# Types of atoms, and alchemical potentials.

### This page gives hints on how to specify the types of atoms that form the system with the ABINIT package.

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

Mentioned in topic_PseudosPAW, topic_crystal, help_features#2.1.

### Table of content:

- 1. Introduction.
- 2. Related lesson(s) of the tutorial.
- 3. Related input variables.
- 4. Selected input files.

### 1. Introduction.

ABINIT needs to know the different types of atoms that form the system.

The atoms assembled in a molecule or a solid are physically specified by their nuclear charge (and their mass for dynamical properties).

However, in a pseudopotential or PAW approach, the knowledge of the nuclear charge does not define the potential felt by the electron, only the atomic data file (pseudopotential or PAW) defines it. Thus, in addition to the number of types of atoms ntypat, and their nuclear charge znucl, ABINIT requires to know the pseudopotential/PAW to use for each type of atom. The latters are specified in the "files" file. Unless alchemical potentials are used (see later), the number of pseudopotentials to be read, npsp, is the same as ntypat. Note that one cannot mix norm-conserving pseudopotentials with PAW atomic data files in a single ABINIT run, even for different datasets. One has to stick either to norm-conserving pseudopotentials or to PAW.
More on the pseudos/PAW in PseudosPAW.

ABINIT also has a default table of the atomic masses, but this can be superceded by specifying amu.

Alchemical potentials

For norm-conserving pseudopotentials, ABINIT can mix the pseudopotentials, as described in the ABINIT wiki, to create so-called "alchemical potentials", see mixalch.
In this case, the number of pseudopotentials to be given, npsp, will usually be larger than the number of types of atoms, ntypat. Using alchemical potentials makes sense to treat alloys in which similar ions are present, and whose specific chemical properties are not crucial for the property of interest. Usually it is done only for isovalent species, and ions of quite similar radii. It is a reasonable interpolation technique for the electronic properties.
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### 2. Related lesson(s) of the tutorial.

- Lesson on polarization and finite electric fields. Polarization, and responses to finite electric fields for AlAs. In the present topic, it is an example of the definition of several atom types ...
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### 3. Related input variables.

Compulsory input variables:

... ntypat [Number of TYPes of AToms]
... znucl [charge -Z- of the NUCLeus]

Basic input variables:

... amu [Atomic Mass Units]
... typat [TYPe of AToms]

Useful input variables:

... mixalch [MIXing coefficients for ALCHemical potentials]
... npsp [Number of PSeudoPotentials]
... ntypalch [Number of TYPe of atoms that are "ALCHemical"]

Relevant internal variables:

... %npspalch [Number of PSeudoPotentials that are "ALCHemical"]
... %ntyppure [Number of TYPe of atoms that are "PURe"]
... %ziontypat [Z (charge) of the IONs for the different TYPes of AToms]

Input variables for experts:

... algalch [ALGorithm for generating ALCHemical pseudopotentials]
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### 4. 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/v3/Input: t92.in t93.in t94.in t95.in t96.in t97.in

tests/v5/Input: t44.in

tests/v6/Input: t28.in
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