Selasa, 11 Oktober 2011

ABINIT on Nanohub

             ABINIT on Nanohub

ABINIT can now be run, by anybody, on a virtual facility in the USA, called Nanohub
Nanohub is an NSF sponsored project to make HPC and educational resources available to the general public. After registering you can run a variety of ab initio and other softwares, directly on the cluster behind the web interface. There is also a lot of teaching material, tutorials and courses.
Execution times are fairly limited, but you will get direct access (e.g. along with a class of your students) to an efficient computational infrastructure, with a graphical tool to set up, run, and analyze ABINIT calculations. Cool!
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Main ABINIT code, input variables:

 

Main ABINIT code, input variables:

Complete list.

This document lists the names (keywords) of all input variables to be used in the main input file of the abinit code.
The new user is advised to read first the new user's guide, before reading the present file. It will be easier to discover the present file with the help of the tutorial.
When the user is sufficiently familiarized with ABINIT, the reading of the ~abinit/doc/users/tuning file might be useful. For response-function calculations using abinit, please read the response function help file
Copyright (C) 1998-2011 ABINIT group (DCA,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 .
Files which describe the input variables:
  • Basic variables, VARBAS
  • Developpement variables, VARDEV
  • Files handling variables, VARFIL
  • Geometry builder + symmetry related variables, VARGEO
  • Ground-state calculation variables, VARGS
  • GW variables, VARGW
  • Internal variables, VARINT
  • Parallelisation variables, VARPAR
  • Projector-Augmented Wave variables, VARPAW
  • Response Function variables, VARRF
  • Structure optimization variables, VARRLX
  • Wannier90 interface variables, VARW90
See also the Space group table

Alphabetical list of all input variables and some internal variables.

