Particle-related classes¶

`Particle`	A simulation particle.
`ParticleBond`	A bond between two particles.
`ParticleAngle`	A bond involving three particles.
`ParticleDihedral`	A bond involving four particles.
`ParticleSet`	A set of particles.
`System`	A single configuration.

class baggianalysis.core.Particle(*args, **kwargs)¶

Bases: pybind11_builtins.pybind11_object

A simulation particle.

Overloaded function.

__init__(self: baggianalysis.core.Particle, index: int) -> None

Build a new particle by specifying its index.

Parameters: index (int) – The index of the particle. Note that this value cannot be changed later on.

__init__(self: baggianalysis.core.Particle, index: int, type: str) -> None

Build a new particle by specifying its index and type.

Parameters

index (int) – The index of the particle. Note that this value cannot be changed later on.
type (str) – The type of the particle.
type –

__init__(self: baggianalysis.core.Particle, index: int, type: str, position: glm::tvec3<scalar, P>) -> None

Build a new particle by specifying its index, type and position.

Parameters

index (int) – The index of the particle. Note that this value cannot be changed later on.
type (str) – The type of the particle.
position (numpy.ndarray) – The position of the particle

__init__(self: baggianalysis.core.Particle, index: int, type: str, position: glm::tvec3<scalar, P>, velocity: glm::tvec3<scalar, P>) -> None

Build a new particle by specifying its index, type, position and velocity.

Parameters

index (int) – The index of the particle. Note that this value cannot be changed later on.
type (str) – The type of the particle.
position (numpy.ndarray) – The position of the particle.
velocity (numpy.ndarray) – The velocity of the particle.

add_bonded_angle(*args, **kwargs)¶

Overloaded function.

add_bonded_angle(self: baggianalysis.core.Particle, type: str, p1: baggianalysis.core.Particle, p2: baggianalysis.core.Particle, p3: baggianalysis.core.Particle) -> None

Add an angle of the given type (defined by three particles) this particle is involved in. Note that the current particle must be one of the three particles given as parameters.

Parameters

type (str) – The type of the angle.
p1 (Particle) – The first particle participating in the angle.
p2 (Particle) – The second particle participating in the angle.
p3 (Particle) – The third particle participating in the angle.

add_bonded_angle(self: baggianalysis.core.Particle, p1: baggianalysis.core.Particle, p2: baggianalysis.core.Particle, p3: baggianalysis.core.Particle) -> None

Add an angle of the default type (defined by three particles) this particle is involved in. Note that the current particle must be one of the three particles given as parameters.

Parameters

p1 (Particle) – The first particle participating in the angle.
p2 (Particle) – The second particle participating in the angle.
p3 (Particle) – The third particle participating in the angle.

add_bonded_dihedral(*args, **kwargs)¶

Overloaded function.

add_bonded_dihedral(self: baggianalysis.core.Particle, type: str, p1: baggianalysis.core.Particle, p2: baggianalysis.core.Particle, p3: baggianalysis.core.Particle, p4: baggianalysis.core.Particle) -> None

Add a dihedral of the given type (defined by four particles) this particle is involved in. Note that the current particle must be one of the four particles given as parameters.

Parameters

type (str) – The type of the dihedral.
p1 (Particle) – The first particle participating in the dihedral.
p2 (Particle) – The second particle participating in the dihedral.
p3 (Particle) – The third particle participating in the dihedral.
p4 (Particle) – The fourth particle participating in the dihedral.

add_bonded_dihedral(self: baggianalysis.core.Particle, p1: baggianalysis.core.Particle, p2: baggianalysis.core.Particle, p3: baggianalysis.core.Particle, p4: baggianalysis.core.Particle) -> None

Add a dihedral of the default type (defined by four particles) this particle is involved in. Note that the current particle must be one of the four particles given as parameters.

Parameters

p1 (Particle) – The first particle participating in the dihedral.
p2 (Particle) – The second particle participating in the dihedral.
p3 (Particle) – The third particle participating in the dihedral.
p4 (Particle) – The fourth particle participating in the dihedral.

add_bonded_neighbour(*args, **kwargs)¶

Overloaded function.

add_bonded_neighbour(self: baggianalysis.core.Particle, type: str, q: baggianalysis.core.Particle) -> None

Add a bond of the given type between the current particle and q.

