Python API

pack([n, radii, container, density, ...])	Packs spheres (disks in 2D) with the Lubachevsky-Stillinger algorithm.
Packing(positions, radii, container, status, ...)	A sphere (disk) packing.
Box(lengths[, periodic, ball])	Rectangular box spanning [0, L_k) along each axis.
PeriodicBox(lengths[, dim])	Fully periodic box.
PackingWarning	A packing run stopped before reaching its target.
PackingError(message, packing)	Raised with strict=True when a run stops before its target.
load(path)	Loads a packing written by save().

neighbor_pairs(packing, cutoff)	All pairs closer than cutoff (centre to centre).
contacts(packing[, tol])	Pairs in contact: centre distance at most (r_i + r_j) * (1 + tol).
contact_numbers(packing[, tol])	Number of contacts of every sphere (see contacts() for tol).
rattlers(packing[, tol, method, force_threshold])	Boolean mask of rattlers: spheres that carry no force in a jammed packing.
radial_distribution(packing[, r_max, bins])	Pair distribution function of the sphere centres.
radial_profile(packing[, bins, n_theta])	Local solid fraction as a function of the distance from the axis of a cylinder, or from the centre of a spherical container or disk.
bond_order(packing[, l, cutoff])	Bond-orientational order parameter of order l.
crystalline(packing[, cutoff, threshold, ...])	Boolean mask of spheres in a crystalline environment.
isostaticity(packing[, tol, method])	Ratio of the number of contacts among non-rattlers to the isostatic number.
density_profile(packing[, axis, bins])	Local volume (area) fraction as a function of position along axis.

write_xyz(packing, path, *[, species, ...])	Writes an extended XYZ file (Lattice, pbc and a radius column).
write_lammps_dump(packing, path, *[, types, ...])	Writes a LAMMPS text dump (id type x y z radius), one frame.
write_lammps_data(packing, path, *[, ...])	Writes a LAMMPS data file for atom_style sphere (id type diameter density x y z).
write_vtp(packing, path, *[, ...])	Writes the sphere centres as VTK XML PolyData with radius and diameter.
write_container_vtp(packing_or_container, path)	Writes the outline of the container (box edges, or circles and generators of a cylinder, or great circles of a sphere) as VTK lines, to show with the spheres.
write_stl(packing, path, *[, subdivisions, ...])	Writes the sphere surfaces as a binary STL mesh (icospheres, 20 * 4**subdivisions triangles per sphere; 320 for the default).
write_pov(packing, path, *[, ...])	Writes a POV-Ray scene with camera, light and one sphere per particle.
save(packing, path)	Saves a packing, its container and run statistics to a NumPy .npz file.
load(path)	Loads a packing written by save().

System([positions, n, density, box, kT, ...])	Particles interacting with a pair potential in a periodic box, sampled with the rejection-free method.
radial_distribution(system, n_samples, interval)	Pair distribution function averaged over n_samples configurations taken every interval of simulation time (the system advances by n_samples * interval).
PairPotential(kind[, epsilon, sigma, ...])	Isotropic pair potential with at most one minimum and zero at the cutoff.
LennardJones([epsilon, sigma, cutoff])	Truncated and shifted Lennard-Jones potential, \(4\epsilon[(\sigma/r)^{12} - (\sigma/r)^6] - U_\mathrm{LJ}(r_c)\) for \(r < r_c\).
WCA([epsilon, sigma])	Weeks-Chandler-Andersen potential: Lennard-Jones truncated and shifted at its minimum.
DPD([a, cutoff])	Conservative DPD potential \(\frac{a}{2}(1 - r/r_c)^2\) for \(r < r_c\).
SoftSpheres([epsilon, sigma, alpha])	Soft repulsion \(\frac{\epsilon}{\alpha}(1 - r/\sigma)^\alpha\) for \(r < \sigma\) (harmonic for \(\alpha = 2\), Hertzian for \(\alpha = 5/2\)).
HardSpheres([diameter])	Hard spheres: every approach to contact reflects (event-driven hard-sphere dynamics).

Jammed([pressure, relax_windows, step, ...])	Compress quasi-statically until the packing is jammed.
Pressure([value])	Stop when the reduced pressure Z = PV/(N kT) exceeds value.
Stall([tol, window])	Stop when the radii grew by less than tol (relative) during the last window collisions per sphere.
Collisions([total, per_particle])	Stop after total collisions, or per_particle collisions per sphere.
Timeout(seconds)	Stop after seconds of wall-clock time (not reproducible between machines).