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SIESTA (computer program)

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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.

It uses a density functional theory code that predicts the physical properties of a collection of atoms.

Its main characteristics are:

  • 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)

Properties that can be predicted using the code include Kohn–Sham band-structures, electron density, and Mulliken populations.

Applications

SIESTA has been applied to study the structure, dynamics and electronic properties of large biomolecules and bimolecular assemblies.[1][2][3]

See also

References

  • 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). 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" (abstract). 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.
  1. ^ Mashaghi A et al. Hydration strongly affects the molecular and electronic structure of membrane phospholipids J. Chem. Phys. 136, 114709 (2012) [1]
  2. ^ 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 [2]
  3. ^ Mashaghi A et al. Enhanced Autoionization of Water at Phospholipid Interfaces. J. Phys. Chem. C, 2013, 117 (1), pp 510–514 [3]


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