lammpsio.Angles¶

class lammpsio.Angles(N, num_types=None)¶

Angle connections between particles.

All values of indexes follow the LAMMPS 1-indexed convention, but the arrays themselves are 0-indexed.

Parameters:

N (int) – Number of angles.
num_types (int) – Number of angle types. Default of None means the number of types is determined from the unique typeids.

Example

Create angles:

angles = lammpsio.topology.Angles(N=3, num_types=1)
angles.id = [1, 2, 3]
angles.typeid = [1, 1, 1]
angles.members = [[1, 2, 3], [2, 3, 1], [3, 1, 2]]

This creates a molecule with three angles of the same type. The angles are defined between particles IDs 1-2-3, 2-3-1, and 3-1-2 to form a triangle structure.

Methods:

`has_id`()	Check if configuration has connection IDs.
`has_members`()	Check if configuration has connection members.
`has_typeid`()	Check if configuration has connection typeids.
`reorder`(order[, check_order])	Reorder the connections in place.

Attributes:

`N`	Number of connections.
`id`	Unique identifiers (IDs).
`members`	Connection members.
`num_types`	Number of connection types.
`type_label`	Labels of connection type IDs.
`typeid`	Connection type IDs.

property N¶

Number of connections.

Type:: int

has_id()¶

Check if configuration has connection IDs.

Returns:: True if connection IDs have been initialized.
Return type:: bool

has_members()¶

Check if configuration has connection members.

Returns:: True if particle members have been initialized.
Return type:: bool

has_typeid()¶

Check if configuration has connection typeids.

Returns:: True if connection typeids have been initialized.
Return type:: bool

property id¶

Unique identifiers (IDs).

The default value on initialization runs from 1 to N.

Type:: (N,) numpy.ndarray of int

property members¶

Connection members.

The default value on initialization is 1 for all entries. M is the number of members in the connection.

Type:: (N, M) numpy.ndarray of int

property num_types¶

Number of connection types.

Type:: int

reorder(order, check_order=True)¶

Reorder the connections in place.

Parameters:

order (list) – New order of indexes.
check_order (bool) – If True, validate the new order before applying it.

property type_label¶

Labels of connection type IDs.

Type:: LabelMap

property typeid¶

Connection type IDs.

The default value on initialization is 1 for all entries.

Type:: (N,) numpy.ndarray of int