ABINIT. List of features.
This file describes the major features of the ABINIT package.
Copyright (C) 1998-2009 ABINIT group (DCA,XG)
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 .
Goto :
ABINIT home Page
|
Suggested acknowledgments
|
List of input variables
|
Tutorial home page
|
Bibliography
Help files :
New user's guide
|
Abinis (main)
|
Abinis (respfn)
|
Mrgddb
|
Anaddb
|
AIM (Bader)
|
Cut3D
|
Optic
|
Mrgscr
Contents:
- 0. Related documentation.
- 1. Available physical properties.
- 1.A. Total energy of an assembly of nuclei and electrons placed in a repeated cell.
- 1.B. Derivatives of the total energy and eigenenergies.
- 1.C. Excited states.
- 1.D. Displacement of atoms, and changes of cell parameters.
- 1.E. Analysis and graphical tools.
- 1.F. Interfacing with other codes.
- 2. Speed and memory.
- 2.A. Speed in the sequential version.
- 2.B. Speed in the parallel version.
- 2.C. Memory.
- 3. The user's point of view.
- 3.A. The Web site.
- 3.B. Portability.
- 3.C. Running jobs, input and output files.
- 3.D. Documentation.
- 3.E. Generation of the k-points, geometries, and starting wavefunctions.
- 3.F. Automatic determination of input parameters.
- 4. The programmer's point of view.
0. Related documentation
Besides the documentation available on the Web,
there is a wealth of information inside the package itself, see the
directory "doc".
The reader might consult the latest version of the "doc/users/context.txt" file
for the description of the ABINIT project and its history.
The latest version of the "doc/developers/planning.txt" file will give an idea of
possible future developments.
The different versions of the "doc/release_notes/*html" files will allow to
see the actual development of the project since version 1.5,
released in August 1998.
1. Available physical properties
1.A. Computation of the total energy of an assembly of nuclei and electrons
placed in a repeated cell.
-
1.A.1. The computation can be done using plane waves and norm-conserving
pseudopotentials, or, alternatively, so-called
"Projector-Augmented Waves" (PAW method), with appropriate pseudoatomic data.
-
1.A.2. The total energy computation is done according to the Density Functional
Theory. Most of the important local approximations (LDA) are
available, including the Perdew-Zunger one. Two different local spin density
(LSD) are available, including the Perdew Wang 92, and one due to M. Teter.
The Perdew-Burke-Ernzerhof, the revPBE, the RPBE
and the HCTH GGAs (spin unpolarized as well as polarized)
are also available.
-
1.A.3. Self-consistent calculations will generate the DFT ground-state,
with associated energy and density. Afterwards, a non-self-consistent
calculation might generate eigenenergies at a large number
of k-points, for band structures. The electronic Density-Of-States
can be computed either within the tetrahedron method, or using a smearing
technique.
-
1.A.4. The program admits many different types of pseudopotentials.
There are two complete sets of pseudopotentials available for
the whole periodic table, one of the Troullier-Martins type,
one of the Goedecker type (this one include the spin-orbit coupling).
Four codes are available to generate
new pseudopotentials when needed. Two of them are able to generate
pseudopotentials with a core hole, in order to compute core-level shifts.
Two of them are able to generate GGA pseudopotentials.
No ultra-soft pseudopotential can be used.
Pseudopotentials can be mixed, to generate "alchemical" pseudoatoms.
-
1.A.5. Metallic as well as insulating systems can be treated. Schemes for
determination of the occupation number include the Fermi broadening,
the Gaussian broadening, the Gaussian-Hermite broadening, as well as
the modifications proposed by Marzari. Finite temperatures
can also be treated using a smearing scheme (Verstraete scheme).
-
1.A.6. The cell may be orthogonal or non-orthogonal.
Any kind of symmetries and corresponding sets of k-point can be input,
and taken into account in the computation.
-
1.A.7. The electronic system may be computed in the
spin-unpolarized or spin-polarized
case, with the possibility to impose occupation numbers of majority and
minority spins, and the spins of the starting configuration.
A specific option for efficient treatment of
anti-ferromagnetism (Shubnikov groups) is available.
The treatment of non-collinear magnetism is available, but only for
the total energy (no forces, stresses, reponse-functions ...).
