U s e r’ s Guide

SIESTA 4.1-b4

November 07, 2018

http://www.uam.es/siesta

SIESTA Steering Committee:

Emilio Artacho CIC-Nanogune and University of Cambridge

José María Cela Barcelona Supercomputing Center
Julian D. Gale Curtin University of Technology, Perth
Alberto García Institut de Ciència de Materials, CSIC, Barcelona
Javier Junquera Universidad de Cantabria, Santander
Richard M. Martin University of Illinois at Urbana-Champaign
Pablo Ordejón Centre de Investigació en Nanociència
i Nanotecnologia, (CSIC-ICN), Barcelona
Nick Rübner Papior Technical University of Denmark
Daniel Sánchez-Portal Unidad de Física de Materiales,
Centro Mixto CSIC-UPV/EHU, San Sebastián
José M. Soler Universidad Autónoma de Madrid

SIESTA is Copyright © 1996-2018 by The Siesta Group

Contributors to SIESTA

The SIESTA project was initiated by Pablo Ordejon (then at the Univ. de Oviedo), and Jose M.
Soler and Emilio Artacho (Univ. Autonoma de Madrid, UAM). The development team was then
joined by Alberto Garcia (then at Univ. del Pais Vasco, Bilbao), Daniel Sanchez-Portal (UAM),
and Javier Junquera (Univ. de Oviedo and later UAM), and sometime later by Julian Gale (then at
Imperial College, London). In 2007 Jose M. Cela (Barcelona Supercomputing Center, BSC) became
a core developer and member of the Steering Committee.
The original TranSIESTA module was developed by Pablo Ordejon and Jose L. Mozos (then
at ICMAB-CSIC), and Mads Brandbyge, Kurt Stokbro, and Jeremy Taylor (Technical Univ. of
Denmark).
The current TranSIESTA module within SIESTA is developed by Nick R. Papior and Mads Brand-
byge. Nick R. Papior became a core developer and member of the Steering Committee in 2015.
Other contributors (we apologize for any omissions):
Eduardo Anglada, Thomas Archer, Luis C. Balbas, Xavier Blase, Ramon Cuadrado, Michele Ceriotti,
Fabiano Corsetti, Raul de la Cruz, Gabriel Fabricius, Marivi Fernandez-Serra, Jaime Ferrer, Chu-
Chun Fu, Sandra Garcia, Victor M. Garcia-Suarez, Rogeli Grima, Rainer Hoft, Georg Huhs, Jorge
Kohanoff, Richard Korytar, In-Ho Lee, Lin Lin, Nicolas Lorente, Miquel Llunell, Eduardo Machado,
Maider Machado, Jose Luis Martins, Volodymyr Maslyuk, Juana Moreno, Frederico Dutilh Novaes,
Micael Oliveira, Magnus Paulsson, Oscar Paz, Andrei Postnikov, Tristana Sondon, Andrew Walker,
Andrew Walkingshaw, Toby White, Francois Willaime, Chao Yang.
O.F. Sankey, D.J. Niklewski and D.A. Drabold made the FIREBALL code available to P. Ordejon.
Although we no longer use the routines in that code, it was essential in the initial development of
SIESTA, which still uses many of the algorithms developed by them.

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Contents

Contributors to SIESTA 2

1 INTRODUCTION 8

2 COMPILATION 10
2.1 The build directory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.1.1 Multiple-target compilation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2 The arch.make file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.3 Parallel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.3.1 MPI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.3.2 OpenMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.4 Library dependencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

3 EXECUTION OF THE PROGRAM 17

3.1 Specific execution options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

4 THE FLEXIBLE DATA FORMAT (FDF) 19

5 PROGRAM OUTPUT 21
5.1 Standard output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.2 Output to dedicated files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

6 DETAILED DESCRIPTION OF PROGRAM OPTIONS 22

6.1 General system descriptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
6.2 Pseudopotentials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
6.3 Basis set and KB projectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
6.3.1 Overview of atomic-orbital bases implemented in SIESTA . . . . . . . . . . . 24
6.3.2 Type of basis sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
6.3.3 Size of the basis set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
6.3.4 Range of the orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
6.3.5 Generation of multiple-zeta orbitals . . . . . . . . . . . . . . . . . . . . . . . 29
6.3.6 Soft-confinement options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
6.3.7 Kleinman-Bylander projectors . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
6.3.8 The PAO.Basis block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
6.3.9 Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

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 6.3.10 Saving and reading basis-set information . . . . . . . . . . . . . . . . . . . . . 36
6.3.11 Tools to inspect the orbitals and KB projectors . . . . . . . . . . . . . . . . . 36
6.3.12 Basis optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
6.3.13 Low-level options regarding the radial grid . . . . . . . . . . . . . . . . . . . 37
6.4 Structural information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
6.4.1 Traditional structure input in the fdf file . . . . . . . . . . . . . . . . . . . . . 38
6.4.2 Z-matrix format and constraints . . . . . . . . . . . . . . . . . . . . . . . . . 40
6.4.3 Output of structural information . . . . . . . . . . . . . . . . . . . . . . . . . 43
6.4.4 Input of structural information from external files . . . . . . . . . . . . . . . 45
6.4.5 Input from a FIFO file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
6.4.6 Precedence issues in structural input . . . . . . . . . . . . . . . . . . . . . . . 46
6.4.7 Interatomic distances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
6.5 k-point sampling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
6.5.1 Output of k-point information . . . . . . . . . . . . . . . . . . . . . . . . . . 47
6.6 Exchange-correlation functionals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
6.7 Spin polarization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
6.8 Spin–Orbit coupling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
6.9 The self-consistent-field loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
6.9.1 Harris functional . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
6.9.2 Mixing options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
6.9.3 Mixing of the Charge Density . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
6.9.4 Initialization of the density-matrix . . . . . . . . . . . . . . . . . . . . . . . . 60
6.9.5 Initialization of the SCF cycle with charge densities . . . . . . . . . . . . . . 63
6.9.6 Output of density matrix and Hamiltonian . . . . . . . . . . . . . . . . . . . 63
6.9.7 Convergence criteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
6.10 The real-space grid and the eggbox-effect . . . . . . . . . . . . . . . . . . . . . . . . 67
6.11 Matrix elements of the Hamiltonian and overlap . . . . . . . . . . . . . . . . . . . . 70
6.11.1 The auxiliary supercell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
6.12 Calculation of the electronic structure . . . . . . . . . . . . . . . . . . . . . . . . . . 71
6.12.1 Diagonalization options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
6.12.2 Output of eigenvalues and wavefunctions . . . . . . . . . . . . . . . . . . . . 75
6.12.3 Occupation of electronic states and Fermi level . . . . . . . . . . . . . . . . . 76
6.12.4 Orbital minimization method (OMM) . . . . . . . . . . . . . . . . . . . . . . 76
6.12.5 Order(N) calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

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 6.13 The PEXSI solver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
6.13.1 Pole handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
6.13.2 Parallel environment and control options . . . . . . . . . . . . . . . . . . . . 81
6.13.3 Electron tolerance and the PEXSI solver . . . . . . . . . . . . . . . . . . . . . 83
6.13.4 Inertia-counting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
6.13.5 Re-use of µ information accross iterations . . . . . . . . . . . . . . . . . . . . 85
6.13.6 Calculation of the density of states by inertia-counting . . . . . . . . . . . . . 86
6.13.7 Calculation of the LDOS by selected-inversion . . . . . . . . . . . . . . . . . 86
6.14 Band-structure analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
6.14.1 Format of the .bands file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
6.14.2 Output of wavefunctions associated to bands . . . . . . . . . . . . . . . . . . 88
6.15 Output of selected wavefunctions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
6.16 Densities of states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
6.16.1 Total density of states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
6.16.2 Partial (projected) density of states . . . . . . . . . . . . . . . . . . . . . . . 90
6.16.3 Local density of states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
6.17 Options for chemical analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
6.17.1 Mulliken charges and overlap populations . . . . . . . . . . . . . . . . . . . . 92
6.17.2 Voronoi and Hirshfeld atomic population analysis . . . . . . . . . . . . . . . . 92
6.17.3 Crystal-Orbital overlap and hamilton populations (COOP/COHP) . . . . . . 93
6.18 Optical properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
6.19 Macroscopic polarization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
6.20 Maximally Localized Wannier Functions . . . . . . . . . . . . . . . . . . . . . . . . . 97
6.21 Systems with net charge or dipole, and electric fields . . . . . . . . . . . . . . . . . . 99
6.22 Output of charge densities and potentials on the grid . . . . . . . . . . . . . . . . . . 102
6.23 Auxiliary Force field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
6.24 Parallel options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
6.24.1 Parallel decompositions for O(N) . . . . . . . . . . . . . . . . . . . . . . . . . 106
6.25 Efficiency options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
6.26 Memory, CPU-time, and Wall time accounting options . . . . . . . . . . . . . . . . . 107
6.27 The catch-all option UseSaveData . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
6.28 Output of information for Denchar . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
6.29 NetCDF (CDF4) output file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

