Observables

BondOrderParameters

ClusterList

Partition particles into clusters and return their size.

ConvexHull

Construct the convex hull of the system, which is the smallest convex set that contains the set of points constituted by the particles’ coordinates of the given system.

FormFactor

PoreSize

RDF

Compute the radial distribution function of a system.

StructureFactor

Compute the structure factor of a system.

class baggianalysis.core.BondOrderParameters(self: baggianalysis.core.BondOrderParameters, orders_to_compute: Set[int], compute_avg_qs: bool = True, compute_qs: bool = False, compute_avg_ws: bool = False, compute_ws: bool = False)None

Bases: pybind11_builtins.pybind11_object

analyse_system(self: baggianalysis.core.BondOrderParameters, arg0: baggianalysis.core.System)None
analyse_trajectory(self: baggianalysis.core.BondOrderParameters, arg0: baggianalysis.core.BaseTrajectory)None
reset(self: baggianalysis.core.BondOrderParameters)None
result(self: baggianalysis.core.BondOrderParameters) → List[List[float]]
class baggianalysis.core.ClusterList(self: baggianalysis.core.ClusterList)None

Bases: pybind11_builtins.pybind11_object

Partition particles into clusters and return their size.

The default constructor takes no parameters

analyse_system(self: baggianalysis.core.ClusterList, arg0: baggianalysis.core.System)None
analyse_trajectory(self: baggianalysis.core.ClusterList, arg0: baggianalysis.core.BaseTrajectory)None
property clusters

Return the list of clusters of the system analysed last.

reset(self: baggianalysis.core.ClusterList)None
result(self: baggianalysis.core.ClusterList) → List[int]
class baggianalysis.core.ConvexHull(self: baggianalysis.core.ConvexHull)None

Bases: pybind11_builtins.pybind11_object

Construct the convex hull of the system, which is the smallest convex set that contains the set of points constituted by the particles’ coordinates of the given system.

analyse_system(self: baggianalysis.core.ConvexHull, arg0: baggianalysis.core.System)None
analyse_trajectory(self: baggianalysis.core.ConvexHull, arg0: baggianalysis.core.BaseTrajectory)None
reset(self: baggianalysis.core.ConvexHull)None
result(self: baggianalysis.core.ConvexHull) → ba::ConvexHullResult
class baggianalysis.core.ConvexHullResult(self: baggianalysis.core.ConvexHullResult)None

Bases: pybind11_builtins.pybind11_object

The actual convex hull.

property area

The area of the convex hull.

property triangles

A list of Triangles that compose the convex hull.

property vertices

The vertices that compose the convex hull. These are a subset of the particles of the system.

property volume

The volume of the convex hull.

class baggianalysis.core.ConvexHullTriangle

Bases: pybind11_builtins.pybind11_object

A triangle of the convex hull mesh. It contains its three vertices as well as its normal (i.e. the normal unit vector pointing outwards).

area(self: baggianalysis.core.ConvexHullTriangle)float

Return the area of the triangle.

property normal

The unit vector orthogonal to the triangle surface which points towards the exterior of convex hull.

property v1

The first vertex.

property v2

The second vertex along the counter-clock-wise contour of the triangle.

property v3

The second vertex along the counter-clock-wise contour of the triangle.

volume(self: baggianalysis.core.ConvexHullTriangle)float

Return the volume of the triangle.

class baggianalysis.core.FormFactor(self: baggianalysis.core.FormFactor, arg0: List[float], arg1: int, arg2: bool)None

Bases: pybind11_builtins.pybind11_object

analyse_particle_set(self: baggianalysis.core.FormFactor, arg0: baggianalysis.core.ParticleSet)None
analyse_system(self: baggianalysis.core.FormFactor, arg0: baggianalysis.core.System)None
analyse_trajectory(self: baggianalysis.core.FormFactor, arg0: baggianalysis.core.BaseTrajectory)None
reset(self: baggianalysis.core.FormFactor)None
result(self: baggianalysis.core.FormFactor) → Dict[float, float]
class baggianalysis.core.PoreSize(self: baggianalysis.core.PoreSize, N_attempts: int, r_cut: float = 1.0, particle_radius: float = 0.5, max_time: float = 1.0)None

