SIESTA (computer program): Difference between revisions

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{{redirect|SIESTA|other uses|Siesta (disambiguation)}}

{{Infobox software

'''SIESTA''' ('''Spanish Initiative for Electronic Simulations with Thousands of Atoms''') is an original method and a software implementation for performing [[electronic structure]] calculations and [[ab initio]] [[molecular dynamics]] simulations of [[molecules]] and solids.

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| released = {{Start date and age|1996|df=yes}}

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| latest release version = 5.4.0<ref>{{cite web|url=https://siesta-project.org/siesta/news/2025/05/28/release-5.4.0/|title=Release of Siesta-5.4.0}}</ref>

| latest release date = {{Start date and age|2025|05|28|df=yes}}

| repo = {{URL|https://gitlab.com/siesta-project/siesta/}}

| qid = Q7390304

| programming language = [[Fortran]]

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| language = English

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| genre = [[Computational Chemistry]]

| license = [[GPLv3]]

| website = {{URL|siesta-project.org}}

| AsOf = 2025

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'''SIESTA''' ('''Spanish Initiative for Electronic Simulations with Thousands of Atoms''') is an original method and its computer program implementation, to efficiently perform [[electronic structure]] calculations and [[ab initio]] [[molecular dynamics]] simulations of [[molecules]] and solids. SIESTA uses strictly localized basis sets and the implementation of [[linear-scaling algorithms]]. Accuracy and speed can be set in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as the [[Plane wave expansion method|plane-wave]] and [[all-electron methods]].

It uses a [[density functional theory]] code that predicts the physical properties of a collection of [[atom]]s.

SIESTA's [[backronym]] is the Spanish Initiative for Electronic Simulations with Thousands of Atoms.

Its main characteristics are:

* It uses the standard Kohn-Sham selfconsistent density functional method in the [[Local-density approximation|local density]] (LDA-LSD) and generalized gradient (GGA) approximations, as well as in a non local functional that includes [[van der Waals interactions]] (VDW-DF).

Since 13 May 2016, with the 4.0 version announcement, SIESTA is released under the terms of the [[GPL]] open-source license. Source packages and access to the development versions can be obtained from the [[DevOps]] platform on [[GitLab]].<ref>{{cite web|url=https://gitlab.com/siesta-project/siesta/|title=SIESTA development platform on GitLab.}}</ref> The latest version, Siesta 5.4.0, was released on 28 May 2025.

* It uses norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.

* It uses [[Atomic orbital|atomic orbitals]] as a basis set, allowing unlimited multiple-zeta and angular momenta, polarization and off-site orbitals. The radial shape of every orbital is numerical and any shape can be used and provided by the user, with the only condition that it has to be of finite support, i.e., it has to be strictly zero beyond a user-provided distance from the corresponding nucleus. Finite-support basis sets are the key for calculating the Hamiltonian and overlap matrices in O(N) operations.

== Features ==

* Projects the electron wavefunctions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements.

ItsSIESTA has these main characteristics are:

* Besides the standard Rayleigh-Ritz eigenstate method, it allows the use of localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), making the computer time and memory scale linearly with the number of atoms. Simulations with several hundred atoms are feasible with modest workstations.

* It uses the standard [[Kohn–Sham equations|Kohn-Sham]] selfconsistentself-consistent [[Density functional theory|density functional]] method in the [[Local-density approximation|local density]] (LDA-LSD) and generalized gradient (GGA) approximations, as well as in a non -local functionalfunction that includes [[van der Waals interactions]] (VDW-DF).

* It uses norm-conserving pseudopotentials[[pseudopotential]]s in their fully nonlocalnon-local (Kleinman-Bylander) form.

* It uses [[Atomicatomic orbital|atomic orbitals]]s as a basis set, allowing unlimited multiple-zeta and angular momenta, polarization, and off-site orbitals. The radial shape of every orbital is numerical, and any shape can be used and provided by the user, with the only condition that it has to be of finite support, i.e., it has to be strictly zero beyond a user-provided distance from the corresponding nucleus. Finite-support basis sets are the key forto calculating the Hamiltonian and overlap matrices in O(N) operations.

* Projects the electron wavefunctionswave functions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements.

