ABINIT new user help file.

This file gives a beginner's introduction to the ABINIT resources, the ABINIT package, and the main ABINIT application.


Copyright (C) 1998-2017 ABINIT group (DCA,XG,RC)

Content of the help file:



1. Foreword

The ABINIT project is a group effort of dozens of people worldwide, whose central outcome is the main ABINIT application, delivered with many other files in the ABINIT package. The ABINIT project includes also resources provided on the ABINIT Web site and the ABINIT Github repository.

Before reading the present file, and get some grasp about the main ABINIT application, you should get some theoretical background. In case you have already used another electronic structure code, or a quantum chemistry code, it might be sufficient to read the introduction of the paper ``Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients'' M. C. Payne, M. P. Teter, D. C. Allan, T. A. Arias, and J. D. Joannopoulos, Rev. Mod. Phys. 64, 1045-1097 (1992).

If you have never used another electronic structure code or a Quantum Chemistry package, you should complete such reading by going (at your own pace) through the Chaps. 1 to 13 , and appendices L and M of the book Electronic Structure. Basic Theory and Practical Methods. R. M. Martin. Cambridge University Press (2004) ISBN 0 521 78285 6.

After having gone through the present New User's Guide, you should follow the ABINIT tutorial (lesson_welcome).

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2. Introduction

ABINIT is a package whose main program allows to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory, using pseudopotentials and a planewave basis, or augmented plane waves, or even wavelets. Some possibilities of ABINIT go beyond Density Functional Theory, i.e. the many-body perturbation theory (GW approximation the Bethe-Salpether equation), Time-Dependent Density Functional Theory, Dynamical Mean-Field Theory, the Allen-Heine-Cardona theory to find temperature-dependent electronic structure. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulation using these forces, or to generate dynamical (vibrations - phonons) properties, dielectric properties, mechanical properties, thermodynamical properties, etc . In addition to the main ABINIT code, different utility programs are provided.

We suppose that you have downloaded the ABINIT package from the Web site, unpacked it and installed it. If not, you might nevertheless continue reading the present Web page, just to get an overview, but it might prove more fruitful to have first downloaded the ABINIT package and at least unpacked it, see the installation notes.

We will use the name "~abinit" to refer to the directory that contains the ABINIT package after download. In practice, a version number is appended to this name, to give for example : abinit-8.4.0 . The ABINIT package versioning scheme is explained later in this file.

~abinit contains different subdirectories. For example, the present file, as well as other descriptive files, should be found in ~abinit/doc/users . Other subdirectories will be described later.

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3. The ABINIT executable : abinit

After compilation, the main code will be present in the package as ~abinit/src/98_main/abinit (or perhaps at another place, depending on your installation).

To run abinit you need four things:

With these items a job can be run.

The full list of input variables, all of which are provided in the single input file, is given in the ABINIT list of all variable.
The detailed description of input variables is given in many "Variable Set" files, including:

A set of examples aimed at guiding the beginner is available in the tutorial (lesson_welcome).

Other test cases (more than 800 input files) can be found in the ~abinit/test subdirectories, e.g. "fast", the "vX" series (v1, v2, ... v67mbpt, v7, v8), "libxc", "paral", the "tutoX" series ...

Many different sorts of pseudopotentials can be used with ABINIT. Most of them can be found on the atomic data files page of the ABINIT web site. There are official recommended pseudopotentials tables (the PAW JTH table, and the norm-conserving table from ONCVPSP), and also some older sets of pseudopotentials. A subset of existing pseudopotentials are used for test cases, and are located in the ~abinit/tests/Psps_for_tests directory, but they are not recommended for production. Information on pseudopotential files can be found in the ABINIT help file and the ~abinit/doc/psp_infos directory.

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4. Other programs in the ABINIT package

In addition to abinit, there are utility programs provided in the ABINIT package.