7 STRUCTURAL RELAXATION, PHONONS, AND MOLECULAR DYNAM-

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 ICS 109
7.1 Compatibility with pre-v4 versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
7.2 Structural relaxation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
7.2.1 Conjugate-gradients optimization . . . . . . . . . . . . . . . . . . . . . . . . . 112
7.2.2 Broyden optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
7.2.3 FIRE relaxation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
7.3 Target stress options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
7.4 Molecular dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
7.5 Output options for dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
7.6 Restarting geometry optimizations and MD runs . . . . . . . . . . . . . . . . . . . . 117
7.7 Use of general constraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
7.8 Phonon calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

8 LDA+U 120

9 External control of SIESTA 122

9.1 Examples of Lua programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
9.2 External MD/relaxation methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

10 TRANSIESTA 126
10.1 Source code structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
10.2 Compilation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
10.3 Brief description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
10.4 Electrodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
10.4.1 Matching coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
10.4.2 Principal layer interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
10.5 TranSIESTA Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
10.5.1 Quick and dirty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
10.5.2 General options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
10.5.3 Algorithm specific options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
10.5.4 Poisson solution for fixed boundary conditions . . . . . . . . . . . . . . . . . 137
10.5.5 Electrode description options . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
10.5.6 Chemical potentials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
10.5.7 Complex contour integration options . . . . . . . . . . . . . . . . . . . . . . . 143
10.5.8 Bias contour integration options . . . . . . . . . . . . . . . . . . . . . . . . . 145
10.6 Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

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 10.7 Utilities for analysis: TBtrans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

11 ANALYSIS TOOLS 146

12 SCRIPTING 147

13 PROBLEM HANDLING 147

13.1 Error and warning messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

14 REPORTING BUGS 147

15 ACKNOWLEDGMENTS 147

16 APPENDIX: Physical unit names recognized by FDF 149

17 APPENDIX: XML Output 151

17.1 Controlling XML output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
17.2 Converting XML to XHTML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

18 APPENDIX: Selection of precision for storage 152

19 APPENDIX: Data structures and reference counting 153

Bibliography 154

Index 156

7
1 INTRODUCTION

This Reference Manual contains descriptions of all the input, output and execution features of
SIESTA, but is not really a tutorial introduction to the program. Interested users can find tu-
torial material prepared for SIESTA schools and workshops at the project’s web page http:
//www.uam.es/siesta.
NOTE: See the description of changes in the logic of the SCF loop
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method
and its computer program implementation, to perform electronic structure calculations and ab initio
molecular dynamics simulations of molecules and solids. Its main characteristics are:

• It uses the standard Kohn-Sham selfconsistent density functional method in the local den-
sity (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).

It routinely provides:

• Total and partial energies.

• Atomic forces.

• Stress tensor.

• Electric dipole moment.

• Atomic, orbital and bond populations (Mulliken).

• Electron density.

8
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 (colinear 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)

Starting from version 3.0, SIESTA includes the TranSIESTA module. TranSIESTA provides
the ability to model open-boundary systems where ballistic electron transport is taking place. Using
TranSIESTA one can compute electronic transport properties, such as the zero bias conductance
and the I-V characteristic, of a nanoscale system in contact with two electrodes at different elec-
trochemical potentials. The method is based on using non equilibrium Greens functions (NEGF),
that are constructed using the density functional theory Hamiltonian obtained from a given electron
density. A new density is computed using the NEGF formalism, which closes the DFT-NEGF self
consistent cycle.
Starting from version 4.1, TranSIESTA is an intrinsic part of the SIESTA code. I.e. a separate
executable is not necessary anymore. See Sec. 10 for details.
For more details on the formalism, see the main TranSIESTA reference cited below. A section
has been added to this User’s Guide, that describes the necessary steps involved in doing transport
calculations, together with the currently implemented input options.

References:

• “Unconstrained minimization approach for electronic computations that scales linearly with
system size” P. Ordejón, D. A. Drabold, M. P. Grumbach and R. M. Martin, Phys. Rev. B 48,
14646 (1993); “Linear system-size methods for electronic-structure calculations” Phys. Rev.
B 51 1456 (1995), and references therein.
Description of the order-N eigensolvers implemented in this code.

• “Self-consistent order-N density-functional calculations for very large systems” P. Ordejón, E.

Artacho and J. M. Soler, Phys. Rev. B 53, 10441, (1996).
Description of a previous version of this methodology.

9
 • “Density functional method for very large systems with LCAO basis sets” D. Sánchez-Portal,
P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quantum Chem., 65, 453 (1997).
Description of the present method and code.

• “Linear-scaling ab-initio calculations for large and complex systems” E. Artacho, D. Sánchez-
Portal, P. Ordejón, A. García and J. M. Soler, Phys. Stat. Sol. (b) 215, 809 (1999).
Description of the numerical atomic orbitals (NAOs) most commonly used in the code, and
brief review of applications as of March 1999.

• “Numerical atomic orbitals for linear-scaling calculations” J. Junquera, O. Paz, D. Sánchez-

Portal, and E. Artacho, Phys. Rev. B 64, 235111, (2001).
Improved, soft-confined NAOs.

• “The SIESTA method for ab initio order-N materials simulation” J. M. Soler, E. Artacho,
J.D. Gale, A. García, J. Junquera, P. Ordejón, and D. Sánchez-Portal, J. Phys.: Condens.
Matter 14, 2745-2779 (2002)
Extensive description of the SIESTA method.

• “Computing the properties of materials from first principles with SIESTA”, D. Sánchez-Portal,
P. Ordejón, and E. Canadell, Structure and Bonding 113, 103-170 (2004).
Extensive review of applications as of summer 2003.

• “Improvements on non-equilibrium and transport Green function techniques: The next-

generation TranSIESTA”, Nick Papior, Nicolas Lorente, Thomas Frederiksen, Alberto Gar-
cÃŋa and Mads Brandbyge, Computer Physics Communications, 212, 8–24 (2017).
Description of the TranSIESTA method.

• “Density-functional method for nonequilibrium electron transport”, Mads Brandbyge, Jose-

Luis Mozos, Pablo Ordejón, Jeremy Taylor, and Kurt Stokbro, Phys. Rev. B 65, 165401
(2002).
Description of the original TranSIESTA method (prior to 4.1).

For more information you can visit the web page http://www.uam.es/siesta.

2 COMPILATION

2.1 The build directory

Rather than using the top-level Src directory as building directory, the user has to use an ad-hoc
building directory (by default the top-level Obj directory, but it can be any (new) directory in the
top level). The building directory will hold the object files, module files, and libraries resulting from
the compilation of the sources in Src. The VPATH mechanism of modern make programs is used.
This scheme has many advantages. Among them:

• The Src directory is kept pristine.

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 • Many different object directories can be used concurrently to compile the program with differ-
ent compilers or optimization levels.

If you just want to compile the program, go to Obj and issue the command:

sh ../Src/obj_setup.sh

to populate this directory with the minimal scaffolding of makefiles, and then make sure that you
create or generate an appropriate arch.make file (see below, in Sec. 2.2). Then, type

make

The executable should work for any job. (This is not exactly true, since some of the parameters in
the atomic routines are still hardwired (see Src/atmparams.f), but those would seldom need to be
changed.)
To compile utility programs (those living in Util), you can just simply use the provided makefiles,
typing “make” as appropriate.