The total magnetic moment of the unit cell can be constrained.
-
1.A.8. The total energy, forces, stresses, and electronic structure
can be provided with the spin-orbit coupling included (the latter not for PAW).
-
1.A.9. A finite electric field can be imposed on insulators, using the proper
Hamiltonian for periodic systems based on Berry's phase (not for PAW).
-
1.A.10. The decomposition of energy in its different component (local potential,
XC, hartree ...) is provided.
-
1.A.11. Inner electronic eigenvalues can be computed thanks to the
minimisation of the residual with respect to a target energy value.
-
1.A.12. The charge density of states close to the Fermi energy can be output,
and provide a simple approach to STM image calculations (not for PAW).
-
1.A.13. The lifetime of positrons can be computed.
1.B. Derivatives of the total energy and eigenenergies (incl. linear and non-linear DFPT responses)
-
1.B.1. Hellman-Feynman forces are computed from an analytical formula,
and corresponds exactly to the limit of finite differences of energy
for infinitesimally small atomic displacements when the ground-state
calculation is at convergence. This feature is available for all the
cases where the total energy can be computed (except non-collinear
magnetism).
A correction for non-converged
cases allows to get accurate forces with less converged wavefunctions
than without it. The decomposition of the forces in their different
components can be provided.
-
1.B.2. Stress can also be computed. This feature is available for all
the cases where the total energy can be computed, except
non-collinear magnetism.
The decomposition of the stresses in their different
components can be provided. A smearing scheme applied to the kinetic
energy allows to get smooth energy curves as a function of
lattice parameters and angles.
Alternatively, a facility for correcting the computed stress
by the Pulay stress is provided.
-
1.B.3. The polarization can be computed within the Berry phase
formulation. This feature is available for insulators,
magnetic or non-magnetic, but not yet when spin-orbit splitting
is present or for PAW. The localisation tensor can also be computed.
Constrained-polarization calculations can be performed, following Na Sai
et al, PRB 66, 104108 (2002).
-
1.B.4. For norm-conserving pseudopotentials, accurate responses
to atomic displacements and homogeneous electric fields
are available, and allows to compute the interatomic force constants,
the Born effective charges, the dielectric constant, the phonon band
structure. Symmetry characters of the phonons at Gamma
are computed. Thermodynamical properties, like the free energy,
the heat capacity or the entropy, can also be computed, in the
quasi-harmonic approximation. Available for the GGAs (except the HCTH
one), while for spin-orbit, only responses to atomic displacements are
available.
-
1.B.5. For norm-conserving pseudopotentials, accurate responses
to strain perturbations are available,
and allow to compute, presently, the elastic constants
("rigid-ion" as well as "relaxed"), the piezoelectricity tensor,
as well as the so-called "internal strains", change of forces to atoms
due to a strain, or change of the stress due to an atomic displacement.
(no treatment of spin-orbit coupling yet).
-
1.B.6. For norm-conserving pseudopotentials, approximate or accurate susceptibility matrix
and dielectric matrix can be computed, thanks to a sum over states.
(no treatment of spin-polarized cases or spin-orbit coupling yet)
-
1.B.7. For norm-conserving pseudopotentials, derivatives of the
electronic eigenenergies with respect
to the wavevector can be computed analytically.
-
1.B.8. For norm-conserving pseudopotentials, optical conductivity
can be computed, thanks to the Kubo-Greenwood formula.
(no treatment of spin-polarized cases or spin-orbit coupling yet)
-
1.B.9. For norm-conserving pseudopotentials,
the band-by-band decomposition of the Born effective charges,
and the localisation tensor is available.
(no treatment of spin-polarized cases or spin-orbit coupling yet)
-
1.B.10. For norm-conserving pseudopotentials, selected non-linear
response coefficients can be computed thanks to the
2n+1 theorem of perturbation theory. At present :
- the electro-optic coefficients
- the Raman cross sections
(no treatment of spin-polarized cases or spin-orbit coupling yet)
-
1.B.11. For norm-conserving pseudopotentials,
electron-phonon matrix elements are available directly from the
output of a linear-response phonon calculation. They can be analyzed
to give e.g. the phonon linewidth or superconducting temperature.
