# Atom manipulator

### This page gives hints on how to manipulate atoms and groups of atoms to generate the set of atomic positions with the ABINIT package.

##### Copyright (C) 2016-2017 ABINIT group (FJ)

Mentioned in topic_crystal, help_features#2.1.

### Table of content:

- 1. Introduction.
- 2. Related input variables.
- 3. Selected input files.

### 1. Introduction.

ABINIT has some (non-graphical) capabilities to manipulate atoms and group of atoms, to help establishing the set of atomic positions in the input file when big cells are considered.

Explicitly, one or two groups of atoms, forming e.g. a molecule, a cluster, or a small primitive cell, can be repeated in arbitrary number, then translated and rotated. Then, atoms can be removed, to form e.g. vacancies. See nobj as entry point.

The related input variables being used for preprocessing of the input file, they are not echoed in the output file (INPUT_ONLY characteristics).
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### 2. Related input variables.

Compulsory input variables:

... nobj [Number of OBJects]

Basic input variables:

... natrd [Number of AToms ReaD]
... objaat [OBJect A : list of AToms]
... objan [OBJect A : Number of atoms]
... objarf [OBJect A : Repetition Factors]

Useful input variables:

... objaax [OBJect A : AXis]
... objaro [OBJect A : ROtations]
... objatr [OBJect A : TRanslations]
... objbat [OBJect B : list of AToms]
... objbax [OBJect B : AXis]
... objbn [OBJect B : Number of atoms]
... objbrf [OBJect B : Repetition Factors]
... objbro [OBJect B : ROtations]
... objbtr [OBJect B : TRanslations]
... vaclst [VACancies LiST]
... vacnum [VACancies NUMber]
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### 3. Selected input files.

WARNING : as of ABINITv8.6.x, the list of input files provided in the specific section of the topics Web pages is still to be reviewed/tuned. In some cases, it will be adequate, and in other cases, it might be incomplete, or perhaps even useless.
The user can find some related example input files in the ABINIT package in the directory /tests, or on the Web:

tests/v1/Input: t40.in t42.in t43.in
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