A review of the present status, recent enhancements, and applicability of the Siesta program is presented. Since its debut in the mid-1990s, Siesta’s flexibility, efficiency, and free distribution have given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of Siesta combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here, we describe the more recent implementations on top of that core scheme, which include full spin–orbit interaction, non-repeated and multiple-contact ballistic electron transport, density functional theory (DFT)+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as wannier90 and the second-principles modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering Siesta runs, and various post-processing utilities. Siesta has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low-level libraries, as well as data standards and support for them, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments.

1.
J. M.
Soler
,
E.
Artacho
,
J. D.
Gale
,
A.
García
,
J.
Junquera
,
P.
Ordejón
, and
D.
Sánchez-Portal
, “
The SIESTA method for ab initio order-n materials simulation
,”
J. Phys.: Condens. Matter
14
,
2745
2779
(
2002
).
2.
E.
Artacho
,
E.
Anglada
,
O.
Diéguez
,
J. D.
Gale
,
A.
García
,
J.
Junquera
,
R. M.
Martin
,
P.
Ordejón
,
J. M.
Pruneda
,
D.
Sánchez-Portal
, and
J. M.
Soler
, “
The SIESTA method; developments and applicability
,”
J. Phys.: Condens. Matter
20
,
064208
(
2008
).
3.
G.
Galli
, “
Linear scaling methods for electronic structure calculations and quantum molecular dynamics simulations
,”
Curr. Opin. Solid State Mater. Sci.
1
,
864
874
(
1996
).
4.
S.
Goedecker
, “
Linear scaling electronic structure methods
,”
Rev. Mod. Phys.
71
,
1085
1123
(
1999
).
5.
P.
Ordejón
,
E.
Artacho
, and
J. M.
Soler
, “
Self-consistent order-n density-functional calculations for very large systems
,”
Phys. Rev. B
53
,
R10441
R10444
(
1996
).
6.
D.
Sánchez-Portal
,
P.
Ordejón
,
E.
Artacho
, and
J. M.
Soler
, “
Density-functional method for very large systems with LCAO basis sets
,”
Int. J. Quantum Chem.
65
,
453
461
(
1997
).
7.
O. F.
Sankey
and
D. J.
Niklewski
, “
Ab initio multicenter tight-binding model for molecular-dynamics simulations and other applications in covalent systems
,”
Phys. Rev. B
40
,
3979
3995
(
1989
).
8.
E.
Artacho
,
D.
Sánchez-Portal
,
P.
Ordejón
,
A.
García
, and
J. M.
Soler
, “
Linear-scaling ab initio calculations for large and complex systems
,”
Phys. Status Solidi B
215
,
809
817
(
1999
).
9.
J.
Junquera
,
O.
Paz
,
D.
Sánchez-Portal
, and
E.
Artacho
, “
Numerical atomic orbitals for linear-scaling calculations
,”
Phys. Rev. B
64
,
235111
(
2001
).
10.
E.
Anglada
,
J. M.
Soler
,
J.
Junquera
, and
E.
Artacho
, “
Systematic generation of finite-range atomic basis sets for linear-scaling calculations
,”
Phys. Rev. B
66
,
205101
(
2002
).
11.
See http://www.openmx-square.org/ for information about the OpenMX code.
12.
See https://www.synopsys.com/silicon/quantumatk.html for information about the QuantumATK package.
13.
V.
Blum
,
R.
Gehrke
,
F.
Hanke
,
P.
Havu
,
V.
Havu
,
X.
Ren
,
K.
Reuter
, and
M.
Scheffler
, “
Ab initio molecular simulations with numeric atom-centered orbitals
,”
Comput. Phys. Commun.
180
,
2175
2196
(
2009
).
14.
A.
Carreras
,
S.
Conejeros
,
A.
Camón
,
A.
García
,
N.
Casañ-Pastor
,
P.
Alemany
, and
E.
Canadell
, “
Charge delocalization, oxidation states, and silver mobility in the mixed silver–copper oxide AgCuO2
,”
Inorg. Chem.
58
,
7026
7035
(
2019
).
15.
M.
Brandbyge
,
J.-L.
Mozos
,
P.
Ordejón
,
J.
Taylor
, and
K.
Stokbro
, “
Density-functional method for nonequilibrium electron transport
,”
Phys. Rev. B
65
,
165401
(
2002
).
16.
F.
Corsetti
,
E.
Artacho
,
J. M.
Soler
,
S. S.
Alexandre
, and
M.-V.
Fernández-Serra
, “
Room temperature compressibility and diffusivity of liquid water from first principles
,”
J. Chem. Phys.
139
,
194502
(
2013
).
17.
X.
Gonze
,
B.
Amadon
,
P.-M.
Anglade
,
J.-M.
Beuken
,
F.
Bottin
,
P.
Boulanger
,
F.
Bruneval
,
D.
Caliste
,
R.
Caracas
,
M.
Côté
,
T.
Deutsch
,
L.
Genovese
,
P.
Ghosez
,
M.
Giantomassi
,
S.
Goedecker
,
D. R.
Hamann
,
P.
Hermet
,
F.
Jollet
,
G.
Jomard
,
S.
Leroux
,
M.
Mancini
,
S.
Mazevet
,
M. J. T.
Oliveira
,
G.
Onida
,
Y.
Pouillon
,
T.
Rangel
,
G.-M.
Rignanese
,
D.
Sangalli
,
R.
Shaltaf
,
M.
Torrent
,
M. J.
Verstraete
,
G.
Zerah
, and
J. W.
Zwanziger
, “
ABINIT: First-principles approach to material and nanosystem properties
,”
Comput. Phys. Commun.
180
,
2582
2615
(
2009
).
18.
See https://www.gnu.org/licenses/gpl-3.0.html for more details about the GPL.
19.
See https://launchpad.net/siesta for more details about the Launchpad platform for Siesta development.
20.
See https://gitlab.com/siesta-project for more details about the Gitlab platform for Siesta development.
21.
A.
García
,
M. J.
Verstraete
,
Y.
Pouillon
, and
J.
Junquera
, “
The PSML format and library for norm-conserving pseudopotential data curation and interoperability
,”
Comput. Phys. Commun.
227
,
51
71
(
2018
).
22.
See https://siesta-project.github.io/psml-docs for more information about the PSML ecosystem; accessed November 2019.
23.
D. R.
Hamann
, “
Optimized norm-conserving Vanderbilt pseudopotentials
,”
Phys. Rev. B
88
,
085117
(
2013
).
24.
ATOM code for the generation of norm-conserving pseudopotentials. The version maintained by the SIESTA project can be accessed at http://icmab.es/siesta/Pseudopotentials/index.html. An alternative version is available at http://bohr.inesc-mn.pt/jlm/pseudo.html; accessed July 2017.
25.
M. J.
van Setten
,
M.
Giantomassi
,
E.
Bousquet
,
M. J.
Verstraete
,
D. R.
Hamann
,
X.
Gonze
, and
G.-M.
Rignanese
, “
The PSEUDODOJO: Training and grading a 85 element optimized norm-conserving pseudopotential table
,”
Comput. Phys. Commun.
