Crystalline structure, atomic positions and symmetries

This page gives hints on how to to specify a crystal, with atomic positions and symmetries with the ABINIT package.

Copyright (C) 2016-2017 ABINIT group (FJ)
Mentioned in   help_features#2.1.

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1. Introduction.

In addition to the Specification of the unit cell and Atom types, ABINIT must know the number of atoms inside the cell, their type, and position. This is described by natom, typat and one of xred, xcart and xangst.

ABINIT can automatically detect the Bravais lattice and space group, and generate symmetries (e.g. nsym,symrel,tnons), from the primitive cell and the position of atoms (provided they are not too inaccurate, see tolsym). For this purpose, in the magnetic case, ABINIT will also take into account the input atomic spin, through the knowledge of spinat.

Alternatively, ABINIT can start from the specification of symmetries (either from spgroup or from the list of symmetries - nsym,symrel,tnons) and generate the atomic positions from the asymmetric (irreducible) part of the primitive cell. This is described in the Smart Symmetrizer topic.

ABINIT can treat antiferromagnetic symmetry operations, see symafm.

In ABINIT, a database with the 230 spatial groups of symmetry (see spgroup) and the 1191 Shubnikov anti-ferromagnetic space groups is present (see also spgroupma and genafm).

There is also a (non-graphical) atom manipulator in ABINIT, see AtomManipulator.

ABINIT can read XYZ files, see xyzfile.

Atomic positions can also be generated at random, see random_atpos.

Details about the way the crystal structure is defined in ABINIT can be found here.

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2. Related lesson(s) of the tutorial.

  • The lesson 1 deals with the H2 molecule : get the total energy, the electronic energies, the charge density, the bond length, the atomisation energy
  • The lesson 2 deals again with the H2 molecule: convergence studies, LDA versus GGA
  • The lesson 3 deals with crystalline silicon (an insulator): the definition of a k-point grid, the smearing of the cut-off energy, the computation of a band structure, and again, convergence studies ...
  • The lesson 4 deals with crystalline aluminum (a metal), and its surface: occupation numbers, smearing the Fermi-Dirac distribution, the surface energy, and again, convergence studies ...


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    3. Related input variables.

    Compulsory input variables:

    ... xangst [vectors (X) of atom positions in cartesian coordinates -length in ANGSTrom-]
    ... xcart [vectors (X) of atom positions in CARTesian coordinates]
    ... xred [vectors (X) of atom positions in REDuced coordinates]

    Basic input variables:

    ... natom [Number of ATOMs]
    ... ntypat [Number of TYPes of AToms]
    ... typat [TYPe of AToms]

    Useful input variables:

    ... chkprim [CHecK whether the cell is PRIMitive]
    ... nsym [Number of SYMmetry operations]
    ... spgroup [SPace GROUP number]
    ... spinat [SPIN for AToms]
    ... symrel [SYMmetry in REaL space]
    ... tnons [Translation NON-Symmorphic vectors]
    ... tolsym [TOLERANCE for SYMmetries]
    ... xyzfile [XYZ FILE input for geometry]

    Input variables for experts:

    ... maxnsym [MAXimum Number of SYMetries]
    ... random_atpos [RANDOM ATomic POSitions]
    ... symmorphi [SYMMORPHIc symmetry operation selection]


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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: t21.in t23.in t39.in

    tests/v5/Input: t14.in


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