* Besides the standard [[Rayleigh–Ritz method|Rayleigh-Ritz eigenstate method]], it allows the use of localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), making the computer time and memory scale linearly with the number of atoms. Simulations with several hundred atoms are feasible with modest workstations.

* It is written in [[Fortran 95]] and memory is allocated dynamically.

* It may be compiled for serial or parallel execution (under MPI parallelization, OpenMP threading, and GPU offloading).

SIESTA routinely provides:

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* Stress tensor.

* Electric dipole moment.

* Atomic, orbital, and bond populations ([[Mulliken population analysis|Mulliken]]).

* Electron density.

And also (though not all options are compatible):

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* Constant-temperature molecular dynamics (Nose thermostat).

* Variable cell dynamics (Parrinello-Rahman).

* [[Spin polarization|Spin -polarized]] calculations (collinear or not).

* k-sampling of the [[Brillouin zone]].

* LocalThe local and orbital-projected [[density of states]].

* COOP and COHP curves for chemical bonding analysis.

* [[Dielectric polarization]].

* Vibrations (phonons).

* [[Electronic band structure|Band structure]].

* Ballistic electron transport under non-equilibrium (through TranSIESTA)

* Density functional Bogoliubov-de Gennes theory for superconductors

== Strengths of SIESTA ==

Properties that can be predicted using the code include [[Kohn–Sham equations|Kohn–Sham]] band-structures, electron density, and [[Mulliken population analysis|Mulliken]] populations.

SIESTA's main strengths are:

# Flexible accuracy and speed.

# It can tackle computationally demanding systems (systems currently out of the reach of plane-wave codes).{{Citation needed|date=November 2021}}

# Efficient parallelization.

The use of a linear combination of numerical atomic orbitals makes SIESTA a DFT code. SIESTA can produce very fast calculations with small basis sets, allowing the computation of systems with thousands of atoms. Alternatively, the use of more complete and accurate bases achieves accuracies comparable to those of standard plane wave calculations, with competitive performance.

== Implemented Solutions ==

SIESTA is in continuous development since it was implemented in 1996. The main solutions implemented in the current version are:

* Collinear and non-collinear spin-polarised calculations

* Efficient implementation of Van der Waals functional

* [[Wannier function]] implementation

* TranSIESTA/TBTrans module with any number of electrodes N>=1

* On-site Coulomb corrections (DFT+U)

* Description of strongly localized electrons, transition metal oxides

* [[Spin-orbit coupling]] (SOC)

* Topological insulator, semiconductor structures, and quantum-transport calculations

* NEB (Nudged Elastic Band) (interfacing with [https://github.com/siesta-project/flos LUA])

== Solutions under development ==

* [[GW approximation]]

* Time Dependent DFT ([[TDDFT]])

* [[Hybrid functional|Hybrid Functionals]]

* Band unfolding

* Poisson solver in real space

== Post-processing tools ==

Several post-processing tools for SIESTA have been developed. These programs process SIESTA output or provide additional features.

== Applications ==

Since its implementation, SIESTA has been appliedused toby studyresearchers thein structuregeosciences, dynamicsbiology, and electronicengineering properties(extending ofbeyond largematerials biomoleculesphysics and bimolecularchemistry) and has been applied to a large variety of systems including surfaces, adsorbates, nanotubes, nanoclusters, biological molecules, amorphous semiconductors, ferroelectric films, low-dimensional metals, assembliesetc.<ref>Mashaghi A et al. Hydration strongly affects the molecular and electronic structure of membrane phospholipids J. Chem. Phys. 136, 114709 (2012) [http://scitation.aip.org/content/aip/journal/jcp/136/11/10.1063/1.3694280]</ref><ref>Mashaghi A et al. Interfacial Water Facilitates Energy Transfer by Inducing Extended Vibrations in Membrane Lipids, J. Phys. Chem. B, 2012, 116 (22), pp 6455–6460 [http://pubs.acs.org/doi/abs/10.1021/jp302478a]</ref><ref>Mashaghi A et al. Enhanced Autoionization of Water at Phospholipid Interfaces. J. Phys. Chem. C, 2013, 117 (1), pp 510–514 [http://pubs.acs.org/doi/abs/10.1021/jp3119617]</ref>