(no treatment of spin-polarized cases or spin-orbit coupling yet)
-
1.B.12. For norm-conserving pseudopotentials,
the computation of responses with respect to atomic displacement
is possible when a finite electric field is present.
This feature is available for insulators,
non-magnetic, no spin-orbit coupling.
Computation of other linear or non-linear responses within
an electric field is not yet possible.
1.C. Excited states.
(Note : at present, for norm-conserving pseudopotentials only)
-
1.C.1. Computation of ionisation energies (N -> N-1 electrons)
and affinities (N -> N+1 electrons) in the GW approximation.
Three plasmon pole models are available, but that calculation
can also be done by a full integration over frequencies.
ABINIT is able to treat insulators as well as metals, but
should be improved to treat polymers or clusters.
In the GW implementation, it is possible to disable the full computation,
and actually do an Hartree-Fock, screened exchange or COHSEX calculation.
Self-consistency is implemented at a very primitive level.
The Faleev method, see PRL 93, 126406 (2004), is implemented.
-
1.C.2. Excited states of atoms and molecules (spin-singlet as well
as spin-triplet) can be computed within TDDFT. Oscillator strengths
are available.
-
1.C.3. Frequency-dependent linear optical response is available,
for all components of the tensor (xx,yy,zz,xy,yz,zx),
real as well as imaginary part. This property is computed within the very simple
"sum-over-state" approximation (i.e. without local field corrections).
-
1.C.4. Frequency-dependent non-linear optical response is available,
for all components of the tensor (xxx,yyy,zzz,xyz ... ),
real as well as imaginary part. This property is computed within the very simple
"sum-over-state" approximation (i.e. without local field corrections).
1.D. Displacement of atoms, and changes of cell parameters.
-
1.D.1. Different algorithms (Broyden; modified Broyden; Verlet with sudden
stop of atoms) allows to find the equilibrium configuration
of the nuclei, for which the forces vanish. The cell parameters
can also be optimized concurently with the atomic positions.
Specified lattice parameters, or angles, or atomic positions,
can be kept fixed if needed.
-
1.D.2. Two molecular dynamics algorithm (Numerov or Verlet)
allow to perform simulations in real
(simulated) time. The displacement of atoms may be computed according to
Newton's law, or by adding a friction force to it.
Nose-Hoover thermostat is available with Verlet algorithm.
Langevin dynamics is also available.
-
1.D.3. The code can provide an automatic analysis of bond lengths and angles,
and the atomic coordinates in a format suitable for vizualisation with XMOL.
1.E. Analysis and graphical tools.
-
1.E.1. A post-processor, called "cut3d", is available to analyse density,
potential and wavefunction files. It is able to change the format of these
files, to extract the data on a 2D plane, or along a 1D line.
It can perform the Hirshfeld computation of atomic charges.
It can analyse the charge contained in an atomic sphere,
and determine the angular momentum projected charge (l=0 to 4)
contained in that sphere.
(only available for norm-conserving pseudopotentials)
-
1.E.2. Another post-processor, called "aim", is available to
perform the Bader "Atom-In-Molecule" analysis of the density.
(only available for norm-conserving pseudopotentials)
-
1.E.3. A special part in the tutorial (see later) indicates how
to generate properly formatted data for the visualisation of :
- the band structure (visualisation thanks to XMGR)
- total energies vs different parameters (also using XMGR)
- the charge density (3D isosurfaces)
(the cut3d postprocessor must be used, followed by matlab)
The cut3d postprocessor also allows to prepare 2D charge density plots.
-
1.E.4. The post-processor band2eps allows to draw phonon dispersion
curves automatically, in a file written in Encapsulated PostScript (eps).
Moreover, a color code allows to emphasize the contribution of individual
atoms to the corresponding eigenvector (at most three types of atoms).
-
1.E.5. Utilities to view the structures and make the band structure
are available (StructureViewer, BandStructureMaker).
1.F. Interfacing with other codes.
-
1.F.1. ABINIT is interfaced with WanT (see http://www.wannier-transport.org).
WanT, as a postprocessor of ABINIT results, allows to compute
maximally localized Wannier functions, as well as transport
properties through nanostructures.