226
,
39
54
(
2018
).
26.
See http://www.pseudo-dojo.org for information about the Pseudo-Dojo project and database.
27.
X.
Gonze
,
F.
Jollet
,
F.
Abreu Araujo
,
D.
Adams
,
B.
Amadon
,
T.
Applencourt
,
C.
Audouze
,
J.-M.
Beuken
,
J.
Bieder
,
A.
Bokhanchuk
,
E.
Bousquet
,
F.
Bruneval
,
D.
Caliste
,
M.
Côté
,
F.
Dahm
,
F.
Da Pieve
,
M.
Delaveau
,
M.
Di Gennaro
,
B.
Dorado
,
C.
Espejo
,
G.
Geneste
,
L.
Genovese
,
A.
Gerossier
,
M.
Giantomassi
,
Y.
Gillet
,
D. R.
Hamann
,
L.
He
,
G.
Jomard
,
J.
Laflamme Janssen
,
S.
Le Roux
,
A.
Levitt
,
A.
Lherbier
,
F.
Liu
,
I.
Lukačević
,
A.
Martin
,
C.
Martins
,
M. J. T.
Oliveira
,
S.
Poncé
,
Y.
Pouillon
,
T.
Rangel
,
G.-M.
Rignanese
,
A. H.
Romero
,
B.
Rousseau
,
O.
Rubel
,
A. A.
Shukri
,
M.
Stankovski
,
M.
Torrent
,
M. J.
Van Setten
,
B.
Van Troeye
,
M. J.
Verstraete
,
D.
Waroquiers
,
J.
Wiktor
,
B.
Xu
,
A.
Zhou
, and
J. W.
Zwanziger
, “
Recent developments in the ABINIT software package
,”
Comput. Phys. Commun.
205
,
106
131
(
2016
).
28.
V. I.
Anisimov
,
J.
Zaanen
, and
O. K.
Andersen
, “
Band theory and Mott insulators: Hubbard U instead of stoner I
,”
Phys. Rev. B
44
,
943
954
(
1991
).
29.
B.
Himmetoglu
,
A.
Floris
,
S.
de Gironcoli
, and
M.
Cococcioni
, “
Hubbard-corrected DFT energy functionals: The LDA+U description of correlated systems
,”
Int. J. Quantum Chem.
114
,
14
49
(
2014
).
30.
S. L.
Dudarev
,
G. A.
Botton
,
S. Y.
Savrasov
,
C. J.
Humphreys
, and
A. P.
Sutton
, “
Electron-energy-loss spectra and the structural stability of nickel oxide: An LSDA+U study
,”
Phys. Rev. B
57
,
1505
1509
(
1998
).
31.
M.
Cococcioni
and
S.
de Gironcoli
, “
Linear response approach to the calculation of the effective interaction parameters in the LDA+U method
,”
Phys. Rev. B
71
,
035105
(
2005
).
32.
R. J.
Powell
and
W. E.
Spicer
, “
Optical properties of NiO and CoO
,”
Phys. Rev. B
2
,
2182
2193
(
1970
).
33.
H. A.
Alperin
,
J. Phys. Soc. Jpn. Suppl. B
17
,
12
(
1962
).
34.
A. K.
Cheetham
and
D. A. O.
Hope
, “
Magnetic ordering and exchange effects in the antiferromagnetic solid solutions MnxNi1−xO
,”
Phys. Rev. B
27
,
6964
6967
(
1983
).
35.
M.
Dion
,
H.
Rydberg
,
E.
Schröder
,
D. C.
Langreth
, and
B. I.
Lundqvist
, “
van der Waals density functional for general geometries
,”
Phys. Rev. Lett.
92
,
246401
(
2004
).
36.
K.
Berland
and
P.
Hyldgaard
, “
Exchange functional that tests the robustness of the plasmon description of the van der Waals density functional
,”
Phys. Rev. B
89
,
035412
(
2014
).
37.
G.
Román-Pérez
and
J. M.
Soler
, “
Efficient implementation of a van der Waals density functional: Application to double-wall carbon nanotubes
,”
Phys. Rev. Lett.
103
,
096102
(
2009
).
38.
O. A.
Vydrov
and
T.
Van Voorhis
, “
Nonlocal van der Waals density functional: The simpler the better
,”
J. Chem. Phys.
133
,
244103
(
2010
).
39.
L.
Kong
,
G.
Román-Pérez
,
J. M.
Soler
, and
D. C.
Langreth
, “
Energetics and dynamics of h2 adsorbed in a nanoporous material at low temperature
,”
Phys. Rev. Lett.
103
,
096103
(
2009
).
40.
H.
Gonzalez-Herrero
,
J. M.
Gomez-Rodriguez
,
P.
Mallet
,
M.
Moaied
,
J. J.
Palacios
,
C.
Salgado
,
M. M.
Ugeda
,
J.-Y.
Veuillen
,
F.
Yndurain
, and
I.
Brihuega
, “
Atomic-scale control of graphene magnetism by using hydrogen atoms
,”
Science
352
,
437
441
(
2016
).
41.
J.
Wang
,
G.
Román-Pérez
,
J. M.
Soler
,
E.
Artacho
, and
M.-V.
Fernández-Serra
, “
Density, structure, and dynamics of water: The effect of van der Waals interactions
,”
J. Chem. Phys.
134
,
024516
(
2011
).
42.
J.
Heyd
,
G. E.
Scuseria
, and
M.
Ernzerhof
, “
Hybrid functionals based on a screened Coulomb potential
,”
J. Chem. Phys.
118
,
8207
8215
(
2003
).
43.
J.
Heyd
,
G. E.
Scuseria
, and
M.
Ernzerhof
, “
Erratum: “Hybrid functionals based on a screened Coulomb potential”
,”
J. Chem. Phys.
124
,
219906
(
2006
).
44.
A. V.
Krukau
,
O. A.
Vydrov
,
A. F.
Izmaylov
, and
G. E.
Scuseria
, “
Influence of the exchange screening parameter on the performance of screened hybrid functionals
,”
J. Chem. Phys.
125
,
224106
(
2006
).
45.
H.
Shang
,
Z.
Li
, and
J.
Yang
, “
Implementation of screened hybrid density functional for periodic systems with numerical atomic orbitals: Basis function fitting and integral screening
,”
J. Chem. Phys.
135
,
034110
(
2011
).
46.
See https://sourceforge.net/projects/libint/ for provided by
E.
Valeev
and
J. T.
Fermann
.
47.
S.
Obara
and
A.
Saika
, “
Efficient recursive computation of molecular integrals over cartesian Gaussian functions
,”
J. Chem. Phys.
84
,
3963
3974
(
1986
).
48.
M.
Head-Gordon
and
J. A.
Pople
, “
A method for two-electron Gaussian integral and integral derivative evaluation using recurrence relations
,”
J. Chem. Phys.
89
,
5777
5786
(
1988
).
49.
J. P.
Perdew
,
K.
Burke
, and
M.
Ernzerhof
, “
Generalized gradient approximation made simple
,”
Phys. Rev. Lett.