Some utility programs are written in F90 (like the main abinit program), and their sources is also in ~abinit/src/98_main .
These include : mrgddb, anaddb, aim, conducti, optics, mrgscr, cut3d, and fold2Bloch.

mrgddb and anaddb allow to post-process responses to atomic displacements and/or to homogeneous electric field, and/or to strain perturbation, as generated by abinit, to produce full phonon band structures, thermodynamical functions, piezoelectric properties, superconducting properties, to name a few. "mrgddb" is for "Merge of Derivative DataBases", while "anaddb" is for "Analysis of Derivative DataBases".

cut3d can be used to post-process the three-dimensional density (or potential) files generated by abinit. It allows one to deduce charge density in selected planes (for isodensity plots), along selected lines, or at selected points. It allows one also to make the Hirshfeld decomposition of the charge density in "atomic" contributions.

fold2Bloch is used for unfolding of first-principle electronic band structure obtained with ABINIT code.

aim is also a post-processor of the three-dimensional density files generated by abinit. It performs the Bader Atom-In-Molecule decomposition of the charge density in "atomic" contributions.

conducti allows one to compute the frequency-dependent optical conductivity.

Some utility programs are not written in F90, but in Python. They are contained in ~abinit/scripts, where post-processing (numerous tools) and pre-processing scripts are distinguished. Some allows one to visualize ABINIT outputs, like abinit_eignc_to_bandstructure.py .

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5. Other resources outside the ABINIT package

In addition to the ABINIT package, other resources can be obtained from the ABINIT GitHub site. The sources of the latest version of the ABINIT package are actually mirrored on this site, but for other resources (not in the package) this is the only download point.

abipy is an open-source library for analyzing the results produced by ABINIT (including visualisation), and for preparing input files and workflows to automate ab-initio calculations (so-called high-throughput calculations). It provides interface with pymatgen, developed by the Materials Project. Links for AbiPy : https://github.com/abinit/abipy, and http://abinit.github.io/abipy.

The pseudo-dojo is a Python framework for generating and validating pseudopotentials (or PAW atomic data files). Normal ABINIT users benefit a lot from this project, since the ABINIT recommended table of norm-conserving pseudopotentials has been generated thanks to it, while the PAW recommended table is under control of it. Albeit, only specialized ABINIT experts use it.

abiconfig is a holding area for configuration files used to configure/compile Abinit on clusters. You might benefit from it if you have indeed to install Abinit on a cluster.

abiconda contains conda recipes to build Abinit-related packages (like AbiPy). You might benefit from it if you install Abipy on your machine.

abiflows provides flows for high-throughput calculations with ABINIT.

In addition to the resources that the ABINIT developer provide to the community through the ABINIT packages, portal and Github, many ABINIT-independent commercial or free applications can be used to visualize ABINIT outputs or interact with ABINIT. We provide a (not very well maintained) list of links in https://www.abinit.org/community/links. Of course, you might get more by browsing the Web...

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6. Input variables to abinit

As an overview, the most important input variables, to be provided in the input file, are listed below:

Specification of the geometry of the problem, and types of atoms :
natom           total number of atoms in unit cell
ntypat          number of types of atoms
typat(natom)    sequence of integers, specifying the type of each atom.
                NOTE: the atomic coordinates (xangst, xcart or xred)
                must be specified in the same order
rprim(3,3)      unscaled primitive translations of periodic cell;
                each COLUMN of this array is one primitive translation
xangst(3,natom)  cartesian coordinates (Angstrom) of atoms in unit cell
                NOTE: only used when xred and xcart are absent
xcart(3,natom)  cartesian coordinates (Bohr) of atoms in unit cell
                NOTE: only used when xred and xangst are absent
xred(3,natom)   fractional coordinates for atomic locations;
                NOTE: leave out if xangst or xcart is used
znucl(ntypat)   Nuclear charge of each type of element; must agree with
                nuclear charge found in psp file.

Specification of the planewave basis set, Brillouin zone wavevector sampling, and occupation of the bands:
ecut            planewave kinetic energy cutoff in Hartree
kptopt          option for specifying the k-point grid
                if kptopt=1, automatic generation, using ngkpt and shiftk.
                (for the latter, see the help_abinit file)
ngkpt(3)        dimensions of the three-dimensional grid of k-points
occopt          set the occupation of electronic levels :
                 =1 for semiconductors
                 =3 ... 7  for metals