2.1.1 Multiple-target compilation

The mechanism described here can be repeated in other directories at the same level as Obj, with
different names. In this way one can compile as many different versions of the SIESTA executable
as needed (for example, with different levels of optimization, serial, parallel, debug, etc), by working
in separate building directories.
Simply provide the appropriate arch.make, and issue the setup command above. To compile utility
programs, you need to use the form:

make OBJDIR=ObjName

where ObjName is the name of the object directory of your choice. Be sure to type make clean before
attempting to re-compile a utility program.
(The pristine Src directory should be kept “clean”, without objects, or else the compilation in the
build directories will get confused)

2.2 The arch.make file

The compilation of the program is done using a Makefile that is provided with the code. This
Makefile will generate the executable for any of several architectures, with a minimum of tuning
required from the user and encapsulated in a separate file called arch.make.
You are strongly encouraged to look at Obj/DOCUMENTED-TEMPLATE.make for information about the
fine points of the arch.make file. There are two sample make files for compilation of SIESTA with
gfortran and ifort named Obj/gfortran.make and Obj/intel.make, respectively. Please use
those as guidelines for creating the final arch.make.
Note that Intel compilers default to high optimizations which tends to break SIESTA. We advice
to use -fp-model source flag and not compile with higher optimizations than -O2.

11
2.3 Parallel

To achieve a parallel build of SIESTA one should first determine which type of parallelism one
requires. It is advised to use MPI for calculations with moderate number of cores. If one requires
eXa-scale parallelism SIESTA provides hybrid parallelism using both MPI and OpenMP.

2.3.1 MPI

MPI is a message-passing interface which enables communication between equivalently executed

binaries. This library will thus duplicate all non-distributed data such as local variables etc.
To enable MPI in SIESTA the compilation options are required to be changed accordingly, here is
the most basic changes to the arch.make for standard binary names

CC = mpicc
FC = mpifort # or mpif90
MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = .
FPPFLAGS += -DMPI

Subsequently one may run SIESTA using the mpirun/mpiexec commands:

mpirun -np <> siesta RUN.fdf

where <> is the number of cores used.

2.3.2 OpenMP

OpenMP is shared memory parallelism. It typically does not infer any memory overhead and may
be used if memory is scarce and the regular MPI compilation is crashing due to insufficient memory.
To enable OpenMP, simply add this to your arch.make

# For GNU compiler

FFLAGS += -fopenmp
LIBS += -fopenmp
# or, for Intel compiler < 16
FFLAGS += -openmp
LIBS += -openmp
# or, for Intel compiler >= 16
FFLAGS += -qopenmp
LIBS += -qopenmp

The above will yield the most basic parallelism using OpenMP. However, the BLAS/LAPACK
libraries which is the most time-consuming part of SIESTA also requires to be threaded, please see
Sec. 2.4 for correct linking.
Subsequently one may run SIESTA using OpenMP through the environment variable
OMP_NUM_THREADS which determine the number of threads/cores used in the execution.

12
 OMP_NUM_THREADS=<> siesta RUN.fdf
# or (bash)
export OMP_NUM_THREADS=<>
siesta RUN.fdf
# or (csh)
setenv OMP_NUM_THREADS <>
siesta RUN.fdf

where <> is the number of threads/cores used.

If SIESTA is also compiled using MPI it is more difficult to obtain a good performance. Please
refer to your local cluster how to correctly call MPI with hybrid parallelism. An example for running
SIESTA with good performance using OpenMPI > 1.8.2 and OpenMP on a machine with 2 sockets
and 8 cores per socket, one may do:

# MPI = 2 cores, OpenMP = 8 threads per core (total=16)

mpirun --map-by ppr:1:socket:pe=8 \
-x OMP_NUM_THREADS=8 \
-x OMP_PROC_BIND=true siesta RUN.fdf

# MPI = 4 cores, OpenMP = 4 threads per core (total=16)

mpirun --map-by ppr:2:socket:pe=4 \
-x OMP_NUM_THREADS=4 \
-x OMP_PROC_BIND=true siesta RUN.fdf

# MPI = 8 cores, OpenMP = 2 threads per core (total=16)

mpirun --map-by ppr:4:socket:pe=2 \
-x OMP_NUM_THREADS=2 \
-x OMP_PROC_BIND=true siesta RUN.fdf

If using only 1 thread per MPI core it is advised to compile SIESTA without OpenMP. As such it
may be advantageous to compile SIESTA in 3 variants; OpenMP-only (small systems), MPI-only
(medium to large systems) and MPI+OpenMP (large> systems).
The variable OMP_PROC_BIND may heavily influence the performance of the executable! Please per-
form tests for the architecture used.

2.4 Library dependencies

SIESTA makes use of several libraries. Here we list a set of libraries and how each of them may be
added to the compilation step (arch.make).
SIESTA is distributed with scripts that install the most useful libraries. These installation scripts
may be located in the Docs/ folder with names: install_*.bash. Currently SIESTA is shipped
with these installation scripts:

• install_netcdf4.bash; installs NetCDF with full CDF4 support. Thus it installs zlib, hdf5
and NetCDF C and Fortran.

• install_flook.bash; installs flook which enables interaction with Lua and SIESTA.

13
Note that these scripts are guidance scripts and users are encouraged to check the mailing list for
or seek help there in non-standard. The installation scripts finishes by telling what to add to the
arch.make file to correctly link the just installed libraries.

BLAS it is recommended to use a high-performance library (OpenBLAS or MKL library from Intel)

• If you use your *nix distribution package manager to install BLAS you are bound to have
a poor performance. Please try and use performance libraries, whenever possible!
• If you do not have the BLAS library you may use the BLAS library shipped with SIESTA.
To do so simply add libsiestaBLAS.a to the COMP_LIBS variable.

To add BLAS to the arch.make file you need to add the required linker flags to the LIBS
variable in the arch.make file.
Example variables
# OpenBLAS:
LIBS += -L/opt/openblas/lib -lopenblas
# or for MKL
LIBS += -L/opt/intel/.../mkl/lib/intel64 -lmkl_blas95_lp64 ...

To use the threaded (OpenMP) libraries, change the above linking to

# OpenBLAS:
LIBS += -L/opt/openblas/lib -lopenblasp
# or for MKL
LIBS += -L/opt/intel/.../mkl/lib/intel64 -lmkl_blas95_lp64
-lmkl_<>_thread ...

where <> is the compiler used (intel or gnu).

LAPACK it is recommended to use a high-performance library (OpenBLAS1 or MKL library from

Intel)
If you do not have the LAPACK library you may use the LAPACK library shipped with
SIESTA. To do so simply add libsiestaLAPACK.a to the COMP_LIBS variable.
Example variables
# OpenBLAS (OpenBLAS will default to build in LAPACK 3.6)
LIBS += -L/opt/openblas/lib -lopenblas
# or for MKL
LIBS += -L/opt/intel/.../mkl/lib/intel64 -lmkl_lapack95_lp64 ...

To use the threaded (OpenMP) libraries, change the above linking to

# OpenBLAS (OpenBLAS will default to build in LAPACK 3.6)
LIBS += -L/opt/openblas/lib -lopenblasp
# or for MKL
LIBS += -L/opt/intel/.../mkl/lib/intel64 -lmkl_lapack95_lp64
-lmkl_<>_thread ...

where <> is the compiler used (intel or gnu).

1
OpenBLAS enables the inclusion of the LAPACK routines. This is advised.

14
ScaLAPACK Only required for MPI compilation.
Here one may be sufficient to rely on the NetLIB2 version of ScaLAPACK.
Example variables
# ScaLAPACK
LIBS += -L/opt/scalapack/lib -lscalapack
# or for MKL
LIBS += -L/opt/intel/.../mkl/lib/intel64 -lmkl_scalapack_lp64
-lmkl_blacs_<>_lp64 ...

where <> refers to the MPI version used, (intelmpi, openmpi, sgimpt).

Additionally SIESTA may be compiled with support for several other libraries

fdict This library is shipped with SIESTA and its linking may be enabled by
COMP_LIBS += libfdict.a

NetCDF It is adviced to compile NetCDF in CDF4 compliant mode (thus also linking with HDF5)
as this enables more advanced IO. If you only link against a CDF3 compliant library you will
not get the complete feature set of SIESTA.

3 If the CDF3 compliant library is present one may add this to your arch.make:
LIBS += -L/opt/netcdf/lib -lnetcdff -lnetcdf
FPPFLAGS += -DCDF
4 If the CDF4 compliant library is present the HDF5 libraries are also required at link time:
LIBS += -L/opt/netcdf/lib -lnetcdff -lnetcdf \
-lhdf5_fortran -lhdf5 -lz

ncdf This library is shipped with SIESTA and its linking is required to take advantage of the CDF4
library functionalities. To use this library, ensure that you can compile SIESTA with CDF4
support. Then proceed by adding the following to your arch.make
COMP_LIBS += libncdf.a libfdict.a
FPPFLAGS += -DNCDF -DNCDF_4

If the NetCDF library is compiled with parallel support one may take advantage of parallel IO
by adding this to the arch.make
FPPFLAGS += -DNCDF_PARALLEL

To easily install NetCDF please see the installation file: Docs/install_netcdf4.bash.

