ABINIT: the tutorials

These tutorials are aimed at teaching the use of ABINIT, in the UNIX/Linux OS and its variants (OSF, HP-UX, AIX ...). They might be used for other operating systems, but the commands have to be adapted.

Note that they can be accessed from the ABINIT web site as well as from your local ~abinit/doc/tutorial/welcome.html file. The latter solution is of course preferable, as the response time will not depend on the network traffic.

At present, more than thirty lessons are available. Each of them is at most two hours of student work. Lessons 1-4 cover the basics, other lectures are more specialized.

Copyright (C) 2000-2011 ABINIT group (XG,RC)
This file is distributed under the terms of the GNU General Public License, see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt .
For the initials of contributors, see ~abinit/doc/developers/contributors.txt .

Before following the tutorials, you should have read the "new user's guide", as well as the pages 1045-1058 of the paper "Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients", by M.C. Payne, M.P. Teter, D.C. Allan, T.A. Arias and J.D. Joannopoulos, Rev. Mod. Phys. 64, 1045 (1992) or, if you have more time, you should browse 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. The latter reference is a must if you have not yet used another electronic structure code or a Quantum Chemistry package.

After the tutorial, you might find it useful to learn about the test cases contained in the subdirectories of ~abinit/tests/, e.g. the directories fast, v1, v2, ... v6, that provide many example input files. You should have a look at the README files of these directories.

Additional information can be found in the ~abinit/doc directory, including the description of the ABINIT project, guide lines for developpers, more on the use of the code (tuning) ...

Index

Basic lessons:
lesson 1, lesson 2, lesson 3, lesson 4

Specialized lessons (except response functions and many-body perturbation theory):
spin, TDDFT, Polarization and finite electric field, Analysis Tools, PAW1, PAW2, PAW3, DFT+U, Determination of U, Wannier90, Source code

Specialized lessons (response functions):
Response-Function 1, Response-Function 2, Optic, Electron-phonon interaction, Elastic properties, Static non-linear properties (+finite electric field)

Specialized lessons (many-body perturbation theory):
GW1, GW2, BSE

Using the parallelism in ABINIT:
A first introduction to ABINIT in parallel, ground state with plane waves, ground state with wavelets, molecular dynamics, parallelism on "images", response functions, Many-Body Perturbation Theory

Some lessons depends on other lessons. The following schema should help you to understand these dependencies.

Brief description of each lesson's content

The lessons 1-4 present the basic concepts, and form a global entity: you should not skip any of these.

• 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 ...

Other lessons present more specialized topics.

There is a group of lessons that can be started without any other prerequisite than the lessons 1 to 4, and that you can do in any order:

• The lesson on spin in ABINIT presents the properties related to spin: spin-polarized calculations and spin-orbit coupling.
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• The first lesson on GW deals with the computation of the quasi-particle band gap of Silicon (semiconductor), in the GW approximation (much better than the Kohn-Sham LDA band structure), with a plasmon-pole model.
• The second lesson on GW deals with the computation of the quasi-particule band structure of Aluminum, in the GW approximation (so, much better than the Kohn-Sham LDA band structure) without using the plasmon-pole model.
• The lesson on BSE deals with the computation of the macroscopic dielectric function of Silicon within the Bethe-Salpeter equation.
• The lesson on TDDFT deals with the computation of the excitation spectrum of finite systems, thanks to the Time-Dependent Density Functional Theory approach, in the Cassida formalism.
• The lesson on polarization and finite electric field deals with the computation of the polarization of an insulator (e.g. ferroelectric, or dielectric material) thanks to the Berry phase approach, and also presents the computation of materials properties in the presence of a finite electric field (also thanks to the Berry phase approach).
• The lesson on Analysis Tools deals with the use of the CUT3D utility to analyse wavefunctions and densities, and their graphical representation using Open DX.
• The lesson on the use of PAW (PAW1) presents the Projector-Augmented Wave method, implemented in ABINIT as an alternative to norm-conserving pseudopotentials, with a sizeable CPU time advantage.
• The lesson on the generation of PAW atomic data files (PAW2) presents the generation of atomic data for use with the PAW method.
• The lesson on the validation of a PAW atomic datafile (PAW3) demonstrates how to test a generated PAW dataset using ABINIT, against the ELK all-electron code, for diamond and magnesium.
• The lesson on DFT+U shows how to perform a DFT+U calculation using Abinit, and will lead to compute the projected DOS of NiO.
• The lesson on the determination of U for DFT+U shows how to determine the U value, to be used in the DFT+U approach.
• The lesson on Wannier90 deals with the Wannier90 library to obtain Maximally Localized Wannier Functions.
• The lesson on ABINIT in Parallel presents the use of basic parallelism in ABINIT
• The lesson "Source code" introduces the user to the development of new functionalities in ABINIT: in this lesson, one learns how to add a new input variable ...