== See also ==

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==References==

* {{Cite journal|doi=10.1063/5.0005077|title=Siesta: Recent developments and applications|year=2020|last1=García|first1=Alberto|last2=Papior|first2=Nick|last3=Akhtar|first3=Arsalan|last4=Artacho|first4=Emilio|last5=Blum|first5=Volker|last6=Bosoni|first6=Emanuele|last7=Brandimarte|first7=Pedro|last8=Brandbyge|first8=Mads|last9=Cerdá|first9=J.I.|last10=Corsetti|first10=Fabiano|last11=Cuadrado|first11=Ramón|last12=Dikan|first12=Vladimir|last13=Ferrer|first13=Jaime|last14=Gale|first14=Julian|last15=García-Fernández|first15=Pablo|last16=García-Suárez|first16=V.M.|last17=García|first17=Sandra|last18=Huhs|first18=Georg|last19=Illera|first19=Sergio|last20=Korytár|first20=Richard|last21=Koval|first21=Peter|last22=Lebedeva|first22=Irina|last23=Lin|first23=Lin|last24=López-Tarifa|first24=Pablo|last25=G. Mayo|first25=Sara|last26=Mohr|first26=Stephan|last27=Ordejón|first27=Pablo|last28=Postnikov|first28=Andrei|last29=Pouillon|first29=Yann|last30=Pruneda|first30=Miguel|last31=Robles|first31=Roberto|last32=Sánchez-Portal|first32=Daniel|last33=Soler|first33=Jose M.|last34=Ullah|first34=Rafi|last35=Yu|first35=Victor Wen-zhe|last36=Junquera|first36=Javier|journal=Journal of Chemical Physics|volume=152|issue=20|pages=204108|pmid=32486661 |hdl=10902/20680|s2cid=219179270 |hdl-access=free|arxiv=2006.01270}} Postprint is available at {{hdl|10261/213028}}.

* {{Cite journal|doi=10.1103/PhysRevB.61.13639|title=Systematic ab initio study of the electronic and magnetic properties of different pure and mixed iron systems|year=2000|last1=Izquierdo|first1=J.|last2=Vega|first2=A.|last3=Balbás|first3=L.|last4=Sánchez-Portal|first4=Daniel|last5=Junquera|first5=Javier|last6=Artacho|first6=Emilio|last7=Soler|first7=Jose|last8=Ordejón|first8=Pablo|journal=Physical Review B|volume=61|issue=20|pages=13639|bibcode = 2000PhRvB..6113639I }}

* {{Cite journal|doi=10.1103/PhysRevB.63.172406|title=All-electron and pseudopotential study of the spin-polarization of the V(001) surface: LDA versus GGA|year=2001|last1=Robles|first1=R.|last2=Izquierdo|first2=J.|last3=Vega|first3=A.|last4=Balbás|first4=L.|journal=Physical Review B|volume=63|issue=17|pages=172406|arxiv = cond-mat/0012064 |bibcode = 2001PhRvB..63q2406R |s2cid=17632035 }}

*{{cite journal | url = http://www.iop.org/EJ/abstract/0953-8984/14/11/302/ | title = The SIESTA method for ''ab initio'' order-''N'' materials simulation | journal = Journal of Physics: Condensed Matter | last1 = Soler | first1 = José M. | volume = 14 | pages = 2745–2779 | year = 2002 | doi = 10.1088/0953-8984/14/11/302 | format = abstract |arxiv = cond-mat/0104182 |bibcode = 2002JPCM...14.2745S | last2 = Artacho | first2 = Emilio | last3 = Gale | first3 = Julian D | last4 = García | first4 = Alberto | last5 = Junquera | first5 = Javier | last6 = Ordejón | first6 = Pablo | last7 = Sánchez-Portal | first7 = Daniel | issue = 11 | s2cid = 250812001 }}

{{Reflist}}

== External links ==

* [http://wwwsiesta-project.icmab.es/siestaorg/ SIESTA website]

* [http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf SIESTA tutorial] - an introduction to SIESTA, addressing the tasks for which SIESTA is better suited than other ab initio codes.

* [https://launchpadgitlab.netcom/siesta-project/siesta/ Download SIESTA]

* [httphttps://www.simunesimuneatomistics.eucom Professional support for SIESTA]

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