Metis The Metis library may be used in the Order-N code.

Add these flags to your arch.make file to enable Metis
LIBS += -L/opt/metis/lib -lmetis
FPPFLAGS += -DSIESTA__METIS

2
ScaLAPACKs performance is mainly governed by BLAS and LAPACK.

15
ELPA The ELPA [1;7] library provides faster diagonalization routines.
The required version of ELPA must be 2017.05.003 or later. Add these flags to your arch.make
file to enable ELPA
LIBS += -L/opt/elpa/lib -lelpa <>
FPPFLAGS += -DSIESTA__ELPA -I/opt/elpa/include/elpa-<>/modules

where <> are any libraries that ELPA depend on.

NOTE: ELPA can only be used in the parallel version of SIESTA.
MUMPS The MUMPS library may currently be used with TranSIESTA.
Add these flags to your arch.make file to enable MUMPS
LIBS += -L/opt/mumps/lib -lzmumps -lmumps_common <>
FPPFLAGS += -DSIESTA__MUMPS

where <> are any libraries that MUMPS depend on.

PEXSI The PEXSI library may be used with SIESTA for exa-scale calculations, see Sec. 6.13.
Currently the interface is implemented (tested) as in PEXSI version 0.8.0, 0.9.0 and 0.9.2. If
newer versions retain the same interface they may also be used.
To successfully compile SIESTA with PEXSI support one require the PEXSI fortran interface.
When installing PEXSI copy the f_interface.f90 file to the include directory of PEXSI such
that the module may be found3 when compiling SIESTA.
Add these flags to your arch.make file to enable PEXSI
INCFLAGS += -I/opt/pexsi/include
LIBS += -L/opt/pexsi/lib -lpexsi_linux <>
FPPFLAGS += -DSIESTA__PEXSI

where <> are any libraries that PEXSI depend on. If one experiences linker failures, one
possible solution that may help is
LIBS += -lmpi_cxx -lstdc++

which is due to PEXSI being a C++ library, and the Fortran compiler is the linker. The exact
library name for your MPI vendor may vary.
Additionally the PEXSI linker step may have duplicate objects which can be circumvented by
prefixing the PEXSI libraries with
LIBS += -Wl,--allow-multiple-definition -lpexsi_linux <>

flook SIESTA allows external control via the LUA scripting language. Using this library one may
do advanced MD simulations and much more without changing any code in SIESTA.
Add these flags to your arch.make file to enable flook
LIBS += -L/opt/flook/lib -lflookall -ldl
COMP_LIBS += libfdict.a
FPPFLAGS += -DSIESTA__FLOOK

See Tests/h2o_lua for an example on the LUA interface.

To easily install flook please see the installation file: Docs/install_flook.bash.
3
Optionally the file may be copied to the Obj directory where the compilation takes place.

16
3 EXECUTION OF THE PROGRAM

A fast way to test your installation of SIESTA and get a feeling for the workings of the program
is implemented in directory Tests. In it you can find several subdirectories with pre-packaged fdf
files and pseudopotential references. Everything is automated: after compiling SIESTA you can
just go into any subdirectory and type make. The program does its work in subdirectory work, and
there you can find all the resulting files. For convenience, the output file is copied to the parent
directory. A collection of reference output files can be found in Tests/Reference. Please note
that small numerical and formatting differences are to be expected, depending on the compiler.
(For non-standard execution environments, including queuing systems, have a look at the Scripts in
Tests/Scripts, and see also Sec. 2.3.)
Other examples are provided in the Examples directory. This directory contains basically .fdf files
and the appropriate pseudopotential generation input files. Since at some point you will have to
generate your own pseudopotentials and run your own jobs, we describe here the whole process by
means of the simple example of the water-molecule. It is advisable to create independent directories
for each job, so that everything is clean and neat, and out of the SIESTA directory, so that one can
easily update version by replacing the whole SIESTA tree. Go to your favorite working directory
and:

$ mkdir h2o
$ cd h2o
$ cp path-to-package/Examples/H2O/h2o.fdf

You need to make the siesta executable visible in your path. You can do it in many ways, but a
simple one is

$ ln -s path-to-package/Obj/siesta

We need to generate the required pseudopotentials. (We are going to streamline this process for
this time, but you must realize that this is a tricky business that you must master before using
SIESTA responsibly. Every pseudopotential must be thoroughly checked before use. Please refer
to the ATOM program manual for details regarding what follows.)
NOTE: The ATOM program is no longer bundled with SIESTA, but academic users can dowload
it from the SIESTA webpage at www.icmab.es/siesta.
$ cd path/to/atom/package/
(Compile the program following the instructions)
$ cd Tutorial/PS_Generation/O
$ cat O.tm2.inp
This is the input file, for the oxygen pseudopotential, that we have prepared for you. It is in a
standard (but ancient and obscure) format that you will need to understand in the future:

------------------------------------------------------------
pg Oxygen
tm2 2.0

17
 n=O c=ca
0.0 0.0 0.0 0.0 0.0 0.0
1 4
2 0 2.00 0.00
2 1 4.00 0.00
3 2 0.00 0.00
4 3 0.00 0.00
1.15 1.15 1.15 1.15
------------------------------------------------------------

To generate the pseudopotential do the following;

$ sh ../../Utils/pg.sh O.tm2.inp
Now there should be a new subdirectory called O.tm2 (O for oxygen) and O.tm2.vps (binary) and
O.tm2.psf (ASCII) files.
$ cp O.tm2.psf path-to-working-dir/h2o/O.psf
copies the generated pseudopotential file to your working directory. (The unformatted and ASCII
files are functionally equivalent, but the latter is more transportable and easier to look at, if you so
desire.) The same could be repeated for the pseudopotential for H, but you may as well copy H.psf
from Examples/Vps/ to your h2o working directory.
Now you are ready to run the program:
./siesta < h2o.fdf | tee h2o.out
(If you are running the parallel version you should use some other invocation, such as mpirun -np
2 siesta ..., but we cannot go into that here — see Sec. 2.3).
After a successful run of the program, you should have several files in your directory including the
following:

• fdf.log (contains all the data used, explicit or chosen by default)

• O.ion and H.ion (complete information about the basis and KB projectors)

• h2o.XV (contains positions and velocities)

• h2o.STRUCT_OUT (contains the final cell vectors and positions in “crystallographic” format)

• h2o.DM (contains the density matrix to allow a restart)

• h2o.ANI (contains the coordinates of every MD step, in this case only one)

• h2o.FA (contains the forces on the atoms)

• h2o.EIG (contains the eigenvalues of the Kohn-Sham Hamiltonian)

• h2o.xml (XML marked-up output)

The prefix h2o of all these files is the SystemLabel specified in the input h2o.fdf file (see fdf section
below). The standard output of the program, that you have already seen passing on the screen, was
copied to file h2o.out by the tee command. Have a look at it and refer to the output-explanation

18
 section if necessary. You may also want to look at the fdf.log file to see all the default values that
siesta has chosen for you, before studying the input-explanation section and start changing them.
Now look at the other data files in Examples (all with an .fdf suffix) choose one and repeat the
process for it.

3.1 Specific execution options

SIESTA may be executed in different forms. The basic execution form is

siesta < RUN.fdf > RUN.out

which uses a pipe statement. Since 4.1 SIESTA does not require one to pipe in the input file and
the input file may instead be specified on the command line.

siesta RUN.fdf > RUN.out

This allows for SIESTA to accept special flags described in what follows. Each flag may be quoted
if it contains spaces, or one may substitute spaces by .

-h print a help instruction and quit

-L Override, temporarily, the SystemLabel flag.
siesta -L Hello.
-out|-o Specify the output file (instead of printing to the terminal).
siesta -out RUN.out.
-electrode|-elec depends on: TS.HS.Save, TS.DE.Save
denote this as an electrode calculation which forces the SystemLabel.TSHS and SystemLabel.TSDE
files to be saved.
-V depends on: TS.Voltage
specify the bias for the current TranSIESTA run.
siesta -V 0.25:eV or siesta -V "0.25 eV" which sets the applied bias to 0.25 eV.

