Observables¶
Partition particles into clusters and return their size. |
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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. |
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Compute the radial distribution function of a system. |
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Compute the structure factor of a system. |
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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
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analyse_system
(self: baggianalysis.core.BondOrderParameters, arg0: baggianalysis.core.System) → None¶
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analyse_trajectory
(self: baggianalysis.core.BondOrderParameters, arg0: baggianalysis.core.BaseTrajectory) → None¶
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reset
(self: baggianalysis.core.BondOrderParameters) → None¶
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result
(self: baggianalysis.core.BondOrderParameters) → List[List[float]]¶
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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
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analyse_system
(self: baggianalysis.core.ClusterList, arg0: baggianalysis.core.System) → None¶
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analyse_trajectory
(self: baggianalysis.core.ClusterList, arg0: baggianalysis.core.BaseTrajectory) → None¶
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property
clusters
¶ Return the list of clusters of the system analysed last.
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reset
(self: baggianalysis.core.ClusterList) → None¶
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result
(self: baggianalysis.core.ClusterList) → List[int]¶
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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.
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analyse_system
(self: baggianalysis.core.ConvexHull, arg0: baggianalysis.core.System) → None¶
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analyse_trajectory
(self: baggianalysis.core.ConvexHull, arg0: baggianalysis.core.BaseTrajectory) → None¶
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reset
(self: baggianalysis.core.ConvexHull) → None¶
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result
(self: baggianalysis.core.ConvexHull) → ba::ConvexHullResult¶
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class
baggianalysis.core.
ConvexHullResult
(self: baggianalysis.core.ConvexHullResult) → None¶ Bases:
pybind11_builtins.pybind11_object
The actual convex hull.
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property
area
¶ The area of the convex hull.
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property
vertices
¶ The vertices that compose the convex hull. These are a subset of the particles of the system.
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property
volume
¶ The volume of the convex hull.
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property
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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).
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area
(self: baggianalysis.core.ConvexHullTriangle) → float¶ Return the area of the triangle.
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property
normal
¶ The unit vector orthogonal to the triangle surface which points towards the exterior of convex hull.
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property
v1
¶ The first vertex.
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property
v2
¶ The second vertex along the counter-clock-wise contour of the triangle.
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property
v3
¶ The second vertex along the counter-clock-wise contour of the triangle.
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volume
(self: baggianalysis.core.ConvexHullTriangle) → float¶ Return the volume of the triangle.
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class
baggianalysis.core.
FormFactor
(self: baggianalysis.core.FormFactor, arg0: List[float], arg1: int, arg2: bool) → None¶ Bases:
pybind11_builtins.pybind11_object
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analyse_particle_set
(self: baggianalysis.core.FormFactor, arg0: baggianalysis.core.ParticleSet) → None¶
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analyse_system
(self: baggianalysis.core.FormFactor, arg0: baggianalysis.core.System) → None¶
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analyse_trajectory
(self: baggianalysis.core.FormFactor, arg0: baggianalysis.core.BaseTrajectory) → None¶
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reset
(self: baggianalysis.core.FormFactor) → None¶
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result
(self: baggianalysis.core.FormFactor) → Dict[float, float]¶
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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
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analyse_system
(self: baggianalysis.core.PoreSize, arg0: baggianalysis.core.System) → None¶
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analyse_trajectory
(self: baggianalysis.core.PoreSize, arg0: baggianalysis.core.BaseTrajectory) → None¶
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reset
(self: baggianalysis.core.PoreSize) → None¶
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result
(self: baggianalysis.core.PoreSize) → List[float]¶
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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.
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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.
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analyse_trajectory
(self: baggianalysis.core.MSD, arg0: baggianalysis.core.BaseTrajectory) → None¶
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reset
(self: baggianalysis.core.MSD) → None¶
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result
(self: baggianalysis.core.MSD) → Dict[int, float]¶
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class
baggianalysis.core.
RDF
(*args, **kwargs)¶ Bases:
pybind11_builtins.pybind11_object
Compute the radial distribution function of a system.
Overloaded function.
__init__(self: baggianalysis.core.RDF, arg0: float, arg1: List[str], arg2: List[str]) -> None
__init__(self: baggianalysis.core.RDF, arg0: float) -> None
__init__(self: baggianalysis.core.RDF, arg0: float, arg1: float) -> None
__init__(self: baggianalysis.core.RDF, arg0: float, arg1: float, arg2: List[str], arg3: List[str]) -> None
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analyse_system
(self: baggianalysis.core.RDF, arg0: baggianalysis.core.System) → None¶
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analyse_trajectory
(self: baggianalysis.core.RDF, arg0: baggianalysis.core.BaseTrajectory) → None¶
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reset
(self: baggianalysis.core.RDF) → None¶
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result
(self: baggianalysis.core.RDF) → Dict[float, float]¶
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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.
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analyse_system
(self: baggianalysis.core.StructureFactor, arg0: baggianalysis.core.System) → None¶
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analyse_trajectory
(self: baggianalysis.core.StructureFactor, arg0: baggianalysis.core.BaseTrajectory) → None¶
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clear_b_factors
(self: baggianalysis.core.StructureFactor) → None¶ Reset the b-factors to their default values (b = 1 for each particle).
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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
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reset
(self: baggianalysis.core.StructureFactor) → None¶
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result
(self: baggianalysis.core.StructureFactor) → Dict[float, float]¶
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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.
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