Translate

Description

This function moves one or more components of a system by applying a translation vector.

The function allows you to adjust the coordinates of one or more components of a system (chosen via Component to translate) by a vector V. The vector V can be specified in two ways, selected via the Translation mode input:

vector mode: Specify the x, y, and z components of the vector in angstroms.
origin-target mode: Define an origin and a target, and V will be internally calculated as target minus origin. The target point can be set as the min, max, or center of the simulation cell, or defined by an explicit vector. The origin can be defined as the geometric center, min, or max of a set of selected atoms (using Selection for origin point).

If periodic boundary conditions (PBCs) are enabled, the geometric center of each component is moved within the cell. Note that no automatic checks are performed to ensure that atoms do not end up too close to one another. Therefore, if not all components are translated, it is the user’s responsibility to ensure that the translation does not cause atoms to come too close to others.

Latest version

Allowed number of parents: 1

Parameter	Description	Value type	Value restrictions	Default value	Units
Component to translate	The component name that shall be translated.	selector_component	component types, “all”	“all”	N/A
Translation mode	The way by which the system shall be translated: either by a given vector, or by specifying origin and target.	selector	“vector”, “origin-target”	“vector”	N/A
Translation vector	The translation vector. Only needs to be specified if the translation mode is set to “vector”.	float	any float	[0, 0, 0]	Angstrom
Target point for the translation	Target point for the translation vector. Only needed when the translation mode is “origin-target”. All values refer to the 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”]	N/A
Origin point for the translation	Origin point for the translation vector. Only needed when the translation mode is “origin-target”. This point will be in the target point at the end of the translation. 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
Apply periodic boundary conditions	Indicates whether we apply periodic boundary conditions (in x, y and z)after the translation, i.e. whether the atoms shall be moved back to the cell if they lie outside.	boolean	True, False	[True, True, True]	N/A

Parameter

Description

Value type

Value restrictions

Default value

Units

Component to translate

The component name that shall be translated.

selector_component

component types, “all”

“all”

N/A

Translation mode

The way by which the system shall be translated: either by a given vector, or by specifying origin and target.

selector

“vector”, “origin-target”

“vector”

N/A

Translation vector

The translation vector. Only needs to be specified if the translation mode is set to “vector”.

float

any float

[0, 0, 0]

Angstrom

Target point for the translation

Target point for the translation vector. Only needed when the translation mode is “origin-target”. All values refer to the 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”]

N/A

Origin point for the translation

Origin point for the translation vector. Only needed when the translation mode is “origin-target”. This point will be in the target point at the end of the translation. 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

Apply periodic boundary conditions

Indicates whether we apply periodic boundary conditions (in x, y and z)after the translation, i.e. whether the atoms shall be moved back to the cell if they lie outside.

boolean

True, False

[True, True, True]

N/A