4 THE FLEXIBLE DATA FORMAT (FDF)

The main input file, which is read as the standard input (unit 5), contains all the physical data of the
system and the parameters of the simulation to be performed. This file is written in a special format
called FDF, developed by Alberto García and José M. Soler. This format allows data to be given in
any order, or to be omitted in favor of default values. Refer to documentation in ∼/siesta/Src/fdf
for details. Here we offer a glimpse of it through the following rules:

• The fdf syntax is a ’data label’ followed by its value. Values that are not specified in the
datafile are assigned a default value.

• fdf labels are case insensitive, and characters - _ . in a data label are ignored. Thus,
LatticeConstant and lattice_constant represent the same label.

19
 • All text following the # character is taken as comment.

• Logical values can be specified as T, true, .true., yes, F, false, .false., no. Blank is also equivalent
to true.

• Character strings should not be in apostrophes.

• Real values which represent a physical magnitude must be followed by its units. Look at
function fdf_convfac in file ∼/siesta/Src/fdf/fdf.f for the units that are currently supported.
It is important to include a decimal point in a real number to distinguish it from an integer,
in order to prevent ambiguities when mixing the types on the same input line.

• Complex data structures are called blocks and are placed between ‘%block label’ and a ‘%end-
block label’ (without the quotes).

• You may ‘include’ other fdf files and redirect the search for a particular data label to another
file. If a data label appears more than once, its first appearance is used.

• If the same label is specified twice, the first one takes precedence.

• If a label is misspelled it will not be recognized (there is no internal list of “accepted” tags in
the program). You can check the actual value used by siesta by looking for the label in the
output fdf.log file.

These are some examples:

SystemName Water molecule # This is a comment

SystemLabel h2o
SpinPolarized yes
SaveRho
NumberOfAtoms 64
LatticeConstant 5.42 Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
KgridCutoff < BZ_sampling.fdf

# Reading the coordinates from a file

%block AtomicCoordinatesAndAtomicSpecies < coordinates.data

# Even reading more FDF information from somewhere else

%include mydefaults.fdf

The file fdf.log contains all the parameters used by SIESTA in a given run, both those specified in
the input fdf file and those taken by default. They are written in fdf format, so that you may reuse
them as input directly. Input data blocks are copied to the fdf.log file only if you specify the dump
option for them.

20
5 PROGRAM OUTPUT

5.1 Standard output

SIESTA writes a log of its workings to standard output (unit 6), which is usually redirected to an
“output file”.
A brief description follows. See the example cases in the siesta/Tests directory for illustration.
The program starts writing the version of the code which is used. Then, the input fdf file is
dumped into the output file as is (except for empty lines). The program does part of the reading
and digesting of the data at the beginning within the redata subroutine. It prints some of the
information it digests. It is important to note that it is only part of it, some other information being
accessed by the different subroutines when they need it during the run (in the spirit of fdf input).
A complete list of the input used by the code can be found at the end in the file fdf.log, including
defaults used by the code in the run.
After that, the program reads the pseudopotentials, factorizes them into Kleinman-Bylander form,
and generates (or reads) the atomic basis set to be used in the simulation. These stages are docu-
mented in the output file.
The simulation begins after that, the output showing information of the MD (or CG) steps and the
SCF cycles within. Basic descriptions of the process and results are presented. The user has the
option to customize it, however, by defining different options that control the printing of informations
like coordinates, forces, ~k points, etc. The options are discussed in the appropriate sections, but
take into account the behavior of the legacy LongOutput option, as in the current implementation
might silently activate output to the main .out file at the expense of auxiliary files.

LongOutput false (logical)

SIESTA can write to standard output different data sets depending on the values for output
options described below. By default SIESTA will not write most of them. They can be large
for large systems (coordinates, eigenvalues, forces, etc.) and, if written to standard output, they
accumulate for all the steps of the dynamics. SIESTA writes the information in other files (see
Output Files) in addition to the standard output, and these can be cumulative or not.
Setting LongOutput to true changes the default of some options, obtaining more information
in the output (verbose). In particular, it redefines the defaults for the following:
• WriteKpoints
• WriteKbands
• WriteCoorStep
• WriteForces
• WriteEigenvalues
• WriteWaveFunctions
• WriteMullikenPop(it sets it to 1)
The specific changing of any of these options has precedence.

21
5.2 Output to dedicated files

SIESTA can produce a wealth of information in dedicated files, with specific formats, that can be
used for further analysis. See the appropriate sections, and the appendix on file formats. Please take
into account the behavior of LongOutput, as in the current implementation might silently activate
output to the main .out file at the expense of auxiliary files.

6 DETAILED DESCRIPTION OF PROGRAM OPTIONS

Here follows a description of the variables that you can define in your SIESTA input file, with their
data types and default values. For historical reasons the names of the tags do not have an uniform
structure, and can be confusing at times.
Almost all of the tags are optional: SIESTA will assign a default if a given tag is not found when
needed (see fdf.log).

6.1 General system descriptors

SystemLabel siesta (string)
A single word (max. 20 characters without blanks) containing a nickname of the system, used
to name output files.

SystemName 〈None〉 (string)

A string of one or several words containing a descriptive name of the system (max. 150 charac-
ters).

NumberOfSpecies 〈lines in ChemicalSpeciesLabel〉 (integer)

Number of different atomic species in the simulation. Atoms of the same species, but with a
different pseudopotential or basis set are counted as different species.
NOTE: This is not required to be set.

NumberOfAtoms 〈lines in AtomicCoordinatesAndAtomicSpecies〉 (integer)

Number of atoms in the simulation.
NOTE: This is not required to be set.

%block ChemicalSpeciesLabel 〈None〉 (block)

It specifies the different chemical species that are present, assigning them a number for further
identification. SIESTA recognizes the different atoms by the given atomic number.
%block ChemicalSpecieslabel
1 6 C
2 14 Si
3 14 Si_surface
%endblock ChemicalSpecieslabel

The first number in a line is the species number, it is followed by the atomic number, and then by
the desired label. This label will be used to identify corresponding files, namely, pseudopotential
file, user basis file, basis output file, and local pseudopotential output file.

22
 This construction allows you to have atoms of the same species but with different basis or
pseudopotential, for example.
Negative atomic numbers are used for ghost atoms (see PAO.Basis).
For atomic numbers over 200 or below −200 you should read SyntheticAtoms.
NOTE: This block is mandatory.

%block SyntheticAtoms 〈None〉 (block)

This block is an additional block to complement ChemicalSpeciesLabel for special atomic
numbers.
Atomic numbers over 200 are used to represent synthetic atoms (created for example as a
“mixture” of two real ones for a “virtual crystal” (VCA) calculation). In this special case a
new SyntheticAtoms block must be present to give SIESTA information about the “ground
state” of the synthetic atom.
%block ChemicalSpeciesLabel
1 201 ON-0.50000
%endblock ChemicalSpeciesLabel
%block SyntheticAtoms
1 # Species index
2 2 3 4 # n numbers for valence states with l=0,1,2,3
2.0 3.5 0.0 0.0 # occupations of valence states with l=0,1,2,3
%endblock SyntheticAtoms

Pseudopotentials for synthetic atoms can be created using the mixps and fractional programs
in the Util/VCA directory.
Atomic numbers below −200 represent ghost synthetic atoms.

%block AtomicMass 〈None〉 (block)

It allows the user to introduce the atomic masses of the different species used in the calculation,
useful for the dynamics with isotopes, for example. If a species index is not found within the
block, the natural mass for the corresponding atomic number is assumed. If the block is absent
all masses are the natural ones. One line per species with the species index (integer) and the
desired mass (real). The order is not important. If there is no integer and/or no real numbers
within the line, the line is disregarded.
%block AtomicMass
3 21.5
1 3.2
%endblock AtomicMass

The default atomic mass are the natural masses. For ghost atoms (i.e. floating orbitals) the
mass is 1030 a.u.

6.2 Pseudopotentials

SIESTA uses pseudopotentials to represent the electron-ion interaction (as do most plane-wave codes
and in contrast to so-called “all-electron” programs). In particular, the pseudopotentials are of the
“norm-conserving” kind, and can be generated by the Atom program, (see Pseudo/README.ATOM).
Remember that all pseudopotentials should be thoroughly tested before using them. We refer
you to the standard literature on pseudopotentials and to the ATOM manual for more information. A

23
number of other codes (such as APE) can generate pseudopotentials that SIESTA can use directly
(typically in the .psf format).
The pseudopotentials will be read by SIESTA from different files, one for each defined species
(species defined either in block ChemicalSpeciesLabel). The name of the files should be:
Chemical_label.vps (unformatted) or Chemical_label.psf (ASCII)
where Chemical_label corresponds to the label defined in the ChemicalSpeciesLabel block.

