summonGhosts()

Description

summonGhosts() is a function used to generate the ghosts of the membrane molecules, in order to avoid spurious neighbors in the Voronoi tessellation due to the system geometry and the PBC. Extensive explanations on ghosts are provided in the related tutorial.

During a normal use of ML-LPA, ghosts are automatically generated if needed by the doVoro() function. The function summonGhosts() is only used if one wants to extract the ghosts to study them.

Argument, keywords and outputs

Input(s) / Argument(s)

Name	Flag	Type	Description
Systems		list of classes System	Instances of the System classes containing the molecules to save in a file.
Geometry	geometry=	str	(Opt.) Geometry of the system to perform the tessellations on. Complete list is given in the related tutorial. By default, the geometry is set to a (2D) bilayer.
Exclude Ghosts	exclude_ghosts=	list of int	(Opt.) List of systems indices, provided with the same order than in the argument systems, that should be excluded from ghost generation. Default is None.

Output(s)

Name	Type	Description
Ghosts	np.ndarray	Position array of all the molecule ghosts generated for the Voronoi tessellation.

Examples

Tessellate 1 system with a 2D bilayer geometry

The following example will generate the ghosts using one instance of the System class, system_A, based on the given geometry bilayer and return the ghost positions in the array ghost_array.

import mllpa

ghost_array = mllpa.summonGhosts(system_A, geometry='bilayer')

Tessellate 2 systems with a 2D vesicle geometry and exclude one system from the ghost generation

The following example will generate the ghosts using two instances of the System class, system_A and system_B, based on the given geometry vesicle and return the ghost positions in the array ghost_array. The first system of the list (0), system_A, will be excluded from the lipid ghost generation.

ghost_array = mllpa.summonGhosts([system_A, system_B], geometry='vesicle', exclude_ghosts=[0])