-
1.F.2. ABINIT is interfaced with CASINO, a code for Quantum Monte Carlo
calculation of the properties of solids and molecules.
-
1.F.3. XML pseudopotentials can be used, these being common with the SIESTA
code.
-
1.F.4. The _WFK functions can be used as starting basis
by the TDDFT, GW and/or Bethe-Salpether softwares EXC, SELF and DP
code, see http://www.abinit.org/community/?text=links .
2. Speed and memory.
2.A. Speed in the sequential version.
-
2.A.1. Depending on the number of atoms, there are two regimes in the
code : at low number of atoms and electrons,
the CPU time is dominated by Fast Fourier
Transforms with an average scaling O(N^2 log N) where N is some
number characteristics of the size of the system (atoms, electrons);
at large number of atoms and electrons, the CPU time is dominated
by non-local operator aplication and orthogonalisation, with
an average scaling O(N^3).
-
2.A.2. The complex-to-complex Fast Fourier Transform routine for application
of the Hamiltonian has been highly optimized, and take into account
the fact that the wavefunction do not fill the reciprocal space FFT box.
Library FFTs are also available, but they are found to be slower than the
present FFT routine, developed starting from a routine
provided by S. Goedecker.
A real-to-complex FFT is used for treating potential and densities
of the ground state, since they are real.
For selected k-points, invariant under time-reversal symmetry,
( (0 0 0), (1/2 0 0), (0 1/2 0), (0 0 1/2), (1/2 1/2 0) ... (1/2 1/2 1/2) ),
the number of planewave explicitly treated is divided by two. A
real-to-complex FFT is used then.
-
2.A.3. The non-local potential is applied in reciprocal space. It has been
optimized carefully, although there is still some speed-up to be
coded when the k-point is invariant under time-reversal.
The orthogonalisation procedure can be done twice per loop or only once.
-
2.A.4. At the level of the generation of electronic eigenfunctions, an efficient
band-by-band preconditioned conjugate-gradient algorithm is used,
in its non-self-consistent version. An alternative algorithm "lobpcg"
is also available.
-
2.A.5. At the level of the self-consistency loop, an efficient
potential-based preconditioned conjugate-gradient algorithm is used.
Simple mixing is also available, as well as the Anderson algorithm.
Preconditioning of this algorithm is achieved through a model
dielectric function, or through an approximate dielectric matrix.
2.B. Speed in the parallel version.
-
2.B.1. For ground-state calculations, the code has been parallelized
on the k-points, on the spins, on the bands,
and on the FFT grid and plane wave coefficients.
For the k-point and spin parallelisations (using MPI), the communication
load is generally
very small. This allows it to be used on a cluster of workstations.
However, the number of nodes that can be used in parallel might
be small, and depends strongly on the physics of the problem.
The band parallelisation (also using MPI) can be used
concurently with the k point and and spin parallelisation,
but is less efficient.
The FFT grid parallelisation, based on MPI is under development.
-
2.B.2. For response calculations, the code has been parallelized
on k-points, spins, and bands (MPI), as well as
on the FFT grid and plane wave coefficients (OpenMP).
For the k-points, spins and bands parallelisation,
the communication load is rather
small also, and, unlike for the GS calculations, the number
of nodes that can be used in parallel will be large,
nearly independently of the physics of the problem.
The FFT grid parallelisation (using OpenMP) works only
for SMP machines, and is still to be
optimized.
-
2.B.3. GW calculations are parallelized over k-points.
-
2.B.4. A careful study of the speed-up should still be done,
in both the GS and RF cases.
-
2.C.1. The requirements of the different conjugate gradient algorithms
on memory are relatively low, especially when the number of atoms
is large. Optionally, it is even possible to use disk space
to save memory, at the expense of computing time.
In particular, when the number of k points is large, they can
be stored in memory one at a time. Phase factors in the application of
the non-local operator can also be recomputed at each application,
in order to save memory. For k-points that are invariant under
time-reversal symmetry, the storage required for wavefunctions
is half the storage for other k-point.
3. The user's point of view.
3.A. The Web site.
-
3.A.1. A Web site can be accessed. The complete sources (and all the tests)
of the ABINIT package are available there.
Executables for many different platforms are also available,
in specific packages that also include
the 'Infos' directory are also available.