77
,
3865
3868
(
1996
).
50.
C.
Kittel
,
Introduction to Solid State Physics
(
John Wiley & Sons
,
New York
,
1986
).
51.
S. H.
Wemple
, “
Polarization fluctuations and the optical-absorption edge in BaTiO3
,”
Phys. Rev. B
2
,
2679
2689
(
1970
).
52.
R.
Cuadrado
and
J. I.
Cerdá
, “
Fully relativistic pseudopotential formalism under an atomic orbital basis: Spin–orbit splittings and magnetic anisotropies
,”
J. Phys.: Condens. Matter
24
,
086005
(
2012
).
53.
L.
Fernández-Seivane
,
M. A.
Oliveira
,
S.
Sanvito
, and
J.
Ferrer
, “
On-site approximation for spin–orbit coupling in linear combination of atomic orbitals density functional methods
,”
J. Phys.: Condens. Matter
18
,
7999
8013
(
2006
).
54.
F.
Fernández-Seivane
,
M. A.
Oliveira
,
S.
Sanvito
, and
J.
Ferrer
, “
Erratum: “On-site approximation for spin–orbit coupling in LCAO density functional methods”
,”
J. Phys.: Condens. Matter
19
,
489001
(
2007
).
55.
L. A.
Hemstreet
,
C. Y.
Fong
, and
J. S.
Nelson
, “
First-principles calculations of spin-orbit splittings in solids using nonlocal separable pseudopotentials
,”
Phys. Rev. B
47
,
4238
(
1993
).
56.
F.
Zirkelbach
,
P.-Y.
Prodhomme
,
P.
Han
,
R.
Cherian
, and
G.
Bester
, “
Large-scale atomic effective pseudopotential program including an efficient spin-orbit coupling treatment in real space
,”
Phys. Rev. B
91
,
075119
(
2015
).
57.
V. W.-z.
Yu
,
F.
Corsetti
,
A.
García
,
W. P.
Huhn
,
M.
Jacquelin
,
W.
Jia
,
B.
Lange
,
L.
Lin
,
J.
Lu
,
W.
Mi
,
A.
Seifitokaldani
,
Á.
Vázquez-Mayagoitia
,
C.
Yang
,
H.
Yang
, and
V.
Blum
, “
ELSI: A unified software interface for Kohn-Sham electronic structure solvers
,”
Comput. Phys. Commun.
222
,
267
285
(
2018
).
58.
V. W.
zhe Yu
,
C.
Campos
,
W.
Dawson
,
A.
García
,
V.
Havu
,
B.
Hourahine
,
W. P.
Huhn
,
M.
Jacquelin
,
W.
Jia
,
M.
Keçeli
,
R.
Laasner
,
Y.
Li
,
L.
Lin
,
J.
Lu
,
J.
Moussa
,
J. E.
Roman
,
Á.
Vázquez-Mayagoitia
,
C.
Yang
, and
V.
Blum
, “
ELSI—An open infrastructure for electronic structure solvers
,” arXiv:1912.13403 [physics.comp-ph] (
2019
).
59.
J.
Choi
,
J.
Demmel
,
I.
Dhillon
,
J.
Dongarra
,
S.
Ostrouchov
,
A.
Petitet
,
K.
Stanley
,
D.
Walker
, and
R. C.
Whaley
, “
SCALAPACK: A portable linear algebra library for distributed memory computers—Design issues and performance
,”
Comput. Phys. Commun.
97
,
1
15
(
1996
).
60.
T.
Auckenthaler
,
V.
Blum
,
H.-J.
Bungartz
,
T.
Huckle
,
R.
Johanni
,
L.
Krämer
,
B.
Lang
,
H.
Lederer
, and
P. R.
Willems
, “
Parallel solution of partial symmetric eigenvalue problems from electronic structure calculations
,”
Parallel Comput.
37
,
783
794
(
2011
).
61.
A.
Marek
,
V.
Blum
,
R.
Johanni
,
V.
Havu
,
B.
Lang
,
T.
Auckenthaler
,
A.
Heinecke
,
H.-J.
Bungartz
, and
H.
Lederer
, “
The ELPA library: Scalable parallel eigenvalue solutions for electronic structure theory and computational science
,”
J. Phys.: Condens. Matter
26
,
213201
(
2014
).
62.
P.
Kuṡ
,
A.
Marek
,
S.
Koecher
,
H.-H.
Kowalski
,
C.
Carbogno
,
C.
Scheurer
,
K.
Reuter
,
M.
Scheffler
, and
H.
Lederer
, “
Optimizations of the eigensolvers in the ELPA library
,”
Parallel Comput.
85
,
167
177
(
2019
).
63.
S.
Goedecker
, “
Integral representation of the fermi distribution and its applications in electronic-structure calculations
,”
Phys. Rev. B
48
,
17573
17575
(
1993
).
64.
S.
Mohr
,
W.
Dawson
,
M.
Wagner
,
D.
Caliste
,
T.
Nakajima
, and
L.
Genovese
, “
Efficient computation of sparse matrix functions for large-scale electronic structure calculations: The CheSS library
,”
J. Chem. Theory Comput.
13
,
4684
4698
(
2017
).
65.
L.
Genovese
,
A.
Neelov
,
S.
Goedecker
,
T.
Deutsch
,
S. A.
Ghasemi
,
A.
Willand
,
D.
Caliste
,
O.
Zilberberg
,
M.
Rayson
,
A.
Bergman
, and
R.
Schneider
, “
Daubechies wavelets as a basis set for density functional pseudopotential calculations
,”
J. Chem. Phys.
129
,
014109
(
2008
).
66.
L.
Lin
,
M.
Chen
,
C.
Yang
, and
L.
He
, “
Accelerating atomic orbital-based electronic structure calculation via pole expansion and selected inversion
,”
J. Phys.: Condens. Matter
25
,
295501
(
2013
).
67.
L.
Lin
,
A.
García
,
G.
Huhs
, and
C.
Yang
, “
SIESTA-PEXSI: Massively parallel method for efficient and accurate ab initio materials simulation without matrix diagonalization
,”
J. Phys.: Condens. Matter
26
,
305503
(
2014
).
68.
W.
Hu
,
L.
Lin
,
C.
Yang
, and
J.
Yang
, “
Electronic structure and aromaticity of large-scale hexagonal graphene nanoflakes
,”
J. Chem. Phys.
141
,
214704
(
2014
).
69.
F.
Corsetti
, “
The orbital minimization method for electronic structure calculations with finite-range atomic basis sets
,”
Comput. Phys. Commun.
185
,
873
883
(
2014
).
70.
T.
Imamura
,
S.
Yamada
, and
M.
Machida
, “
Development of a high-performance eigensolver on a peta-scale next-generation supercomputer system
,”
Prog. Nucl. Sci. Technol.
2
,
643
650
(
2011
).
71.
J.
Dongarra
,
M.
Gates
,
A.
Haidar
,
J.
Kurzak
,
P.
Luszczek
,
S.
Tomov
, and
I.
