subvolume_charge

Calculate the net charge of cubic subvolumes of the simulation box.

Divide the simulation box into as many cubic subvolumes of the given cube lengths as possible and calculate the net charge of all Atoms inside these subvolumes.

Options

-f

Trajectory file. See supported coordinate formats of MDAnalysis.

-s

Topology file. See supported topology formats of MDAnalysis.

-o

Output filename.

-b

First frame to read from the trajectory. Frame numbering starts at zero. Default: 0.

-e

Last frame to read from the trajectory. This is exclusive, i.e. the last frame read is actually END - 1. A value of -1 means to read the very last frame. Default: -1.

--every

Read every n-th frame from the trajectory. Default: 1.

--sel

Selection string to select a group of atoms for the analysis. See MDAnalysis’ selection syntax for possible choices. Default: 'all'.

--updating-sel

Use an UpdatingAtomGroup for the analysis. Selection expressions of UpdatingAtomGroups are re-evaluated every time step. This is e.g. useful for position-based selections like 'type Li and prop z <= 2.0'.

--bin-start

First cube length to use (in Angstrom). If set to None, --bin-start is set to --bin-step. Default: None.

--bin-stop

Last cube length to use (in Angstrom). If set to None, go up to the minimum box length for each frame. Default: None.

--bin-step

Increment the cube length by this amount (in Angstrom). Default: 1.0.

Notes

Works only with orthogonal simulation boxes.

Functions

net_charge_of_cubes

Get the net charges of cubic subvolumes.