Parameters

type (str) – The type of bond shared by the two particles.
q (Particle) – The new bonded neighbour.

add_bonded_neighbour(self: baggianalysis.core.Particle, q: baggianalysis.core.Particle) -> None

Add a bond of the default type between the current particle and q.

Parameters: q (Particle) – The new bonded neighbour.

add_neighbour(*args, **kwargs)¶

Overloaded function.

add_neighbour(self: baggianalysis.core.Particle, type: str, q: baggianalysis.core.Particle) -> None

Add particle q as a bond of the given type to the list of this particle’s neighbours. Contrary to add_bonded_neighbour(), the current particle is not added to the list of q’s neighbours.

Parameters

type (str) – The type of bond shared by the two particles.
q (Particle) – The new neighbour.

add_neighbour(self: baggianalysis.core.Particle, q: baggianalysis.core.Particle) -> None

Add particle q as a bond of the default type to the list of this particle’s neighbours. Contrary to add_bonded_neighbour(), the current particle is not added to the list of q’s neighbours.

Parameters: q (Particle) – The new neighbour.

add_orientation_vector(self: baggianalysis.core.Particle, v: glm::tvec3<scalar, P>) → None ¶

The molecule to which this particle belongs.

Parameters: v (numpy.ndarray) – The new orientation vector.

property angular_velocity¶

The particle’s angular velocity.

Type: numpy.ndarray

property bonded_angles¶

A list of ParticleAngle s storing the angles (i.e. triplets of particles) this particle is involved in.

Type: Set(ParticleAngle)

property bonded_dihedrals¶

A list of ParticleDihedral s storing the dihedrals (i.e. list of four particles) this particle is involved in.

Type: Set(ParticleDihedral)

property bonded_neighbours¶

A list of this particle’s bonded neighbours.

Type: Set(ParticleBond)

property charge¶

The particle’s charge.

Type: float

has_bonded_neighbour(self: baggianalysis.core.Particle, q: baggianalysis.core.Particle) → bool ¶

Check whether q is a bonded neighbour.

Parameters: q (Particle) – Another particle.
Returns: True if q is a bonded neighbour, False otherwise.
Return type: bool

has_neighbour(self: baggianalysis.core.Particle, q: baggianalysis.core.Particle) → bool ¶

Check whether q is a neighbour.

Parameters: q (Particle) – Another particle.
Returns: True if q is a neighbour, False otherwise.
Return type: bool

property index¶

The particle’s index. This is a read-only property because changing the index of the particle should be done with the methods provided by ParticleSet and System only.

type

int

make_copy(self: baggianalysis.core.Particle, index: int) → baggianalysis.core.Particle ¶

Return a copy of this particle with the given index. Note that neighbours and bonded neighbours, angles and dihedrals are not copied.

Parameters: index (int) – The index of the new particle.

property mass¶

The particle’s mass.

Type: float

property molecule¶

The molecule to which this particle belongs.

Type: ParticleSet

property neighbours¶

A list of this particle’s neighbours.

Type: Set(ParticleBond)

property orientation_vectors¶

A list of vectors related to the particle’s orientation. Depending on the specific model it may contain the list of interaction centres or the components of the orientation matrix.

type

List(numpy.ndarray)

property position¶

The particle’s position.

Type: numpy.ndarray

remove_bonded_neighbour(*args, **kwargs)¶

Overloaded function.

remove_bonded_neighbour(self: baggianalysis.core.Particle, link: baggianalysis.core.ParticleBond) -> None

Remove the given ParticleBond from the list of current particle’s bonds.

Parameters: link (ParticleBond) – The bond that should be removed.

remove_bonded_neighbour(self: baggianalysis.core.Particle, q: baggianalysis.core.Particle) -> None

Remove q from the list of current particle’s bonded neighbours.