(Keywords with a % sign are internal variables contained in the dtset array - whose description is useful for the user, but to which no direct access is provided in the input files)
A. accesswff   acell   algalch   amu   angdeg   atvshift   awtr  
B. bandpp   bdberry   bdeigrf   bdgw   berryopt   berrystep   bfield   bmass   boxcenter   boxcutmin   brvltt   bxctmindg  
E. ecut   ecuteps   ecutsigx   ecutsm   ecutwfn   effmass   efield   elph2_imagden   enunit   eshift   esmear   etsfgroups   etsfmain   exchn2n3d   exchmix  
H.
I. iatcon   iatfix   iatfixx   iatfixy   iatfixz   iatsph   iboxcut   icoulomb   icutcoul   idyson   ieig2rf   ikhxc   inclvkb   intexact   intxc   imgmov   ionmov   iprcch   iprcel   iprctfvw   iprcfc   iqpt   irdddk   irdden   ird1den   irdqps   irdkss   irdscr   irdsuscep   irdwfk   irdwfq   ird1wf   iscf   isecur   istatr   istatshft   istwfk   ixc   ixcpositron  
J. jdtset   jellslab   jpawu  
K. kberry   kpt   kptbounds   kptgw   kptnrm   %kptns   kptopt   kptrlatt   kptrlen   kssform  
L. ldgapp   lexexch   localrdwf   lpawu  
M. macro_uj   maxnsym   %mband   mdftemp   mditemp   mdwall   mffmem   %mgfft   %mgfftdg   mixalch   mkmem   mkqmem   mk1mem   %mpw   mqgrid   mqgriddg  
N. natcon   natfix   natfixx   natfixy   natfixz   natom   %natpawu   natrd   natsph   natvshift   nband   nbandkss   nbandsus   nbdblock   nbdbuf   nberry   nconeq   nctime   ndivk   ndivsm   ndtset   ndyson   %ndynimage   %nelect   %nfft   %nfftdg   nfreqim   nfreqre   nfreqsp   nfreqsus   ngfft   ngfftdg   ngkpt   ngqpt   ngroup_rf   nimage   nkpt   nkptgw   nline   nloalg   nnos   nnsclo   nobj   nomegasf   nomegasi   nomegasrd   normpawu   noseinert   npband   npfft   npimage   npkpt   npsp   %npspalch   npulayit   npweps   npwkss   npwsigx   npwwfn   nqpt   nqptdm   nscforder   nsheps   nshiftk   nshiftq   nshsigx   nshwfn   nspden   nspinor   nsppol   nstep   nsym   ntime   ntimimage   ntypalch   ntypat   %ntyppure   nwfshist  
P. papiopt   paral_kgb   paral_rf   pawcpxocc   pawecutdg   pawfatbnd   pawlcutd   pawlmix   pawmixdg   pawnhatxc   pawnphi   pawntheta   pawnzlm   pawovlp   pawoptmix   pawprtden   pawprtdos   pawprtvol   pawprtwf   pawprt_b   pawprt_k   pawspnorb   pawstgylm   pawujat   pawujrad   pawujv   pawusecp   pawxcdev   pitransform   positron   posnstep posocc postoldfe postoldff ppmfrq   ppmodel   prepanl   prepgkk   prepscphon   prtbbb   prtbltztrp   prtcml   prtcif   prtden   prtdensph   prtdipole   prtdos   prtdosm   prtefg   prteig   prtelf   prtfc   prtfsurf   prtgden   prtgeo   prtgkk   prtkden   prtkpt   prtlden   prtnabla   prtnest   prtposcar   prtpot   prtspcur   prtstm   prtvha   prtvhxc   prtvol   prtvxc   prtwant   prtwf   prtxangst   prtxcart   prtxml   prtxred   prt1dm   ptcharge   %ptgroupma  
Q. qmass   qprtrb   qpt   qptdm   %qptn   qptnrm   qptopt   qptrlatt   quadmom  
R. random_atpos   ratsph   recefermi   recgratio   recnpath   recnrec   recptrott   recrcut   rectesteg   rectolden   restartxf   rfasr   rfatpol   rfddk   rfdir   rfelfd   rfmeth   rfphon   rfstrs   rfuser   rf1atpol   rf1dir   rf1elfd   rf1phon   rf2atpol   rf2dir   rf2elfd   rf2phon   rf3atpol   rf3dir   rf3elfd   rf3phon   rhoqpmix   rprim   %rprimd  
T. td_maxene   td_mexcit   tfkinfunc   timopt   tl_nprccg   tl_radius   tnons   toldfe   toldff   tolimg   tolmxf   tolrff   tolsym   tolvrs   tolwfr   tphysel   tsmear   typat  
V. vaclst   vacnum   vacuum   vacwidth   vcutgeo   vel   vis   vdw_supercell   vdw_nfrag   vdw_typfrag   vdw_xc   vprtrb  
X. xangst   xcart   %xclevel   xred   xyzfile  
Y.
Z. zcut   zeemanfield   %ziontypat   znucl  
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Tutorial Abinit

 

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 be independent on the network traffic.
At present, more than a dozen 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 useful to learn about the tests cases contained in directories ~abinit/test/fast, ~abinit/test/v1, ~abinit/test/v2, ~abinit/test/v3, ~abinit/test/v4 and ~abinit/test/v5, that provide many example input files. You should have a look at the README files of these directories.
Additional informations 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 : 

Specialized lessons (except response functions): 


Specialized lessons (response functions): 



Brief description of each lesson's content :

    The lessons 1-4 present the basic concepts, and form a global entity : you should not skip one 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 pick at random:
    * The lesson on spin in ABINIT presents the properties related to spin : spin-polarized calculations and spin-orbit coupling.
    * The first lesson on GW deals with the computation of the quasi-particule band gap of Silicon (semiconductor), in the GW approximation (so, 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 plasmon-pole model
    * 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's 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) demonstrate how to test a generated PAW dataset using ABINIT, against the ELK all-electron code, for diamond and magnesium.
    * The lesson on DFT+U aims at showing how to perform a DFT+U calculation using Abinit, and will lead to to compute the projected DOS of NiO.
    * The lesson on the determination of U for DFT+U show 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 teaches 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).
    * 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.
The following topics should be covered later :
    * the choice of pseudopotentials
NOTE that not all functionalities of ABINIT are covered by these tutorials. For a complete list of functionalities, please see the directory ~abinit/doc/features . For examples on how to use these functionalities, please see the ~abinit/tests directories, and their accompanying README files.
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