Yamazaki
, “
Accelerating numerical dense linear algebra calculations with GPUs
,” in
Numerical Computations with GPUs
(
Springer, Cham
,
2014
), pp.
1
26
.
72.
V.
Hernandez
,
J. E.
Roman
, and
V.
Vidal
, “
SLEPc: A scalable and flexible toolkit for the solution of eigenvalue problems
,”
ACM Trans. Math. Software
31
,
351
362
(
2005
).
73.
W.
Dawson
and
T.
Nakajima
, “
Massively parallel sparse matrix function calculations with NTPoly
,”
Comput. Phys. Commun.
225
,
154
165
(
2018
).
74.
A.
Tsolakidis
,
D.
Sánchez-Portal
, and
R. M.
Martin
, “
Calculation of the optical response of atomic clusters using time-dependent density functional theory and local orbitals
,”
Phys. Rev. B
66
,
235416
(
2002
).
75.
E.
Artacho
and
D. D.
O’Regan
, “
Quantum mechanics in an evolving Hilbert space
,”
Phys. Rev. B
95
,
115155
(
2017
).
76.
J. K.
Tomfohr
and
O. F.
Sankey
, “
Time-dependent simulation of conduction through a molecule
,”
Phys. Status Solidi B
226
,
115
123
(
2001
).
77.
A. A.
Correa
,
J.
Kohanoff
,
E.
Artacho
,
D.
Sánchez-Portal
, and
A.
Caro
, “
Nonadiabatic forces in ion-solid interactions: The initial stages of radiation damage
,”
Phys. Rev. Lett.
108
,
213201
(
2012
).
78.
M. A.
Zeb
,
J.
Kohanoff
,
D.
Sánchez-Portal
,
A.
Arnau
,
J. I.
Juaristi
, and
E.
Artacho
, “
Electronic stopping power in gold: The role of d electrons and the H/He anomaly
,”
Phys. Rev. Lett.
108
,
225504
(
2012
).
79.
R.
Ullah
,
F.
Corsetti
,
D.
Sánchez-Portal
, and
E.
Artacho
, “
Electronic stopping power in a narrow band gap semiconductor from first principles
,”
Phys. Rev. B
91
,
125203
(
2015
).
80.
J.
Halliday
and
E.
Artacho
, “
Anisotropy of electronic stopping power in graphite
,”
Phys. Rev. B
100
,
104112
(
2019
).
81.
F.
Corsetti
, “
Performance analysis of electronic structure codes on HPC systems: A case study of siesta
,”
PLoS One
9
,
1
8
(
2014
).
83.
E.
Anderson
,
A.
Benzoni
,
J.
Dongarra
,
S.
Moulton
,
S.
Ostrouchov
,
B.
Tourancheau
, and
R.
van de Geijn
, “
Basic linear algebra communication subprograms
,” in
1991 Proceedings of the Sixth Distributed Memory Computing Conference
(
IEEE
,
1991
), pp.
287
290
.
84.
L. S.
Blackford
,
J.
Choi
,
A.
Cleary
,
E.
D’Azevedo
,
J.
Demmel
,
I.
Dhillon
,
J.
Dongarra
,
S.
Hammarling
,
G.
Henry
,
A.
Petitet
,
K.
Stanley
,
D.
Walker
, and
R. C.
Whaley
,
ScaLAPACK Users’ Guide
(
Society for Industrial and Applied Mathematics
,
Philadelphia, PA
,
1997
).
85.
F.
Tisseur
and
J.
Dongarra
, “
A parallel divide and conquer algorithm for the symmetric eigenvalue problem on distributed memory architectures
,”
SIAM J. Sci. Comput.
20
,
2223
2236
(
1999
).
86.
T. N.
Todorov
, “
Time-dependent tight binding
,”
J. Phys.: Condens. Matter
13
,
10125
10148
(
2001
).
87.
I.
Tavernelli
,
U. F.
Röhrig
, and
U.
Rothlisberger
, “
Molecular dynamics in electronically excited states using time-dependent density functional theory
,”
Mol. Phys.
103
,
963
981
(
2005
).
88.
CPMD v3.13, Copyright IBM Corp (1990–2008), copyright MPI fuer Festkoerperforschung Stuttgart (1997–2001).
89.
P.
López-Tarifa
,
M.-A.
Hervé du Penhoat
,
R.
Vuilleumier
,
M.-P.
Gaigeot
,
I.
Tavernelli
,
A.
Le Padellec
,
J.-P.
Champeaux
,
M.
Alcamí
,
P.
Moretto-Capelle
,
F.
Martín
, and
M.-F.
Politis
, “
Ultrafast nonadiabatic fragmentation dynamics of doubly charged uracil in a gas phase
,”
Phys. Rev. Lett.
107
,
023202
(
2011
).
90.
P.
López-Tarifa
,
M.-A.
Penhoat
,
R.
Vuilleumier
,
M.-P.
Gaigeot
,
U.
Rothlisberger
,
I.
Tavernelli
,
A.
Le Padellec
,
J.-P.
Champeaux
,
M.
Alcami
,
P.
Moretto Capelle
,
F.
Martín
, and
M.
Politis
, “
Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase
,”
Cent. Eur. J. Phys.
12
,
97
102
(
2014
).
91.
M.-P.
Gaigeot
,
P.
Lopez-Tarifa
,
F.
Martin
,
M.
Alcami
,
R.
Vuilleumier
,
I.
Tavernelli
,
M.-A.
Hervé du Penhoat
, and
M.-F.
Politis
, “
Theoretical investigation of the ultrafast dissociation of ionised biomolecules immersed in water: Direct and indirect effects
,”
Mutat. Res.
704
,
45
53
(
2010
).
92.
A. D.
Becke
, “
Density-functional exchange-energy approximation with correct asymptotic behavior
,”
Phys. Rev. A
38
,
3098
3100
(
1988
).
93.
C.
Lee
,
W.
Yang
, and
R. G.
Parr
, “
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
,”
Phys. Rev. B
37
,
785
789
(
1988
).
94.
J. M.
Pruneda
,
D.
Sánchez-Portal
,
A.
Arnau
,
J. I.
Juaristi
, and
E.
Artacho
, “
Electronic stopping power in LiF from first principles
,”
Phys. Rev. Lett.
99
,
235501
(
2007
).
95.
A. A.
Correa
, “
Calculating electronic stopping power in materials from first principles
,”
Comput. Mater. Sci.
150
,
291
303
(
2018
).
96.
J. M.
Pruneda
,
S. K.
Estreicher
,
J.
Junquera
,
J.
Ferrer
, and
P.
Ordejón
, “
Ab initio local vibrational modes of light impurities in silicon
,”
Phys. Rev. B
65
,
075210
(
2002
).
97.
N.
Papior
,
N.
Lorente
,
T.
Frederiksen
,
A.
García
, and
M.
Brandbyge
, “
Improvements on non-equilibrium and transport green function techniques: The next-generation transiesta
,”
Comput. Phys. Commun.
212
,
8
24
(
2017
).
98.
N.
Papior
,
G.
Calogero
,
S.
Leitherer
, and
M.