Bases: pybind11_builtins.pybind11_object

analyse_system(self: baggianalysis.core.PoreSize, arg0: baggianalysis.core.System)None
analyse_trajectory(self: baggianalysis.core.PoreSize, arg0: baggianalysis.core.BaseTrajectory)None
radius(self: baggianalysis.core.PoreSize, arg0: glm::tvec3<scalar, P>)float
reset(self: baggianalysis.core.PoreSize)None
result(self: baggianalysis.core.PoreSize) → List[float]
class baggianalysis.core.MSD(self: baggianalysis.core.MSD, arg0: int, arg1: bool)None

Bases: pybind11_builtins.pybind11_object

Compute the mean-squared displacement of a system.

analyse_and_print(self: baggianalysis.core.MSD, trajectory: baggianalysis.core.BaseTrajectory, output_file: str)None

Analyse the trajectory and print the MSD directly to the given file.

analyse_trajectory(self: baggianalysis.core.MSD, arg0: baggianalysis.core.BaseTrajectory)None
reset(self: baggianalysis.core.MSD)None
result(self: baggianalysis.core.MSD) → Dict[int, float]
class baggianalysis.core.RDF(*args, **kwargs)

Bases: pybind11_builtins.pybind11_object

Compute the radial distribution function of a system.

Overloaded function.

  1. __init__(self: baggianalysis.core.RDF, arg0: float, arg1: List[str], arg2: List[str]) -> None

  2. __init__(self: baggianalysis.core.RDF, arg0: float) -> None

  3. __init__(self: baggianalysis.core.RDF, arg0: float, arg1: float) -> None

  4. __init__(self: baggianalysis.core.RDF, arg0: float, arg1: float, arg2: List[str], arg3: List[str]) -> None

analyse_system(self: baggianalysis.core.RDF, arg0: baggianalysis.core.System)None
analyse_trajectory(self: baggianalysis.core.RDF, arg0: baggianalysis.core.BaseTrajectory)None
reset(self: baggianalysis.core.RDF)None
result(self: baggianalysis.core.RDF) → Dict[float, float]
class baggianalysis.core.StructureFactor(self: baggianalysis.core.StructureFactor, arg0: float, arg1: int, arg2: float)None

Bases: pybind11_builtins.pybind11_object

Compute the structure factor of a system.

analyse_system(self: baggianalysis.core.StructureFactor, arg0: baggianalysis.core.System)None
analyse_trajectory(self: baggianalysis.core.StructureFactor, arg0: baggianalysis.core.BaseTrajectory)None
clear_b_factors(self: baggianalysis.core.StructureFactor)None

Reset the b-factors to their default values (b = 1 for each particle).

destructured_from_system(self: baggianalysis.core.StructureFactor, system: baggianalysis.core.System)baggianalysis.core.DestructuredStructureFactor

Compute and return the single-particle contributions (splitted as cosine and sine contributions stored in a DestructuredStructureFactor instance) that make up the structure factor.

Parameters

system (System) – The input system.

Returns

The final result of the computation.

Return type

DestructuredStructureFactor

reset(self: baggianalysis.core.StructureFactor)None
result(self: baggianalysis.core.StructureFactor) → Dict[float, float]
set_b_factors(self: baggianalysis.core.StructureFactor, b_factors: List[float])None

Set the particles’ b-factors (that is, the scattering amplitudes) that will be used to compute the structure factor.

Parameters

b_factors (List(float)) – The vector of b-factors to be used in the calculation of the S(q). The length of the vector should be equal to the number of particles in the system.

class baggianalysis.core.DestructuredStructureFactor(self: baggianalysis.core.DestructuredStructureFactor)None

Bases: pybind11_builtins.pybind11_object

property cos_contribs
property q_modules
property sin_contribs