6.3 Basis set and KB projectors

6.3.1 Overview of atomic-orbital bases implemented in SIESTA

The main advantage of atomic orbitals is their efficiency (fewer orbitals needed per electron for
similar precision) and their main disadvantage is the lack of systematics for optimal convergence, an
issue that quantum chemists have been working on for many years. They have also clearly shown
that there is no limitation on precision intrinsic to LCAO. This section provides some information
about how basis sets can be generated for SIESTA.
It is important to stress at this point that neither the SIESTA method nor the program are bound
to the use of any particular kind of atomic orbitals. The user can feed into SIESTA the atomic basis
set he/she choses by means of radial tables (see User.Basis below), the only limitations being: (i)
the functions have to be atomic-like (radial functions mutiplied by spherical harmonics), and (ii)
they have to be of finite support, i.e., each orbital becomes strictly zero beyond some cutoff radius
chosen by the user.
Most users, however, do not have their own basis sets. For these users we have devised some schemes
to generate basis sets within the program with a minimum input from the user. If nothing is specified
in the input file, Siesta generates a default basis set of a reasonable quality that might constitute
a good starting point. Of course, depending on the accuracy required in the particular problem,
the user has the degree of freedom to tune several parameters that can be important for quality
and efficiency. A description of these basis sets and some performance tests can be found in the
references quoted below.
“Numerical atomic orbitals for linear-scaling calculations”, J. Junquera, O. Paz, D. Sánchez-Portal,
and E. Artacho, Phys. Rev. B 64, 235111, (2001)
An important point here is that the basis set selection is a variational problem and, therefore,
minimizing the energy with respect to any parameters defining the basis is an “ab initio” way to
define them.
We have also devised a quite simple and systematic way of generating basis sets based on specifying
only one main parameter (the energy shift) besides the basis size. It does not offer the best NAO
results one can get for a given basis size but it has the important advantages mentioned above. More
about it in:
“Linear-scaling ab-initio calculations for large and complex systems”, E. Artacho, D. Sánchez-Portal,
P. Ordejón, A. García and J. M. Soler, Phys. Stat. Sol. (b) 215, 809 (1999).
In addition to SIESTA we provide the program Gen-basis , which reads SIESTA’s input and
generates basis files for later use. Gen-basis can be found in Util/Gen-basis. It should be run
from the Tutorials/Bases directory, using the gen-basis.sh script. It is limited to a single species.

24
Of course, as it happens for the pseudopotential, it is the responsibility of the user to check that
the physical results obtained are converged with respect to the basis set used before starting any
production run.
In the following we give some clues on the basics of the basis sets that SIESTA generates. The
starting point is always the solution of Kohn-Sham’s Hamiltonian for the isolated pseudo-atoms,
solved in a radial grid, with the same approximations as for the solid or molecule (the same exchange-
correlation functional and pseudopotential), plus some way of confinement (see below). We describe
in the following three main features of a basis set of atomic orbitals: size, range, and radial shape.
Size: number of orbitals per atom
Following the nomenclature of Quantum Chemistry, we establish a hierarchy of basis sets, from
single-ζ to multiple-ζ with polarization and diffuse orbitals, covering from quick calculations of low
quality to high precision, as high as the finest obtained in Quantum Chemistry. A single-ζ (also
called minimal) basis set (SZ in the following) has one single radial function per angular momentum
channel, and only for those angular momenta with substantial electronic population in the valence
of the free atom. It offers quick calculations and some insight on qualitative trends in the chemical
bonding and other properties. It remains too rigid, however, for more quantitative calculations
requiring both radial and angular flexibilization.
Starting by the radial flexibilization of SZ, a better basis is obtained by adding a second function per
channel: double-ζ (DZ). In Quantum Chemistry, the split valence scheme is widely used: starting
from the expansion in Gaussians of one atomic orbital, the most contracted Gaussians are used
to define the first orbital of the double-ζ and the most extended ones for the second. For strictly
localized functions there was a first proposal of using the excited states of the confined atoms, but it
would work only for tight confinement (see PAO.BasisType nodes below). This construction was
proposed and tested in D. Sánchez-Portal et al., J. Phys.: Condens. Matter 8, 3859-3880 (1996).
We found that the basis set convergence is slow, requiring high levels of multiple-ζ to achieve what
other schemes do at the double-ζ level. This scheme is related with the basis sets used in the
OpenMX project [see T. Ozaki, Phys. Rev. B 67, 155108 (2003); T. Ozaki and H. Kino, Phys. Rev.
B 69, 195113 (2004)].
We then proposed an extension of the split valence idea of Quantum Chemistry to strictly localized
NAO which has become the standard and has been used quite successfully in many systems (see
PAO.BasisType split below). It is based on the idea of suplementing the first ζ with, instead of a
gaussian, a numerical orbital that reproduces the tail of the original PAO outside a matching radius
rm , and continues smoothly towards the origin as rl (a − br2 ), with a and b ensuring continuity and
differentiability at rm . Within exactly the same Hilbert space, the second orbital can be chosen to
be the difference between the smooth one and the original PAO, which gives a basis orbital strictly
confined within the matching radius rm (smaller than the original PAO!) continuously differentiable
throughout.
Extra parameters have thus appeared: one rm per orbital to be doubled. The user can again
introduce them by hand (see PAO.Basis below). Alternatively, all the rm ’s can be defined at
once by specifying the value of the tail of the original PAO beyond rm , the so-called split norm.
Variational optimization of this split norm performed on different systems shows a very general and
stable performance for values around 15% (except for the ∼ 50% for hydrogen). It generalizes to
multiple-ζ trivially by adding an additional matching radius per new zeta.
Note: What is actually used is the norm of the tail plus the norm of the parabola-like inner function.

25
Angular flexibility is obtained by adding shells of higher angular momentum. Ways to generate these
so-called polarization orbitals have been described in the literature for Gaussians. For NAOs there
are two ways for SIESTA and Gen-basis to generate them: (i) Use atomic PAO’s of higher angular
momentum with suitable confinement, and (ii) solve the pseudoatom in the presence of an electric
field and obtain the l + 1 orbitals from the perturbation of the l orbitals by the field.
So-called diffuse orbitals, that might be important in the description of open systems such as surfaces,
can be simply added by specifying extra “n” shells. [See S. Garcia-Gil, A. Garcia, N. Lorente, P.
Ordejon, Phys. Rev. B 79, 075441 (2009)]
Finally, the method allows the inclusion of off-site (ghost) orbitals (not centered around any specific
atom), useful for example in the calculation of the counterpoise correction for basis-set superposition
errors. Bessel functions for any radius and any excitation level can also be added anywhere to the
basis set.
Range: cutoff radii of orbitals.
Strictly localized orbitals (zero beyond a cutoff radius) are used in order to obtain sparse Hamiltonian
and overlap matrices for linear scaling. One cutoff radius per angular momentum channel has to be
given for each species.
A balanced and systematic starting point for defining all the different radii is achieved by giving one
single parameter, the energy shift, i.e., the energy increase experienced by the orbital when confined.
Allowing for system and physical-quantity variablity, as a rule of thumb ∆EPAO ≈ 100 meV gives
typical precisions within the accuracy of current GGA functionals. The user can, nevertheless,
change the cutoff radii at will.
Shape
Within the pseudopotential framework it is important to keep the consistency between the pseu-
dopotential and the form of the pseudoatomic orbitals in the core region. The shape of the orbitals
at larger radii depends on the cutoff radius (see above) and on the way the localization is enforced.
The first proposal (and quite a standard among SIESTA users) uses an infinite square-well potential.
It was originally proposed and has been widely and successfully used by Otto Sankey and collabora-
tors, for minimal bases within the ab initio tight-binding scheme, using the Fireball program, but
also for more flexible bases using the methodology of SIESTA. This scheme has the disadavantage,
however, of generating orbitals with a discontinuous derivative at rc . This discontinuity is more
pronounced for smaller rc ’s and tends to disappear for long enough values of this cutoff. It does
remain, however, appreciable for sensible values of rc for those orbitals that would be very wide
in the free atom. It is surprising how small an effect such a kink produces in the total energy of
condensed systems. It is, on the other hand, a problem for forces and stresses, especially if they are
calculated using a (coarse) finite three-dimensional grid.
Another problem of this scheme is related to its defining the basis starting from the free atoms.
Free atoms can present extremely extended orbitals, their extension being, besides problematic, of
no practical use for the calculation in condensed systems: the electrons far away from the atom can
be described by the basis functions of other atoms.
A traditional scheme to deal with this is one based on the radial scaling of the orbitals by suitable
scale factors. In addition to very basic bonding arguments, it is soundly based on restoring the
virial’s theorem for finite bases, in the case of Coulombic potentials (all-electron calculations). The
use of pseudopotentials limits its applicability, allowing only for extremely small deviations from