Specification of the type of calculation to be done:
ionmov          when ionmov = 0 : the ions and cell shape are fixed
                            = 2 : search for the equilibrium geometry
                            = 6 : molecular dynamics
iscf            either a positive number for defining self-consistent
                algorithm (usual), or -2 for band structure in fixed potential
optdriver       when == 3 and 4 : will do GW calculations (many-body perturbation theory)
rfelfd          when /= 0 : will do response calculation to electric field
rfphon          when = 1 : will do response calculation to atomic displacements

Specification of the numerical convergency of the calculation:
nstep           maximal number of self-consistent cycles (on the order of 20)
tolvrs          tolerance on self-consistent convergence
ntime           number of molecular dynamics or relaxation steps
tolmxf          force tolerance for structural relaxation in Hartree/Bohr


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7. Output files

Output from an abinit run shows up in several files and in the standard output. Usually one runs the command with a pipe of standard output to a log file, which can be inspected for warnings or error messages if anything goes wrong or otherwise can be discarded at the end of a run. The more easily readable formatted output goes to the output file whose name is given in the "files" file, i.e. you provide the name of the formatted output file. No error message is reported in the latter file. On the other hand, this is the file that is usually kept for archival purposes.

In addition, wavefunctions can be input (starting point) or output (result of the calculation), and possibly, charge density and/or electrostatic potential, if they have been asked for. These three sets of data are stored in unformatted files.
The Density Of States (DOS) can also be an output as a formatted (readable) file.
An analysis of geometry can also be provided (GEO file)
The name of these files is constructed from a "root" name, that must be different for input files and output files, and that is provided by the user, to which the code will append a descriptor, like WFK for wavefunctions, DEN for the density, POT for the potential, DOS for the density of states ...

There are also different temporary files. A "root" name should be provided by the user, from which the code generates a full name. Amongst these files, there is a "status" file, summarizing the current status of advancement of the code, in long jobs. The ABINIT help file contains more details.

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8. What does the code do?

The simplest sort of job computes an electronic structure for a fixed set of atomic positions within a periodic unit cell. By electronic structure, we mean a set of eigenvalues and wavefunctions which achieve the lowest (DFT) energy possible for that basis set (that number of planewaves). The code takes the description of the unit cell and atomic positions and assembles a crystal potential from the input atomic pseudopotentials, then uses either an input wavefunction or simple gaussians to generate the initial charge density and screening potential, then uses a self-consistent algorithm to iteratively adjust the planewave coefficients until a sufficient convergence is reached in the energy.

Analytic derivatives of the energy with respect to atomic positions and unit cell primitive translations yield atomic forces and the stress tensor. The code can optionally adjust atomic positions to move the forces toward zero and adjust unit cell parameters to move toward zero stress. It can performs molecular dynamics. It can also be used to find responses to atomic displacements and homogeneous electric field, so that the full phonon band structure can be constructed...

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9. Versioning logic

We finish this "help for new user" with a brief explanation of the logic of ABINIT version releases.

The full name of a version has three digits (for example, 8.4.0). The first digit is the slowly varying one (in average, it is changed after two or three years). It indicates the major efforts and trends in that version. At the level of 1.x.y ABINIT (before 2000 !), the major effort was placed on the "ground-state" properties (total energy, forces, geometry optimisation, molecular dynamics ...). With version 2.x.y , response-function features (phonons, dielectric response, effective charges, interatomic force constants ...) were included. The main additional characteristics of version 3.x.y were the distribution under the GNU General Public Licence, the set-up of the documentation and help to the user through the Web site in html format, and the availability of GW capabilities. The version 4.x.y put a lot of effort in the speed of ABINIT (e.g. PAW), and its parallelisation. These historical developments explain why the tests are gathered in directories "v1", "v2", "v3", etc. Every 4 to 8 months, we release a "production version" of ABINIT in which the second digit, an even number, is incremented, which usually goes with additional features. A release notes document is issued, with the list of additional capabilities, and other information with respect to modifications with the previous release. The odd second digits are used for internal management only, so-called "development versions" of ABINIT (for example 8.5.0). Two versions differing by the last (third) digit have the same capabilities, but the one with the largest last digit is more debugged than the other : version 8.4.1 is more debugged than 8.4.0, but no new features has been added (so likely, no additional bug!).

 


In order to start using ABINIT, please follow the tutorial (lesson_welcome)

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