Brandbyge
, “
Removing all periodic boundary conditions: Efficient nonequilibrium Green’s function calculations
,”
Phys. Rev. B
100
,
195417
(
2019
).
99.
K. W.
Jacobsen
,
J. T.
Falkenberg
,
N.
Papior
,
P.
Bøggild
,
A.-P.
Jauho
, and
M.
Brandbyge
, “
All-graphene edge contacts: Electrical resistance of graphene t-junctions
,”
Carbon
101
,
101
106
(
2016
).
100.
M.
Kolmer
,
P.
Brandimarte
,
J.
Lis
,
R.
Zuzak
,
S.
Godlewski
,
H.
Kawai
,
A.
Garcia-Lekue
,
N.
Lorente
,
T.
Frederiksen
,
C.
Joachim
,
D.
Sanchez-Portal
, and
M.
Szymonski
, “
Electronic transport in planar atomic-scale structures measured by two-probe scanning tunneling spectroscopy
,”
Nat. Commun.
10
,
1573
(
2019
).
101.
P.
Brandimarte
,
M.
Engelund
,
N.
Papior
,
A.
Garcia-Lekue
,
T.
Frederiksen
, and
D.
Sánchez-Portal
, “
A tunable electronic beam splitter realized with crossed graphene nanoribbons
,”
J. Chem. Phys.
146
,
092318
(
2017
).
102.
N.
Papior
, SISL: v0.9.7,
2019
.
103.
See https://github.com/tfrederiksen/inelastica/ for more information about the Inelastica package.
104.
T.
Frederiksen
,
M.
Paulsson
,
M.
Brandbyge
, and
A.-P.
Jauho
, “
Inelastic transport theory from first principles: Methodology and application to nanoscale devices
,”
Phys. Rev. B
75
,
205413
(
2007
).
105.
See http://www.wannier.org for information about the Wannier90 code.
106.
G.
Pizzi
,
V.
Vitale
,
R.
Arita
,
S.
Blügel
,
F.
Freimuth
,
G.
Géranton
,
M.
Gibertini
,
D.
Gresch
,
C.
Johnson
,
T.
Koretsune
,
J.
Ibañez-Azpiroz
,
H.
Lee
,
J.-M.
Lihm
,
D.
Marchand
,
A.
Marrazzo
,
Y.
Mokrousov
,
J. I.
Mustafa
,
Y.
Nohara
,
Y.
Nomura
,
L.
Paulatto
,
S.
Poncé
,
T.
Ponweiser
,
J.
Qiao
,
F.
Thöle
,
S. S.
Tsirkin
,
M.
Wierzbowska
,
N.
Marzari
,
D.
Vanderbilt
,
I.
Souza
,
A. A.
Mostofi
, and
J. R.
Yates
, “
Wannier90 as a community code: New features and applications
,”
J. Phys.: Condens. Matter
32
,
165902
(
2020
).
107.
N.
Marzari
and
D.
Vanderbilt
, “
Maximally localized generalized wannier functions for composite energy bands
,”
Phys. Rev. B
56
,
12847
12865
(
1997
).
108.
N.
Marzari
,
A. A.
Mostofi
,
J. R.
Yates
,
I.
Souza
, and
D.
Vanderbilt
, “
Maximally localized wannier functions: Theory and applications
,”
Rev. Mod. Phys.
84
,
1419
1475
(
2012
).
109.
D.
Vanderbilt
,
Berry Phases in Electronic Structure Theory
(
Cambridge University Press
,
2018
).
110.
See https://github.com/romerogroup/DMFTwDFT for information about the DMFTwDFT code.
111.
V.
Singh
,
U.
Herath
,
B.
Wah
,
X.
Liao
,
A. H.
Romero
, and
H.
Park
, “
DMFTWDFT: An open-source code combining dynamical mean field theory with various density functional theory packages
,” arXiv:2002.00068v1 (
2020
).
112.
X.
Wu
,
A.
Selloni
, and
R.
Car
, “
Order-n implementation of exact exchange in extended insulating systems
,”
Phys. Rev. B
79
,
085102
(
2009
).
113.
P.
García-Fernández
,
J. C.
Wojdeł
,
J.
Íñiguez
, and
J.
Junquera
, “
Second-principles method for materials simulations including electron and lattice degrees of freedom
,”
Phys. Rev. B
93
,
195137
(
2016
).
114.
J. C.
Wojdeł
,
P.
Hermet
,
M. P.
Ljungberg
,
P.
Ghosez
, and
J.
Íñiguez
, “
First-principles model potentials for lattice-dynamical studies: General methodology and example of application to ferroic perovskite oxides
,”
J. Phys.: Condens. Matter
25
,
305401
(
2013
).
115.
P.
Torres
,
J. A.
Seijas-Bellido
,
C.
Escorihuela-Sayalero
,
J.
Íñiguez
, and
R.
Rurali
, “
Theoretical investigation of lattice thermal conductivity and electrophononic effects in SrTiO3
,”
Phys. Rev. Mater.
3
,
044404
(
2019
).
116.
J. A.
Seijas-Bellido
,
J.
Íñiguez
, and
R.
Rurali
, “
Anisotropy-driven thermal conductivity switching and thermal hysteresis in a ferroelectric
,”
Appl. Phys. Lett.
115
,
192903
(
2019
).
117.
J. A.
Seijas-Bellido
,
H.
Aramberri
,
J.
Íñiguez
, and
R.
Rurali
, “
Electric control of the heat flux through electrophononic effects
,”
Phys. Rev. B
97
,
184306
(
2018
).
118.
S.
Das
,
Y. L.
Tang
,
Z.
Hong
,
M. A. P.
Gonçalves
,
M. R.
McCarter
,
C.
Klewe
,
K. X.
Nguyen
,
F.
Gómez-Ortiz
,
P.
Shafer
,
E.
Arenholz
,
V. A.
Stoica
,
S.-L.
Hsu
,
B.
Wang
,
C.
Ophus
,
J. F.
Liu
,
C. T.
Nelson
,
S.
Saremi
,
B.
Prasad
,
A. B.
Mei
,
D. G.
Schlom
,
J.
Íñiguez
,
P.
García-Fernández
,
D. A.
Muller
,
L. Q.
Chen
,
J.
Junquera
,
L. W.
Martin
, and
R.
Ramesh
, “
Observation of room-temperature polar skyrmions
,”
Nature
568
,
368
372
(
2019
).
119.
A. K.
Yadav
,
K. X.
Nguyen
,
Z.
Hong
,
P.
García-Fernández
,
P.
Aguado-Puente
,
C. T.
Nelson
,
S.
Das
,
B.
Prasad
,
D.
Kwon
,
S.
Cheema
,
A. I.
Khan
,
C.
Hu
,
J.
Íñiguez
,
J.
Junquera
,
L.-Q.
Chen
,
D. A.
Muller
,
R.
Ramesh
, and
S.
Salahuddin
, “
Spatially resolved steady-state negative capacitance
,”
Nature
565
,
468
471
(
2019
).
120.
R.
Ierusalimschy
,
Programming in Lua
, 4th ed. (
Feisty Duck Digital Book Distribution
,
2016
).
