapped_by_trap(mobile, defects, trapped, T)

probability_of_occupation

—

calculate_mobile_steady_state

model.calculate_mobile_steady_state(mobile, defects, trapped, T)

calculate_steady_state

[mobile, trapped] = model.calculate_steady_state(mobile, defects, trapped, T)

Diagnostics

report

model.report(verbose)

Lib_Palioxis_init_MPI

—

echo_message

—

Usage

Install from a downloaded ZIP:

% Unzip the platform archive, then add the extracted folder to your path.
unzip('palioxis-matlab-mexmaca64.zip', '~/palioxis-matlab')
addpath('~/palioxis-matlab/palioxis-matlab')

Example:

% Set the Palioxis data root once per session.
palioxis.set_root('/path/to/palioxis');

% Construct a model from an XML configuration file.
m = palioxis.MultipleDefectModel('input.xml');

% Cached metadata available as read-only properties.
disp(m.n_gas);
disp(m.gas_names);
disp(m.defect_names);

% State vectors — sizes follow the cached dimensions.
mobile  = zeros(m.n_gas, 1);
defects = zeros(m.n_trap_types, 1);
trapped = zeros(m.n_ne_traps, 1);
T = 800;  % Kelvin

% Effective diffusion coefficient prefactor matrix (n_gas × n_gas).
D_eff = m.effective_diffusion_prefactor(mobile, defects, T);

% Both mobile and trapped time derivatives in a single call.
[trapped_dy, mobile_dy] = m.get_time_derivatives(mobile, defects, trapped, T);
% trapped_dy — trapped rates  [n_ne_traps × 1]
% mobile_dy  — mobile rates   [n_gas × 1]