SIESTA (computer program)
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is an original method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA's efficiency stems from the use of 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 accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods.
4.1.5 / 4 February 2021
SIESTA's backronym is 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.
SIESTA has these main characteristics:
- It uses the standard Kohn-Sham selfconsistent density functional method in the 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).
- It uses norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.
- It uses 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.
- 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.
- 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 is written in Fortran 95 and memory is allocated dynamically.
- It may be compiled for serial or parallel execution (under MPI).
SIESTA routinely provides:
- Total and partial energies.
- Atomic forces.
- Stress tensor.
- Electric dipole moment.
- Atomic, orbital and bond populations (Mulliken).
- Electron density.
And also (though not all options are compatible):
- Geometry relaxation, fixed or variable cell.
- Constant-temperature molecular dynamics (Nose thermostat).
- Variable cell dynamics (Parrinello-Rahman).
- Spin polarized calculations (collinear or not).
- k-sampling of the Brillouin zone.
- Local and orbital-projected density of states.
- COOP and COHP curves for chemical bonding analysis.
- Dielectric polarization.
- Vibrations (phonons).
- Band structure.
- Ballistic electron transport under non-equilibrium (through TranSIESTA)
Strengths of SIESTAEdit
SIESTA main strengths are:
- Flexible code in accuracy
- It can tackle computationally demanding systems (systems currently out of the reach of plane-wave codes)
- High efficient parallelization
- Support for a professional use
The use of linear combination of numerical atomic orbitals makes SIESTA a flexible and efficient DFT code. SIESTA is able to produce very fast calculations with small basis sets, allowing computing systems with a thousand of atoms. At the same time, the use of more complete and accurate bases allows to achieve accuracies comparable to those of standard plane waves calculations, still at an advantageous computational cost.
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 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 strong localized electrons, transition metal oxides
- Spin-orbit coupling (SOC)
- Topological insulator, semiconductor structures, and quantum-transport calculations
- NEB (Nudged Elastic Band) (interfacing with LUA)
Solutions under developmentEdit
A number of post-processing tools for SIESTA have been developed. These programs can be helpful to process SIESTA output, or to supplement the functionality of the program.
Since its implementation, SIESTA has become quite popular, being increasingly used by researchers in geosciences, biology, and engineering (apart from those in its natural habitat of 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.
- García, Alberto; Papior, Nick; Akhtar, Arsalan; Artacho, Emilio; Blum, Volker; Bosoni, Emanuele; Brandimarte, Pedro; Brandbyge, Mads; Cerdá, J.I.; Corsetti, Fabiano; Cuadrado, Ramón; Dikan, Vladimir; Ferrer, Jaime; Gale, Julian; García-Fernández, Pablo; García-Suárez, V.M.; García, Sandra; Huhs, Georg; Illera, Sergio; Korytár, Richard; Koval, Peter; Lebedeva, Irina; Lin, Lin; López-Tarifa, Pablo; G. Mayo, Sara; Mohr, Stephan; Ordejón, Pablo; Postnikov, Andrei; Pouillon, Yann; Pruneda, Miguel; Robles, Roberto; Sánchez-Portal, Daniel; Soler, Jose M.; Ullah, Rafi; Yu, Victor Wen-zhe; Junquera, Javier (2020). "Siesta: Recent developments and applications". Journal of Chemical Physics. 152 (20): 204108. doi:10.1063/5.0005077. hdl:10902/20680. Postprint available at hdl:10261/213028.
- Izquierdo, J.; Vega, A.; Balbás, L.; Sánchez-Portal, Daniel; Junquera, Javier; Artacho, Emilio; Soler, Jose; Ordejón, Pablo (2000). "Systematic ab initio study of the electronic and magnetic properties of different pure and mixed iron systems". Physical Review B. 61 (20): 13639. Bibcode:2000PhRvB..6113639I. doi:10.1103/PhysRevB.61.13639.
- Robles, R.; Izquierdo, J.; Vega, A.; Balbás, L. (2001). "All-electron and pseudopotential study of the spin-polarization of the V(001) surface: LDA versus GGA". Physical Review B. 63 (17): 172406. arXiv:cond-mat/0012064. Bibcode:2001PhRvB..63q2406R. doi:10.1103/PhysRevB.63.172406.
- Soler, José M.; Artacho, Emilio; Gale, Julian D; García, Alberto; Junquera, Javier; Ordejón, Pablo; Sánchez-Portal, Daniel (2002). "The SIESTA method for ab initio order-N materials simulation". Journal of Physics: Condensed Matter. 14 (11): 2745–2779. arXiv:cond-mat/0104182. Bibcode:2002JPCM...14.2745S. doi:10.1088/0953-8984/14/11/302.
- "Release of Siesta-4.1.5".
- "SIESTA development platform on GitLab".
- Mashaghi A et al. Hydration strongly affects the molecular and electronic structure of membrane phospholipids J. Chem. Phys. 136, 114709 (2012) 
- 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 
- Mashaghi A et al. Enhanced Autoionization of Water at Phospholipid Interfaces. J. Phys. Chem. C, 2013, 117 (1), pp 510–514