SIESTA (computer program): Difference between revisions

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

{{Peacock|date=November 2021}}

{{Infobox software

| name = SIESTA

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| discontinued = <!-- Set to yes, if software is discontinued, otherwise omit. -->

| latest release version = 5.4.1.50<ref>{{cite web|url=https://siesta-project.org/siesta/2021news/022025/0405/28/release-4.1.5.html4.0/|title=Release of Siesta-5.4.1.50}}</ref>

| latest release date = {{Start date and age|20212025|0205|0428|df=yes}}

<!--| latest preview version = 4.1-b4<ref>{{cite web|url=https://siesta-project.org/siesta/2018/11/04/release-4.1-b4.html|title=Release of Siesta-4.1-b4.}}</ref>

| latest preview date = {{Start date and age|2018|11|04|df=yes}}

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

| qid = Q7390304

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| license = [[GPLv3]]

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

| AsOf = 20212025

}}

'''SIESTA''' ('''Spanish Initiative for Electronic Simulations with Thousands of Atoms''') is an original method and its computer program implementation, to performefficiently efficientperform [[electronic structure]] calculations and [[ab initio]] [[molecular dynamics]] simulations of [[molecules]] and solids. SIESTA's efficiency stems from the use ofuses strictly localized basis sets and from the implementation of [[linear-scaling algorithms which can be applied to suitable systems]]. A very important feature of the code is that its accuracyAccuracy and costspeed can be tunedset 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]].

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

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- 5.4.1.50, was released on 428 FebruaryMay 20212025.

== Features ==

SIESTA has these main characteristics:

* 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 [[pseudopotential]]s in their fully non -local (Kleinman-Bylander) form.

* It uses [[atomic orbital]]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]].

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

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

* Density functional Bogoliubov-de Gennes theory for superconductors

== Strengths of SIESTA ==

SIESTA's main strengths are:

# Flexible codeaccuracy inand accuracyspeed.

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

# High efficientEfficient parallelization.

The use of a linear combination of numerical atomic orbitals makes SIESTA a flexible and efficient DFT code. SIESTA is able tocan produce very fast calculations with small basis sets, allowing computingthe computation of systems with a thousandthousands of atoms. At the same timeAlternatively, the use of more complete and accurate bases allows to achieveachieves accuracies comparable to those of standard plane waveswave calculations, still at an advantageouswith computationalcompetitive costperformance.

== 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 polarized-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 strongstrongly localized electrons, transition metal oxides

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

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

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== Post-processing tools ==

ASeveral number of '''post-processing tools for SIESTA''' have been developed. These programs can be helpful to process SIESTA output, or to supplement the functionality ofprovide theadditional programfeatures.

== Applications ==

Since its implementation, SIESTA has become quite popular, being increasinglybeen used by researchers in geosciences, biology, and engineering (apart from those in its natural habitatextending ofbeyond materials physics and chemistry) and has been applied to a large variety of systems including surfaces, adsorbates, nanotubes, nanoclusters, biological molecules, amorphous semiconductors, ferroelectric films, low-dimensional metals, etc.<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 }}

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{{Chemistry software}}

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