Installation notes, current features of ABINIT,
the tutorial, on-line help can be vizualized directly from the web.
-
3.A.2. Also available from the Web site :
- the pseudopotentials
- some utilities (including cut3d, a density analyser)
- five mailing lists
(one for "official announcements", one for the developpers, one for the developers using the GNU Arch repository, one "forum mailing list" , one for the advisory committee)
- the ABINIT bibliography database, that contains references of papers
in which ABINIT or one of its predecessors have been used
- the FAQ (frequently asked questions) database
- ... (many more infos)
3.B. Portability.
-
3.B.1. The ABINIT package has been installed successfully on the
following different platforms :
- PC/Linux based on PPro, PII, PIII, PIV processors, with
pghpf compiler, Intel compiler, fujitsu compiler, NAG compiler, g95 compiler and gfort compiler.
- PC under Windows
- ItaniumII
- HP/SPP1600, HP/S-class, HP/N-class based on the HP 7200, 8000
and 8500 processors
- Compaq/DEC alpha workstations under OSF, based on EV56, EV6, EV67 or EV68
- Compaq/DEC alpha workstations under Linux, based on EV56
- IBM RS6000 based on Power 2, 3+, 4 and 5 processors
- SGI Origin 2000 and O2
- CRAY T3E
- FUJITSU VPP-700
- Sun ultrasparc II
- NEC
- HITACHI SR8000
- Mac OS X
-
3.B.2. In particular, the parallel version is available on clusters of
Intel/Linux, DEC or IBM workstations, as well as on
CRAY T3E, SGI Origin 2000, HP/SPP1600, HP/S-class, HP/N-class,
FUJITSU VPP-700 machines, HITACHI SR8000, IBM 44P, Sun ultrasparc.
-
3.B.3. Installation is made thanks to the autotools (autoconf and automake)
as well as different scripts. All machine-dependent parameters
are grouped in one single short file for each machine.
The parallel and sequential
version of the code, as well as the different versions for the different
machines, are prepared on-the-fly,
so that there is only one unique source code.
-
3.B.4. Binaries for different machines can be managed in the
same main directory, as they might be placed automatically in different
sub-directories.
3.C. Running jobs, input and output files.
-
3.C.1. The input variables are gathered in one unique file,
read by a text processing facility build in the code.
Many defaults values are provided, so that
the input file can be kept rather short.
-
3.C.2. Many different stopping criteria allow the user to target the accuracy
he or she wants to obtain.
-
3.C.3. The outputs are provided to one main file and one auxiliary file,
as well as different specialized files (for density, potential,
wavefunctions, ...) .
The main file is shorter than the auxiliary file, and well formatted,
while all important results are gathered
there. It can be used for archival purposes. The auxiliary (log) file
will contain all exception messages.
-
3.C.4. Exception handling is provided through four different types
of messages : COMMENT, WARNING, BUG and ERROR. In each case, the
accurate meaning of the exception is described, as well as the
eventual action to be taken by the user.
-
3.C.5. Statistics of foreseen memory and disk usage is printed at
the beginning of the run. Statistics of CPU time usage
is printed at the end of the run.
-
3.C.6. There is a facility to stop the run in a clean way at any time.
The user may specify a cpu time limit, after which the job must end
smoothly.
-
3.C.7. A status file, updated very frequently, gives an on-the-fly
report of progress of the current run.
-
3.C.8. The code can handle multiple datasets contained in the input
file, where generic input variables valid for all datasets
can be defined. These calculations for different dataset
can be chained, so that in one run, many complex tasks can be accomplished.
This allows easy convergence studies.
-
3.C.9. The code can start the current run from a wavefunction input file
generated in a previous run. This allows to cut down the number
of iteration to self-consistency, or to perform other tasks.
This can be done even if the previous job
had different computational parameters, like different k points,
different energy cut-off, spin-unpolarized or spin-polarized wavefunctions,
scalr or spinor wavefunctions ... Of course, the restart from
wildly different parameters will not save a lot of CPU time.
-
3.C.10. ABINIT can produce CML (Chemical Markup Language) output files.
It can also read the CML files it produced.
3.D. Documentation.