121.
See https://siesta-project.github.io/flos/ldoc/index.html for more information about the library of Lua scripts for use with Siesta.
122.
S.
Smidstrup
,
A.
Pedersen
,
K.
Stokbro
, and
H.
Jónsson
, “
Improved initial guess for minimum energy path calculations
,”
J. Chem. Phys.
140
,
214106
(
2014
).
123.
D.
Sheppard
,
R.
Terrell
, and
G.
Henkelman
, “
Optimization methods for finding minimum energy paths
,”
J. Chem. Phys.
128
,
134106
(
2008
).
124.
S. A.
Trygubenko
and
D. J.
Wales
, “
A doubly nudged elastic band method for finding transition states
,”
J. Chem. Phys.
120
,
2082
2094
(
2004
).
125.
G.-R.
Qian
,
X.
Dong
,
X.-F.
Zhou
,
Y.
Tian
,
A. R.
Oganov
, and
H.-T.
Wang
, “
Variable cell nudged elastic band method for studying solid-solid structural phase transitions
,”
Comput. Phys. Commun.
184
,
2111
2118
(
2013
).
126.
See https://esl.cecam.org/Flook for more details about the Fortran-Lua bridge, including interoperability of data structures.
127.
G.
Pizzi
,
A.
Cepellotti
,
R.
Sabatini
,
N.
Marzari
, and
B.
Kozinsky
, “
Aiida: Automated interactive infrastructure and database for computational science
,”
Comput. Mater. Sci.
111
,
218
230
(
2016
).
128.
See http://www.aiida.net/ for more information about the AiiDA platform.
129.
See https://aiida.readthedocs.io/ for full details of the implementation and usage of AiiDA.
130.
See https://aiida-siesta-plugin.readthedocs.io/ for documentation on the use of the AiiDA-Siesta plugin.
131.
S. G.
Mayo
,
F.
Yndurain
, and
J. M.
Soler
, “
Band unfolding made simple
,”
J. Phys.: Condens. Matter
32
,
205902
(
2020
).
132.
G.
Calogero
,
N.
Papior
,
M.
Koleini
,
M. H. L.
Larsen
, and
M.
Brandbyge
, “
Multi-scale approach to first-principles electron transport beyond 100 nm
,”
Nanoscale
11
,
6153
6164
(
2019
).
133.
A. H.
Larsen
,
J. J.
Mortensen
,
J.
Blomqvist
,
I. E.
Castelli
,
R.
Christensen
,
M.
Dułak
,
J.
Friis
,
M. N.
Groves
,
B.
Hammer
,
C.
Hargus
,
E. D.
Hermes
,
P. C.
Jennings
,
P. B.
Jensen
,
J.
Kermode
,
J. R.
Kitchin
,
E. L.
Kolsbjerg
,
J.
Kubal
,
K.
Kaasbjerg
,
S.
Lysgaard
,
J. B.
Maronsson
,
T.
Maxson
,
T.
Olsen
,
L.
Pastewka
,
A.
Peterson
,
C.
Rostgaard
,
J.
Schiøtz
,
O.
Schütt
,
M.
Strange
,
K. S.
Thygesen
,
T.
Vegge
,
L.
Vilhelmsen
,
M.
Walter
,
Z.
Zeng
, and
K. W.
Jacobsen
, “
The atomic simulation environment—A python library for working with atoms
,”
J. Phys.: Condens. Matter
29
,
273002
(
2017
).
134.
A.
Kokalj
, “
XCrySDen: A crystalline and molecular structure visualisation program
,” http://www.xcrysden.org.
135.
K.
Momma
, “
VESTA: A 3D visualization program for structural models, volumetric data, and crystal morphologies
,” http://jp-minerals.org/vesta/en/.
136.
A. V.
Postnikov
and
N. B.
Mortazavi Amiri
, “
Calculated vibration spectrum of monoclinic Cu2SnSe3 in comparison with kesterite-type Cu2ZnSnSe4
,”
Phys. Status Solidi A
210
,
1332
1335
(
2013
).
137.
M. N.
Rao
,
D.
Lamago
,
A.
Ivanov
,
M.
d’Astuto
,
A. V.
Postnikov
,
R.
Hajj Hussein
,
T.
Basak
,
S. L.
Chaplot
,
F.
Firszt
,
W.
Paszkowicz
,
S. K.
Deb
, and
O.
Pagés
, “
Lattice dynamics of the model percolation-type (Zn,Be)Se alloy: Inelastic neutron scattering, ab initio study, and shell-model calculations
,”
Phys. Rev. B
89
,
155201
(
2014
).
138.
Bilbao Crystallographic Server → Raman and Hyper-Raman scattering → Spectral Active Modes, https://www.cryst.ehu.es/rep/sam.html.
139.
V.
Kosyak
,
N. B.
Mortazavi Amiri
,
A. V.
Postnikov
, and
M. A.
Scarpulla
, “
Model of native point defect equilibrium in Cu2ZnSnS4 and application to one-zone annealing
,”
J. Appl. Phys.
114
,
124501
(
2013
).
140.
N. B.
Mortazavi Amiri
, “
Relation entre motifs structuraux et dynamique de réseau dans les cristaux mixtes Cu-Zn-Sn-Se: Étude premiers principes
, Ph.D. thesis,
Université de Lorraine
,
2013
.
141.
M. P.
Allen
and
D. J.
Tildesley
,
Computer Simulation of Liquids
(
Oxford University Press
,
Oxford
,
1987
).
142.
A. V.
Postnikov
, “
Vibrations in solids and small particles from first-principles calculations
,” in
Computational Materials Science
, NATO Science Series III (Computer and System Science) Vol. 187, edited by
C. R. A.
Catlow
and
E.
Kotomin
(
IOS Press
,
2003
), pp.
153
166
[Proceedings of the NATO Advanced Study Institute “Computational Materials Science,” Il Ciocco, September 9–22, 2001].
143.
O.
Coulaud
,
P.
Bordat
,
P.
Fayon
,
V.
Le Bris
,
I.
Baraille
, and
R.
Brown
, “
Extensions of the siesta DFT code for simulation of molecules
,” Research Report No. RR-8221,
INRIA
,
2013
.
144.
P.
Koval
,
M.
Barbry
, and
D.
Sánchez-Portal
, “
PySCF-Nao: An efficient and flexible implementation of linear response time-dependent density functional theory with numerical atomic orbitals
,”
Comput. Phys. Commun.
236
,
188
204
(
2019
).
145.
M.
Petersilka
,
U. J.
Gossmann
, and
E. K. U.
Gross
, “
Excitation energies from time-dependent density-functional theory
,”
Phys. Rev. Lett.
76
,
1212
1215
(
1996
).
146.
P.
Koval
,
F.
Marchesin
,
D.
Foerster
, and
D.
Sánchez-Portal
, “
Optical response of silver clusters and their hollow shells from linear-response TDDFT
,”
J. Phys.: Condens. Matter
28
,
214001
(
2016
).
147.
Y.