There is an additional group of lessons on response functions (phonons, optics, dielectric constant, electron-phonon interaction, elastic response, non-linear optics, Raman coefficients, piezoelectricity ...), for which some common additional information are needed:

• The lesson Response-Function 1 (RF1) presents the basics of response-functions within ABINIT. The example given is the study of dynamical and dielectric properties of AlAs (an insulator): phonons at Gamma, dielectric constant, Born effective charges, LO-TO splitting, phonons in the whole Brillouin zone. The creation of the "Derivative Data Base" (DDB) is presented.
• The lesson Response-Function 2 (RF2) presents the analysis of the DDBs that have been introduced in the preceeding lesson RF1. The computation of the interatomic forces and the computation of thermodynamical properties is an outcome of this lesson.
• The additional information given by lesson RF1 opens the door to The lesson on Optic, the utility that allows to obtain the frequency dependent linear optical dielectric function and the frequency dependent second order nonlinear optical susceptibility, in the simple "Sum-Over-State" approximation.
• The additional information given by lesson RF1 and RF2 opens the door to a group of lessons that can be followed independently of each other: The lesson on the electron-phonon interaction presents the use of the utility MRGKK and ANADDB to examine the electron-phonon interaction and the subsequent calculation of superconductivity temperature (for bulk systems).
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• The lesson on the elastic properties presents the computation with respect to the strain perturbation and its responses: elastic constants, piezoelectricity.
• The lesson on static non-linear properties presents the computation of responses beyond the linear order, within Density-Functional Perturbation Theory (beyond the simple Sum-Over-State approximation): Raman scattering efficiencies (non-resonant case), non-linear electronic susceptibility, electro-optic effect. Comparison with the finite field technique (combining the computation of linear response functions with finite difference calculations), is also provided.

Concerning parallelism, there is another set of specialized lessons. For each of these lessons, you are suposed to be familiarized with the corresponding tutorial for the sequential calculation.

• An introduction on ABINIT in Parallel should be read before going to the next lessons about parallelism. One simple example of parallelism in ABINIT will be shown.
• Parallelism for ground-state calculations, with plane waves presents the combined k-point (K), plane-wave (G), band (B), spin/spinor parallelism of ABINIT (so, the "KGB" parallelism), for the computation of total energy, density, and ground state properties
• Parallelism for ground-state calculations, with wavelets presents the parallelism of ABINIT, when wavelets are used as a basis function instead of planewaves, for the computation of total energy, density, and ground state properties
• Parallelism for molecular dynamics calculations
• Parallelism based on "images", e.g. for the determination of transitions paths (string method), that can be activated on top of the "KGB" parallelism for force calculations.
• Parallelism of response-function calculations - you need to be familiarized with the calculation of linear-response properties within ABINIT, see the tutorial Response-Function 1 (RF1)
• Parallelism of Many-Body Perturbation calculations (GW) allows to speed up the calculation of accurate electronic structures (quasi-particle band structure, including many-body effects).

The following topics should be covered later:

• the choice of pseudopotentials

NOTE that not all features of ABINIT are covered by these tutorials. For a complete feature list, please see the ~abinit/doc/features/ directory. For examples on how to use these features, please see the ~abinit/tests/* directories and their accompanying README files.