Parameters: q (Particle) – The particle whose bond with the current particle should be removed.

remove_neighbour(*args, **kwargs)¶

Overloaded function.

remove_neighbour(self: baggianalysis.core.Particle, link: baggianalysis.core.ParticleBond) -> None

Remove the given ParticleBond from the list of this particle’s neighbours.

Parameters: link (ParticleBond) – The link that should be removed.

remove_neighbour(self: baggianalysis.core.Particle, q: baggianalysis.core.Particle) -> None

Remove q from the list of this particle’s neighbours.

Parameters: q (Particle) – The particle that should be removed from the list of neighbous.

shift(self: baggianalysis.core.Particle, delta: glm::tvec3<scalar, P>) → None ¶

Add delta to the particle coordinates.

Parameters: delta (numpy.ndarray) – The shift to be added to the particle’s coordinates.

property type¶

The particle’s type.

Type: string

property velocity¶

The particle’s velocity.

Type: numpy.ndarray

class baggianalysis.core.ParticleBond¶

Bases: pybind11_builtins.pybind11_object

A bond between two particles.

other(self: baggianalysis.core.ParticleBond) → ba::Particle¶: The other particle involved in the bond.

class baggianalysis.core.ParticleAngle¶

Bases: pybind11_builtins.pybind11_object

A bond involving three particles.

class baggianalysis.core.ParticleDihedral¶

Bases: pybind11_builtins.pybind11_object

A bond involving four particles.

class baggianalysis.core.ParticleSet(self: baggianalysis.core.ParticleSet) → None ¶

Bases: pybind11_builtins.pybind11_object

A set of particles.

The constructor takes no parameters.

N(self: baggianalysis.core.ParticleSet) → int ¶: The number of particles stored in the set.

add_particle(self: baggianalysis.core.ParticleSet, p: baggianalysis.core.Particle) → None ¶

Add p to the set.

Parameters: p (Particle) – The particle to be added to the set.

charge(self: baggianalysis.core.ParticleSet) → float ¶: The total charge stored in the set

charges(self: baggianalysis.core.ParticleSet) → List[float]¶

Return a vector containing the charge of all the particles.

The vector is created ex novo every time this method is called. Do not use in performance-critical scenarios (or cache the result).

com(self: baggianalysis.core.ParticleSet) → glm::tvec3<scalar, P>¶: The centre of mass of the set

id_exists(self: baggianalysis.core.ParticleSet, p_idx: int) → bool ¶

Check whether a particle with the given index is stored in the set.

Parameters: p_idx (int) – The index to be checked.
Returns: True if the particle is stored in the set, False otherwise.
Return type: bool

indexes(self: baggianalysis.core.ParticleSet) → List[int]¶

Return a vector containing the index of all the particles.

The vector is created ex novo every time this method is called. Do not use in performance-critical scenarios (or cache the result).

make_copy(self: baggianalysis.core.ParticleSet, indexes_shift: int) → baggianalysis.core.ParticleSet ¶

Make a copy of the set and of the particles therein, shifting all the particle indexes by the given value.

Parameters: indexes_shift (int) – The shift to be added to the index of each particle.

mass(self: baggianalysis.core.ParticleSet) → float ¶: The total mass stored in the set

masses(self: baggianalysis.core.ParticleSet) → List[float]¶

Return a vector containing the mass of all the particles.

The vector is created ex novo every time this method is called. Do not use in performance-critical scenarios (or cache the result).

property name¶: The name of the object. This can be used to keep track of particular particle sets (e.g. when dealing with System.molecules()).

particle_by_id(self: baggianalysis.core.ParticleSet, p_idx: int) → baggianalysis.core.Particle ¶

Retrieve the particle with the given index.

Parameters: p_idx (int) – The index of the particle to be retrieved.
Returns: The particle with the given index.
Return type: Particle

particles(self: baggianalysis.core.ParticleSet) → List[baggianalysis.core.Particle]¶: The list of particles stored in the set

positions(self: baggianalysis.core.ParticleSet) → List[glm::tvec3<scalar, P>]¶

Return a vector containing the position of all the particles.

The vector is created ex novo every time this method is called. Do not use in performance-critical scenarios (or cache the result).

remove_particle(self: baggianalysis.core.ParticleSet, p: baggianalysis.core.Particle) → None ¶

Remove p from the set.