Li
and
C. A.
Ullrich
, “
The particle–hole map: A computational tool to visualize electronic excitations
,”
J. Chem. Theory Comput.
11
,
5838
5852
(
2015
).
148.
R.
Dronskowski
and
P. E.
Bloechl
, “
Crystal orbital Hamilton populations (COHP): Energy-resolved visualization of chemical bonding in solids based on density-functional calculations
,”
J. Phys. Chem.
97
,
8617
8624
(
1993
).
149.
M.
Barbry
,
P.
Koval
,
F.
Marchesin
,
R.
Esteban
,
A. G.
Borisov
,
J.
Aizpurua
, and
D.
Sánchez-Portal
, “
Atomistic near-field nanoplasmonics: Reaching atomic-scale resolution in nanooptics
,”
Nano Lett.
15
,
3410
3419
(
2015
).
150.
F.
Marchesin
,
P.
Koval
,
M.
Barbry
,
J.
Aizpurua
, and
D.
Sánchez-Portal
, “
Optical response of metallic nanojunctions driven by single atom motion
,”
ACS Photonics
3
,
269
277
(
2016
).
151.
M.
Barbry
, “
Plasmons in nanoparticles: Atomistic ab initio theory for large systems
, Ph.D. thesis,
University of Basque Country
,
Donostia-San Sebastián
,
Spain
,
2018
, http://cfm.ehu.es/view/files/MArc_barbry_2-1.pdf; accessed 14 June 2019.
152.
E.
Lampin
,
P. L.
Palla
,
P.-A.
Francioso
, and
F.
Cleri
, “
Thermal conductivity from approach-to-equilibrium molecular dynamics
,”
J. Appl. Phys.
114
,
033525
(
2013
).
153.
S.
Illera
,
M.
Pruneda
,
L.
Colombo
, and
P.
Ordejón
, “
Thermal and transport properties of pristine single-layer hexagonal boron nitride: A first principles investigation
,”
Phys. Rev. Mater.
1
,
044006
(
2017
).
154.
S.
García-Gil
,
A.
García
, and
P.
Ordejón
, “
Calculation of core level shifts within DFT using pseudopotentials and localized basis sets
,”
Eur. Phys. J. B
85
,
239
(
2012
).
155.
S.
Garcia-Gil
,
A.
Arnau
, and
A.
Garcia-Lekue
, “
Exploring large O 1s and N 1s core level shifts due to intermolecular hydrogen bond formation in organic molecules
,”
Surf. Sci.
613
,
102
107
(
2013
).
156.
See https://en.wikipedia.org/wiki/Reference_counting for more information about the reference-counting approach to memory management.
157.
See https://www.max-centre.eu/ for more information about the MaX (Materials at the eXascale) EU Center of Excellence.
158.
See https://esl.cecam.org/ for information about the Electronic Structure Library initiative.
159.
See https://l_sim.gitlab.io/psolver/ for information about the Psolver library for the solution of the Poisson equation.
160.
P.
Zubko
,
N.
Jecklin
,
A.
Torres-Pardo
,
P.
Aguado-Puente
,
A.
Gloter
,
C.
Lichtensteiger
,
J.
Junquera
,
O.
Stéphan
, and
J.-M.
Triscone
, “
Electrostatic coupling and local structural distortions at interfaces in ferroelectric/paraelectric superlattices
,”
Nano Lett.
12
,
2846
2851
(
2012
).
161.
P.
Aguado-Puente
and
J.
Junquera
, “
Structural and energetic properties of domains in pbtio3/srtio3 superlattices from first principles
,”
Phys. Rev. B
85
,
184105
(
2012
).
162.
A. K.
Yadav
,
C. T.
Nelson
,
S. L.
Hsu
,
Z.
Hong
,
J. D.
Clarkson
,
C. M.
Schlepütz
,
A. R.
Damodaran
,
P.
Shafer
,
E.
Arenholz
,
L. R.
Dedon
,
D.
Chen
,
A.
Vishwanath
,
A. M.
Minor
,
L. Q.
Chen
,
J. F.
Scott
,
L. W.
Martin
, and
R.
Ramesh
, “
Observation of polar vortices in oxide superlattices
,”
Nature
530
,
198
201
(
2016
).
163.
P.
Shafer
,
P.
García-Fernández
,
P.
Aguado-Puente
,
A. R.
Damodaran
,
A. K.
Yadav
,
C. T.
Nelson
,
S.-L.
Hsu
,
J. C.
Wojdeł
,
J.
Íñiguez
,
L. W.
Martin
,
E.
Arenholz
,
J.
Junquera
, and
R.
Ramesh
, “
Emergent chirality in the electric polarization texture of titanate superlattices
,”
Proc. Natl. Acad. Sci. U. S. A.
115
,
915
920
(
2018
).
164.
D. W.
Boukhvalov
,
M. I.
Katsnelson
, and
A. I.
Lichtenstein
, “
Hydrogen on graphene: Electronic structure, total energy, structural distortions and magnetism from first-principles calculations
,”
Phys. Rev. B
77
,
035427
(
2008
).
165.
O. V.
Yazyev
and
L.
Helm
, “
Defect-induced magnetism in graphene
,”
Phys. Rev. B
75
,
125408
(
2007
).
166.
M.
Slota
,
A.
Keerthi
,
W. K.
Myers
,
E.
Tretyakov
,
M.
Baumgarten
,
A.
Ardavan
,
H.
Sadeghi
,
C. J.
Lambert
,
A.
Narita
,
K.
Müllen
, and
L.
Bogani
, “
Magnetic edge states and coherent manipulation of graphene nanoribbons
,”
Nature
557
,
691
695
(
2018
).
167.
O. V.
Yazyev
and
S. G.
Louie
, “
Electronic transport in polycrystalline graphene
,”
Nat. Mater.
9
,
806
809
(
2010
).
168.
O. V.
Yazyev
and
S. G.
Louie
, “
Topological defects in graphene: Dislocations and grain boundaries
,”
Phys. Rev. B
81
,
195420
(
2010
).
169.
W. Y.
Kim
and
K. S.
Kim
, “
Prediction of very large values of magnetoresistance in a graphene nanoribbon device
,”
Nat. Nanotechnol.
3
,
408
412
(
2008
).
170.
C.
Moreno
,
M.
Vilas-Varela
,
B.
Kretz
,
A.
Garcia-Lekue
,
M. V.
Costache
,
M.
Paradinas
,
M.
Panighel
,
G.
Ceballos
,
S. O.
Valenzuela
,
D.
Peña
, and
A.
Mugarza
, “
Bottom-up synthesis of multifunctional nanoporous graphene
,”
Science
360
,
199
203
(
2018
).
171.
W.
Hu
,
Y.
Huang
,
X.
Qin
,
L.
Lin
,
E.
Kan
,
X.
Li
,
C.
Yang
, and
J.
Yang
, “
Room-temperature magnetism and tunable energy gaps in edge-passivated zigzag graphene quantum dots
,”
npj 2D Mater. Appl.
3
,
17
(
2019
).
172.
S.
Kim
,
J.
Ihm
,
H. J.
Choi
, and
Y.-W.