-
3.D.1. A new_user_guide and a few rather detailed help files
(abinis_help, respfn_help, anaddb_help, mrgddb_help, newsp_help,
aim_help ... ) are available on-line.
-
3.D.2. A tutorial with more than 15 lessons is available on-line.
It starts with the computation of
different properties of the H2 molecule, describes convergence studies,
then focuses on bulk Silicon, bulk Al and Al surface. It describes
the use of response-function features, the GW calculation of band structures,
the PAW methodology, computation of spin-dependent properties,
analysis tools, the phonon band structure, linear and non-linear optics,
electro-optic effects, electron-phonon coupling, phonon linewidths due
to electron-phonon interaction, Raman scattering efficiencies, piezoelectricity,
the computation of elastic constants, parallelism, the source code, etc ...
-
3.D.3. Many test cases are provided, and can help the user in setting up a run.
-
3.D.4. An ABINIT bibliography database, that contains references of papers
in which ABINIT or one of its predecessors is available on the Web site.
3.E. Generation of the k-points, geometries, and starting wavefunctions.
-
3.E.1. The code can automatically generate symmetries from the primitive cell
and the position of atoms. In this case, it identifies
automatically the Bravais lattice, point group and space group.
Alternatively, it can start from the
symmetries and generate the atomic positions from the irreducible
set. Also, a database of the 230 spatial groups of symmetry
is built inside ABINIT.
-
3.E.2. Anti-ferromagnetic symmetry operations, and associated
magnetic space groups (Shubnikov groups) can be treated with the
same facility as usual space groups, including a database of the
1191 Shubnikov groups.
-
3.E.3. A geometry builder is available inside the code.
It can take one (or two) group
of atoms, rotate it, translate it and repeat it, then create vacancies.
-
3.E.4. The generation of special k point sets (Monkhorst-Pack sets)
and band structure k points can also be done directly inside ABINIT.
A list of interesting k point sets, can be generated automatically,
including a measure of their accuracy in term of integration
within the Brillouin Zone.
-
3.E.5. A utility for generating wavefunctions with new characteristic
(cut-off, k-point) from already existing wavefunctions with
different characteristics is available (newsp).
3.F. Automatic determination of input parameters.
-
3.F.1. Many defaults values are provided.
-
3.F.2. The FFT grid parameters can be automatically generated
from the cut-off energy and geometry of the system.
-
3.F.3. The number of bands and starting occupation numbers can be automatically
generated from the input set of atoms.
-
3.F.4. There is a database of atomic masses.
4. The programmer's point of view.
-
4.A. The code is distributed without charge under the
GNU General Public Licence (GPL). This
garantees that the future modifications of the code
stay available to the developpers and users for free.
This Copyright is often referred to as a "Copyleft".
-
4.B. The code is written in clean Fortran90. Strict programming rules
have been followed. These are documented. Comments are numerous, and
all in english.
-
4.C. Quick, fully automatic, testing of the code is available in the makefile,
giving diagnostics on the validity of computed energy, forces, stresses
and eigenvalues for five typical cases.
-
4.D. More extensive testing is provided in five batteries of tests
(altogether more than 350 different runs), with automatic comparison
with results of preceding versions. A specialized diff script (called
'fldiff') has been written in order to ease the diagnostic on the
suite of tests. A short one-line-per-test file is produced (report file).
In addition to tests of the correctness of the execution,
for the sequential or parallel version of the main code, as well as some
utilities, there are automatic diagnostics of the speed of crucial
routines, and the response to a load of up to 4 instances of the
main code, running concurrently.
-
4.E. Debugging facilities are provided inside the code, and can be directly
accessed from the input file. The compilation can be done in both
debugging or normal mode : the C-preprocessed files are either kept
or removed automatically.
-
4.F. "Design-by-contract" utility routines are present, as well as
a flag to preprocess the sources, and eliminate the design-by-contract
features in production mode.
Goto :
ABINIT home Page
|
Suggested acknowledgments
|
List of input variables
|
Tutorial home page
|
Bibliography
Help files :
New user's guide
|
Abinis (main)
|
Abinis (respfn)
|
Mrgddb
|
Anaddb
|
AIM (Bader)
|
Cut3D
|
Optic
|
Mrgscr