Parameters: p (Particle) – The particle to be removed from the set.

remove_particle_by_id(self: baggianalysis.core.ParticleSet, p_id: int) → None ¶

Remove the particle with given index from the set.

Parameters: p_idx (int) – The index of the particle to be removed from the set.

select(self: baggianalysis.core.ParticleSet, predicate: Callable[[baggianalysis.core.Particle], bool]) → List[baggianalysis.core.Particle]¶

Return all those particles for which the given predicate evaluates to True.

Here is an example that creates a list of particles having a non-negative position along the x axis:

selected = system.select(lambda p: p.position[0] > 0)

Note that the returned list contains references to and not copies of the particles stored in this set.

Parameters: predicate (callable) – A callable that takes a particle and returns True if the particle should be returned, False otherwise.
Returns: The list of particles for which the predicate evaluates to True.
Return type: List(Particle)

set_com(self: baggianalysis.core.ParticleSet, new_com: glm::tvec3<scalar, P>) → None ¶

Set the centre of mass of the set to a new value.

Parameters: new_com (numpy.ndarray) – The new centre of mass of the set.

sort_particles_by_id(self: baggianalysis.core.ParticleSet) → None ¶: Sort the particles according to their index

types(self: baggianalysis.core.ParticleSet) → List[str]¶

Return a vector containing the type of all the particles.

The vector is created ex novo every time this method is called. Do not use in performance-critical scenarios (or cache the result).

velocities(self: baggianalysis.core.ParticleSet) → List[glm::tvec3<scalar, P>]¶

Return a vector containing the velocity of all the particles.

The vector is created ex novo every time this method is called. Do not use in performance-critical scenarios (or cache the result).

velocity(self: baggianalysis.core.ParticleSet) → glm::tvec3<scalar, P>¶: The total velocity of the set

class baggianalysis.core.System(*args, **kwargs)¶

Bases: baggianalysis.core.ParticleSet

A single configuration.

Overloaded function.

__init__(self: baggianalysis.core.System) -> None

The default constructor, which takes no arguments.

__init__(self: baggianalysis.core.System, arg0: baggianalysis.core.System) -> None

The copy constructor.

available_index(self: baggianalysis.core.System) → int ¶

Return a particle index that can be used in the context of this system (that is, that is not used by any of the particles already present in the system).

Returns: A number that can be used as a valid index for a new particle.
Return type: int

property box¶

bring_particles_in_box(self: baggianalysis.core.System, shift_by_half_box: bool = False) → None ¶

Bring the particles back into the box.

Parameters: shift_by_half_box (bool) – If False (the default value) particles will have coordinates ranging from 0 to the length of the box side. If True, the coordinates will range between -box/2 and +box/2.

copy_topology_from(self: baggianalysis.core.System, other: baggianalysis.core.System) → None ¶

Copy the topology details (bonds, angles, dihedrals) from another system.

Parameters: other (System) – The system whence the topology should be copied.

empty_copy(self: baggianalysis.core.System) → baggianalysis.core.System ¶

Return a copy of this system (same time and box, no particles).

Returns: A new system with the same time and box of this one.
Return type: System

molecules(self: baggianalysis.core.System) → List[baggianalysis.core.ParticleSet]¶

Return all the molecules contained in the system in the form of a list of ParticleSet.

Returns: The list of molecules contained in the system.
Return type: list(ParticleSet)

normalise_molecules(self: baggianalysis.core.System) → None ¶: Use periodic boundary conditions to shift particle positions so that bonded neighbours are always as close as possible to each other and not separated by distances that are multiple of box sides.

reindex_particles(self: baggianalysis.core.System, base_idx: int) → None ¶

Sort the particles by index and assign them new indexes so that the first and last ones are base_index and base_index + N() - 1, respectively.

Parameters: base_index (int) – The starting index that should be used.

rescale_lengths(self: baggianalysis.core.System, factor: float) → None ¶

Rescale all lengths (positions, velocities, box sides, etc.) by the given factor.

Parameters: factor (float) – The rescaling factor.

property time¶