API Reference

Main drivers

Problem(options, grid, numerics, prop, geo)	Problem driver for GaPFlow simulations.
Database(md, db[, num_extra_features])	Container for GP training datasets.
integrate	Flux and source term contributions for numerical integration.

Models

gp.GaussianProcessSurrogate(fc, database)	Abstract base class for Gaussian Process (GP) surrogate models.
Pressure(fc, prop, geo[, data, gp])	Pressure model.
BulkStress(fc, prop, geo[, data, gp])	Bulk (gap-averaged) viscous stress model.
WallStress(fc, prop, geo[, direction, data, gp])	Wall stress model (wall shear/stress in xz or yz direction).
pressure	Equation of state (pressure).
sound	Equation of state (sound speed).
viscosity	Viscosity models.
viscous	Viscous stress tensor components.

Molecular dynamics

MolecularDynamics()	Driver for molecular dynamics simulations.
Mock(prop, geo, gp)	Mock implementation of an MD runner.
LennardJones(params)	Run MD simulations with LAMMPS for a pure LJ system.
GoldAlkane(params)	Run MD simulations with LAMMPS for n-alkanes confined between gold surfaces.
moltemplate	Moltemplate helper functions.

Topography

Topography(fc, grid, geo, prop)	Topography container.
ElasticDeformation(E, v, alpha_underrelax, ...)	Thin wrapper around the FFTElasticHalfSpace classes from ContactMechanics.

Visualization

animations	Create animations from simulation output stored as NetCDF files.
plotting	Create line and contour plots of the simulation results.