26
unity (∼ 1%) in the scale factors obtained variationally (with the exception of hydrogen that can
contract up to 25%). This possiblity is available to the user.
Another way of dealing with the above problem and that of the kink at the same time is adding a soft
confinement potential to the atomic Hamiltonian used to generate the basis orbitals: it smoothens
the kink and contracts the orbital as suited. Two additional parameters are introduced for the
purpose, which can be defined again variationally. The confining potential is flat (zero) in the core
region, starts off at some internal radius ri with all derivatives continuous and diverges at rc ensuring
the strict localization there. It is r −r
− c i
e r−ri
V (r) = Vo (1)
rc − r
and both ri and Vo can be given to SIESTA together with rc in the input (see PAO.Basis be-
low). The kink is normally well smoothened with the default values for soft confinement by default
(PAO.SoftDefault true), which are ri = 0.9rc and Vo = 40 Ry.
When explicitly introducing orbitals in the basis that would be empty in the atom (e.g. polarisation
orbitals) these tend to be extremely extended if not completely unbound. The above procedure
produces orbitals that bulge as far away from the nucleus as possible, to plunge abruptly at rc . Soft
confinement can be used to try to force a more reasonable shape, but it is not ideal (for orbitals
peaking in the right region the tails tend to be far too short). Charge confinement produces very
good shapes for empty orbitals. Essentially a Z/r potential is added to the soft confined potential
above. For flexibility the charge confinement option in SIESTA is defined as

Ze−λr
VQ (r) = √ (2)
r2 + δ 2
where δ is there to avoid the singularity (default δ = 0.01 Bohr), and λ allows to screen the potential
if longer tails are needed. The description on how to introduce this option can be found in the
PAO.Basis entry below.
Finally, the shape of an orbital is also changed by the ionic character of the atom. Orbitals in
cations tend to shrink, and they swell in anions. Introducing a δQ in the basis-generating free-atom
calculations gives orbitals better adapted to ionic situations in the condensed systems.
More information about basis sets can be found in the proposed literature.

There are quite a number of options for the input of the basis-set and KB projector specification, and
they are all optional! By default, SIESTA will use a DZP basis set with appropriate choices for the
determination of the range, etc. Of course, the more you experiment with the different options, the
better your basis set can get. To aid in this process we offer an auxiliary program for optimization
which can be used in particular to obtain variationally optimal basis sets (within a chosen basis
size). See Util/Optimizer for general information, and Util/Optimizer/Examples/Basis_Optim
for an example. The directory Tutorials/Bases in the main SIESTA distribution contains some
tutorial material for the generation of basis sets and KB projectors.
Finally, some optimized basis sets for particular elements are available at the SIESTA web page.
Again, it is the responsability of the users to test the transferability of the basis set to their problem
under consideration.

27
6.3.2 Type of basis sets
PAO.BasisType split (string)
The kind of basis to be generated is chosen. All are based on finite-range pseudo-atomic orbitals
[PAO’s of Sankey and Niklewsky, PRB 40, 3979 (1989)]. The original PAO’s were described
only for minimal bases. SIESTA generates extended bases (multiple-ζ, polarization, and diffuse
orbitals) applying different schemes of choice:
- Generalization of the PAO’s: uses the excited orbitals of the finite-range pseudo-atomic
problem, both for multiple-ζ and for polarization [see Sánchez-Portal, Artacho, and Soler,
JPCM 8, 3859 (1996)]. Adequate for short-range orbitals.
- Multiple-ζ in the spirit of split valence, decomposing the original PAO in several pieces of
different range, either defining more (and smaller) confining radii, or introducing Gaussians
from known bases (Huzinaga’s book).
All the remaining options give the same minimal basis. The different options and their fdf
descriptors are the following:
split Split-valence scheme for multiple-zeta. The split is based on different radii.
2
splitgauss Same as split but using gaussian functions e−(x/αi ) . The gaussian widths αi are
read instead of the scale factors (see below). There is no cutting algorithm, so that a large
enough rc should be defined for the gaussian to have decayed sufficiently.
nodes Generalized PAO’s.
nonodes The original PAO’s are used, multiple-zeta is generated by changing the scale-factors,
instead of using the excited orbitals.
filteret Use the filterets as a systematic basis set. The size of the basis set is controlled by the
filter cut-off for the orbitals.
Note that, for the split and nodes cases the whole basis can be generated by SIESTA with
no further information required. SIESTA will use default values as defined in the following
(PAO.BasisSize, PAO.EnergyShift, and PAO.SplitNorm, see below).

6.3.3 Size of the basis set

PAO.BasisSize DZP (string)
It defines usual basis sizes. It has effect only if there is no block PAO.Basis present.
SZ|minimal Use single-ζ basis.
DZ Double zeta basis, in the scheme defined by PAO.BasisType.
SZP Single-zeta basis plus polarization orbitals.
DZP|standard Like DZ plus polarization orbitals. Polarization orbitals are constructed from
perturbation theory, and they are defined so they have the minimum angular momentum l
such that there are not occupied orbitals with the same l in the valence shell of the ground-
state atomic configuration. They polarize the corresponding l − 1 shell.
NOTE: The ground-state atomic configuration used internally by SIESTA is defined in the
source file Src/periodic_table.f. For some elements (e.g., Pd), the configuration might

28
 not be the standard one.

%block PAO.BasisSizes 〈None〉 (block)

Block which allows to specify a different value of the variable PAO.BasisSize for each species.
For example,
%block PAO.BasisSizes
Si DZ
H DZP
O SZP
%endblock PAO.BasisSizes

6.3.4 Range of the orbitals

PAO.EnergyShift 0.02 Ry (energy)
A standard for orbital-confining cutoff radii. It is the excitation energy of the PAO’s due to
the confinement to a finite-range. It offers a general procedure for defining the confining radii
of the original (first-zeta) PAO’s for all the species guaranteeing the compensation of the basis.
It only has an effect when the block PAO.Basis is not present or when the radii specified in
that block are zero for the first zeta.

Write.Graphviz none|atom|orbital|atom+orbital (string)

Write out the sparsity pattern after having determined the basis size overlaps. This will generate
SystemLabel.ATOM.gv or SystemLabel.ORB.gv which both may be converted to a graph using
Graphviz’s program neato:
neato -x -Tpng siesta.ATOM.gv -o siesta_ATOM.png
The resulting graph will list each atom as i(j) where i is the atomic index and j is the number
of other atoms it is connected to.

6.3.5 Generation of multiple-zeta orbitals

PAO.SplitNorm 0.15 (real)
A standard to define sensible default radii for the split-valence type of basis. It gives the amount
of norm that the second-ζ split-off piece has to carry. The split radius is defined accordingly.
If multiple-ζ is used, the corresponding radii are obtained by imposing smaller fractions of the
SplitNorm (1/2, 1/4 ...) value as norm carried by the higher zetas. It only has an effect when
the block PAO.Basis is not present or when the radii specified in that block are zero for zetas
higher than one.

PAO.SplitNormH 〈PAO.SplitNorm〉 (real)

This option is as per PAO.SplitNorm but allows a separate default to be specified for hydrogen
which typically needs larger values than those for other elements.

PAO.NewSplitCode false (logical)

Enables a new, simpler way to match the multiple-zeta radii.
If an old-style (tail+parabola) calculation is being done, perform a scan of the tail+parabola
norm in the whole range of the 1st-zeta orbital, and store that in a table. The construction of
the 2nd-zeta orbital involves simply scanning the table to find the appropriate place. Due to

29
 the idiosyncracies of the old algorithm, the new one is not guaranteed to produce exactly the
same results, as it might settle on a neighboring grid point for the matching.

PAO.FixSplitTable false (logical)

After the scan of the allowable split-norm values, apply a damping function to the tail to make
sure that the table goes to zero at the radius of the first-zeta orbital.

