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 everytime 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
Get the net charges of cubic subvolumes. |