Son
, “
Origin of anomalous electronic structures of epitaxial graphene on silicon carbide
,”
Phys. Rev. Lett.
100
,
176802
(
2008
).
173.
H. S. S.
Ramakrishna Matte
,
A.
Gomathi
,
A. K.
Manna
,
D. J.
Late
,
R.
Datta
,
S. K.
Pati
, and
C. N. R.
Rao
, “
MoS2 and WS2 analogues of graphene
,”
Angew. Chem., Int. Ed.
49
,
4059
4062
(
2010
).
174.
I.
Popov
,
G.
Seifert
, and
D.
Tománek
, “
Designing electrical contacts to mos2 monolayers: A computational study
,”
Phys. Rev. Lett.
108
,
156802
(
2012
).
175.
H.
Liu
,
A. T.
Neal
,
Z.
Zhu
,
Z.
Luo
,
X.
Xu
,
D.
Tománek
, and
P. D.
Ye
, “
Phosphorene: An unexplored 2D semiconductor with a high hole mobility
,”
ACS Nano
8
,
4033
4041
(
2014
).
176.
J.
Guan
,
Z.
Zhu
, and
D.
Tománek
, “
Phase coexistence and metal-insulator transition in few-layer phosphorene: A computational study
,”
Phys. Rev. Lett.
113
,
046804
(
2014
).
177.
W.
Hu
,
L.
Lin
,
C.
Yang
,
J.
Dai
, and
J.
Yang
, “
Edge-modified phosphorene nanoflake heterojunctions as highly efficient solar cells
,”
Nano Lett.
16
,
1675
1682
(
2016
).
178.
I. B.
Guster
, “
A bird’s-eye view of charge and spin density wave from first principles calculations
,” Ph.D. thesis,
Universitat Autonoma de Barcelona
,
2019
.
179.
B.
Guster
,
C.
Rubio-Verdú
,
R.
Robles
,
J.
Zaldívar
,
P.
Dreher
,
M.
Pruneda
,
J. Á.
Silva-Guillén
,
D.-J.
Choi
,
J. I.
Pascual
,
M. M.
Ugeda
,
P.
Ordejón
, and
E.
Canadell
, “
Coexistence of elastic modulations in the charge density wave state of 2H-NbSe2
,”
Nano Lett.
19
,
3027
3032
(
2019
).
180.
B.
Guster
,
M.
Pruneda
,
P.
Ordejón
,
E.
Canadell
, and
J.-P.
Pouget
, “
Evidence for the weak coupling scenario of the Peierls transition in the blue bronze
,”
Phys. Rev. Mater.
3
,
055001
(
2019
).
181.
P. J.
de Pablo
,
F.
Moreno-Herrero
,
J.
Colchero
,
J.
Gómez Herrero
,
P.
Herrero
,
A. M.
Baró
,
P.
Ordejón
,
J. M.
Soler
, and
E.
Artacho
, “
Absence of dc-conductivity in λ-DNA
,”
Phys. Rev. Lett.
85
,
4992
4995
(
2000
).
182.
A.
Crespo
,
D. A.
Scherlis
,
M. A.
Martí
,
P.
Ordejón
,
A. E.
Roitberg
, and
D. A.
Estrin
, “
A DFT-based QM-MM approach designed for the treatment of large molecular systems: Application to chorismate mutase
,”
J. Phys. Chem. B
107
,
13728
13736
(
2003
).
183.
C. F.
Sanz-Navarro
,
R.
Grima
,
A.
García
,
E. A.
Bea
,
A.
Soba
,
J. M.
Cela
, and
P.
Ordejón
, “
An efficient implementation of a QM-MM method in siesta
,”
Theor. Chem. Acc.
128
,
825
833
(
2011
).
184.
G. T.
Feliciano
,
A. J. R.
da Silva
,
G.
Reguera
, and
E.
Artacho
, “
Molecular and electronic structure of the peptide subunit of Geobacter sulfurreducens conductive pili from first principles
,”
J. Phys. Chem. A
116
,
8023
8030
(
2012
).
185.
D. J.
Cole
and
N. D. M.
Hine
, “
Applications of large-scale density functional theory in biology
,”
J. Phys.: Condens. Matter
28
,
393001
(
2016
).
186.
M.
Darvish Ganji
, “
Amino acids interacting with defected carbon nanotubes: Ab initio calculations
,”
J. Pharm. Health Sci.
4
,
157
166
(
2016
).
187.
W.
Li
,
K.
Kotsis
, and
S.
Manzhos
, “
Comparative density functional theory and density functional tight binding study of arginine and arginine-rich cell penetrating peptide TAT adsorption on anatase TiO2
,”
Phys. Chem. Chem. Phys.
18
,
19902
19917
(
2016
).
188.
A.
Hermann
, “
Chemical bonding at high pressure
,” in
Reviews in Computational Chemistry
(
John Wiley & Sons, Ltd.
,
2017
), Chap. 1, pp.
1
41
, https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119356059.ch1.
189.
T.
Liu
,
E.
Artacho
,
F.
Gázquez
,
G.
Walters
, and
D.
Hodell
, “
Prediction of equilibrium isotopic fractionation of the gypsum/bassanite/water system using first-principles calculations
,”
Geochim. Cosmochim. Ac.
244
,
1
11
(
2019
).
190.
E.
Mayoral
,
A.
Rey
,
J.
Klapp
,
A.
Gómez
, and
M.
Mayoral
, “
Ab initio DFT calculations for materials in nuclear research
,” in
High Performance Computing
, edited by
C. J.
Barrios Hernández
,
I.
Gitler
, and
J.
Klapp
(
Springer International Publishing
,
Cham
,
2017
), pp.
329
339
.
191.
R.
Escribano
and
G. M.
Muñoz Caro
, “
Introduction to spectroscopy and astronomical observations
,” in
Laboratory Astrophysics
, edited by
G. M.
Muñoz Caro
and
R.
Escribano
(
Springer International Publishing
,
Cham
,
2018
), pp.
27
47
.
192.
F.
Viñes
,
J. R. B.
Gomes
, and
F.
Illas
, “
Understanding the reactivity of metallic nanoparticles: Beyond the extended surface model for catalysis
,”
Chem. Soc. Rev.
43
,
4922
4939
(
2014
).
193.
F.
Tao
,
W.
Schneider
, and
P.
Kamat
,
Heterogeneous Catalysis at Nanoscale for Energy Applications
(
Wiley
,
2015
).
194.
See https://www.cp2k.org/dbcsr for information about the DBCSR library for optimized sparse-matrix multiplication.
195.
I.
Sivkov
,
P.
Seewald
,
A.
Lazzaro
, and
J.
Hutter
, “
DBCSR: A blocked sparse tensor algebra library
,” , edited by
G. R.
Joubert
, Vol. 36, pp.
331
340
.
196.
See http://esl.cecam.org/libOMM for information about the libOMM library.
197.
A.
Marcolongo
,
P.
Umari
, and
S.
Baroni
, “
Microscopic theory and quantum simulation of atomic heat transport
,”
Nat. Phys.
12
,
80
84
(
2016
).
You do not currently have access to this content.