Modify cell size

Description

This function modifies the cell size of the system. The cell size can either be changed by setting a specific value (set_values ) or by increasing the existing size by a specified amount (increase_values). Additionally, it allows for repositioning the atoms by selecting an origin point and a target point. The repositioning is done without considering periodic boundary conditions (PBCs), so the applied translation may result in some atoms being placed outside the cell.

Latest version

Allowed number of parents: 1

Parameter Description Value type Value restrictions Default value Units

Parameter	Description	Value type	Value restrictions	Default value	Units
Mode to modify the cell size	The cell size can be either changed by setting a specific value or by taking the existing size and adding something	selector	set_values, increase_values	set_values	N/A
Set the cell size	It allows to adjust the cell to the largest and smaller value of the atomic positions in a given axis, to select manually the length of the side of the cell or to keep the original size of a given side of the cell. Available only for `set_values` mode.	selector	set to system size (max-min), manual value selection, keep original size	keep original size	Angstrom
Increase or decrease the cell size	Increase or decrease the cell size. Available only for `increase_values` mode.	float	any float	[0.0, 0.0, 0.0]	Angstrom
Reposition system	Whether to reposition the system within the new cell or not	boolean	True, False	False	N/A
Target point for the repositioning	The target point for the repositioning. Values refer to the NEW simulation box. If “value” is selected, a sub-value where to enter the position in angstrom is activated.	selector	“min”, “max”, “center”, “value”	[min, min, min]	Angstrom
Origin point for the repositioning	The reference point used to decide the repositioning of the system: defines which part of the system is the origin point for the translation vector. All values are referring to the selected atoms for the origin point (see next inputs).	selector	“min”, “max”, “geocen”	[min, min, min]	N/A
Selection for origin point: component name	The component name of the atoms in the group used to determine the origin point. Only needed when the translation mode is “origin-target”.	selector_component	component types, “all”	“all”	N/A
Selection for origin point: atom kind	The atom kind of the atoms in the group used to determine the origin point. Only needed when the translation mode is “origin-target”.	selector_atom_type	atom types, “all”	“all”	N/A
Selection for origin point: atom name	The atom name of the atoms in the group used to determine the origin point. Only needed when the translation mode is “origin-target”.	selector_atom_name	atom names, “all”	“all”	N/A

Mode to modify the cell size

The cell size can be either changed by setting a specific value or by taking the existing size and adding something

selector

set_values, increase_values

set_values

N/A

Set the cell size

It allows to adjust the cell to the largest and smaller value of the atomic positions in a given axis, to select manually the length of the side of the cell or to keep the original size of a given side of the cell. Available only for set_values mode.

selector

set to system size (max-min), manual value selection, keep original size

keep original size

Angstrom

Increase or decrease the cell size

Increase or decrease the cell size. Available only for increase_values mode.

float

any float

[0.0, 0.0, 0.0]

Angstrom

Reposition system

Whether to reposition the system within the new cell or not

boolean

True, False

False

N/A

Target point for the repositioning

The target point for the repositioning. Values refer to the NEW simulation box. If “value” is selected, a sub-value where to enter the position in angstrom is activated.

selector

“min”, “max”, “center”, “value”

[min, min, min]

Angstrom

Origin point for the repositioning

The reference point used to decide the repositioning of the system: defines which part of the system is the origin point for the translation vector. All values are referring to the selected atoms for the origin point (see next inputs).

selector

“min”, “max”, “geocen”

[min, min, min]

N/A

Selection for origin point: component name

The component name of the atoms in the group used to determine the origin point. Only needed when the translation mode is “origin-target”.

selector_component

component types, “all”

“all”

N/A

Selection for origin point: atom kind

The atom kind of the atoms in the group used to determine the origin point. Only needed when the translation mode is “origin-target”.

selector_atom_type

atom types, “all”

“all”

N/A

Selection for origin point: atom name

The atom name of the atoms in the group used to determine the origin point. Only needed when the translation mode is “origin-target”.

selector_atom_name

atom names, “all”

“all”

N/A