PAO.SplitTailNorm false (logical)

Use the norm of the tail instead of the full tail+parabola norm. This is the behavior described
in the JPC paper. (But note that, for numerical reasons, the square root of the tail norm is
used in the algorithm.) This is the preferred mode of operation for automatic operation, as in
non-supervised basis-optimization runs.

As a summary of the above options:

• For complete backwards compatibility, do nothing.

• To exercise the new code, set PAO.NewSplitCode.

• To maintain the old split-norm heuristic, but making sure that the program finds a solution
(even if not optimal, in the sense of producing a second-ζ rc very close to the first-ζ one), set
PAO.FixSplitTable (this will automatically set PAO.NewSplitCode).

• If the old heuristic is of no interest (for example, if only a robust way of mapping split-norms to
radii is needed), set PAO.SplitTailNorm (this will set PAO.NewSplitCode automatically).

PAO.EnergyCutoff 20 Ry (energy)
If the multiple zetas are generated using filterets then only the filterets with an energy lower
than this cutoff are included. Increasing this value leads to a richer basis set (provided the
cutoff is raised above the energy of any filteret that was previously not included) but a more
expensive calculation. It only has an effect when the option PAO.BasisType is set to filteret.

PAO.EnergyPolCutoff 20 Ry (energy)
If the multiple zetas are generated using filterets then only the filterets with an energy lower
than this cutoff are included for the polarisation functions. Increasing this value leads to a
richer basis set (provided the cutoff is raised above the energy of any filteret that was previ-
ously not included) but a more expensive calculation. It only has an effect when the option
PAO.BasisType is set to filteret.

PAO.ContractionCutoff 0|0 − 1 (real)

If the multiple zetas are generated using filterets then any filterets that have a coefficient less
than this threshold within the original PAO will be contracted together to form a single filteret.
Increasing this value leads to a smaller basis set but allows the underlying basis to have a higher
kinetic energy cut-off for filtering. It only has an effect when the option PAO.BasisType is
set to filteret.

6.3.6 Soft-confinement options

PAO.SoftDefault false (logical)

30
 If set to true then this option causes soft confinement to be the default form of potential during
orbital generation. The default potential and inner radius are set by the commands given below.

PAO.SoftInnerRadius 0.9 (real)

For default soft confinement, the inner radius is set at a fraction of the outer confinement radius
determined by the energy shift. This option controls the fraction of the confinement radius to
be used.

PAO.SoftPotential 40 Ry (energy)
For default soft confinement, this option controls the value of the potential used for all orbitals.
NOTE: Soft-confinement options (inner radius, prefactor) have been traditionally used to op-
timize the basis set, even though formally they are just a technical necessity to soften the decay
of the orbitals at rc. To achieve this, it might be enough to use the above global options.

6.3.7 Kleinman-Bylander projectors

%block PS.lmax 〈None〉 (block)
Block with the maximum angular momentum of the Kleinman-Bylander projectors, lmxkb. This
information is optional. If the block is absent, or for a species which is not mentioned inside
it, SIESTA will take lmxkb(is) = lmxo(is) + 1, where lmxo(is) is the maximum angular
momentum of the basis orbitals of species is.
%block Ps.lmax
Al_adatom 3
H 1
O 2
%endblock Ps.lmax

By default lmax is the maximum angular momentum plus one.

%block PS.KBprojectors 〈None〉 (block)

This block provides information about the number of Kleinman-Bylander projectors per angular
momentum, and for each species, that will used in the calculation. This block is optional. If
the block is absent, or for species not mentioned in it, only one projector will be used for
each angular momentum. The projectors will be constructed using the eigenfunctions of the
respective pseudopotentials.
This block allows to specify the number of projector for each l, and also the reference energies of
the wavefunctions used to build them. The specification of the reference energies is optional. If
these energies are not given, the program will use the eigenfunctions with an increasing number
of nodes (if there is not bound state with the corresponding number of nodes, the “eigenstates”
are taken to be just functions which are made zero at very long distance of the nucleus). The
units for the energy can be optionally specified, if not, the program will assumed that are given
in Rydbergs. The data provided in this block must be consistent with those read from the block
PS.lmax. For example,
%block PS.KBprojectors
Si 3
2 1
-0.9 eV

31
 0 2
-0.5 -1.0d4 Hartree
1 2
Ga 1
1 3
-1.0 1.0d5 -6.0
%endblock PS.KBprojectors
The reading is done this way (those variables in brackets are optional, therefore they are only
read if present):
From is = 1 to nspecies
read: label(is), l_shells(is)
From lsh=1 to l_shells(is)
read: l, nkbl(l,is)
read: {erefKB(izeta,il,is)}, from ikb = 1 to nkbl(l,is), {units}
When a very high energy, higher that 1000 Ry, is specified, the default is taken instead. On
the other hand, very low (negative) energies, lower than -1000 Ry, are used to indicate that
the energy derivative of the last state must be used. For example, in the example given above,
two projectors will be used for the s pseudopotential of Si. One generated using a reference
energy of -0.5 Hartree, and the second one using the energy derivative of this state. For the p
pseudopotential of Ga, three projectors will be used. The second one will be constructed from
an automatically generated wavefunction with one node, and the other projectors from states
at -1.0 and -6.0 Rydberg.
The analysis looking for possible ghost states is only performed when a single projector is used.
Using several projectors some attention should be paid to the “KB cosine” (kbcos), given in the
output of the program. The KB cosine gives the value of the overlap between the reference state
and the projector generated from it. If these numbers are very small ( < 0.01, for example) for
all the projectors of some angular momentum, one can have problems related with the presence
of ghost states.
The default is one KB projector from each angular momentum, constructed from the nodeless
eigenfunction.

KB.New.Reference.Orbitals false (logical)

If true, the routine to generate KB projectors will use slightly different parameters for the
construction of the reference orbitals involved (Rmax=60 Bohr both for integration and nor-
malization).

6.3.8 The PAO.Basis block

%block PAO.Basis 〈None〉 (block)
Block with data to define explicitly the basis to be used. It allows the definition by hand
of all the parameters that are used to construct the atomic basis. There is no need to enter
information for all the species present in the calculation. The basis for the species not men-
tioned in this block will be generated automatically using the parameters PAO.BasisSize,
PAO.BasisType, PAO.EnergyShift, PAO.SplitNorm (or PAO.SplitNormH), and the
soft-confinement defaults, if used (see PAO.SoftDefault).

32
Some parameters can be set to zero, or left out completely. In these cases the values will
be generated from the magnitudes defined above, or from the appropriate default values. For
example, the radii will be obtained from PAO.EnergyShift or from PAO.SplitNorm if they
are zero; the scale factors will be put to 1 if they are zero or not given in the input. An example
block for a two-species calculation (H and O) is the following (opt means optional):
%block PAO.Basis # Define Basis set
O 2 nodes 1.0 # Label, l_shells, type (opt), ionic_charge (opt)
n=2 0 2 E 50.0 2.5 # n (opt if not using semicore levels),l,Nzeta,Softconf(opt)
3.50 3.50 # rc(izeta=1,Nzeta)(Bohr)
0.95 1.00 # scaleFactor(izeta=1,Nzeta) (opt)
1 1 P 2 # l, Nzeta, PolOrb (opt), NzetaPol (opt)
3.50 # rc(izeta=1,Nzeta)(Bohr)
H 2 # Label, l_shells, type (opt), ionic_charge (opt)
0 2 S 0.2 # l, Nzeta, Per-shell split norm parameter
5.00 0.00 # rc(izeta=1,Nzeta)(Bohr)
1 1 Q 3. 0.2 # l, Nzeta, Charge conf (opt): Z and screening
5.00 # rc(izeta=1,Nzeta)(Bohr)
%endblock PAO.Basis

The reading is done this way (those variables in brackets are optional, therefore they are only
read if present) (See the routines in Src/basis_specs.f for detailed information):
From js = 1 to nspecies
read: label(is), l_shells(is), { type(is) }, { ionic_charge(is) }
From lsh=1 to l_shells(is)
read:
{ n }, l(lsh), nzls(lsh,is), { PolOrb(l+1) }, { NzetaPol(l+1) },
{SplitNormfFlag(lsh,is)}, {SplitNormValue(lsh,is)}
{SoftConfFlag(lsh,is)}, {PrefactorSoft(lsh,is)}, {InnerRadSoft(lsh,is)},
{FilteretFlag(lsh,is)}, {FilteretCutoff(lsh,is)}
{ChargeConfFlag(lsh,is)}, {Z(lsh,is)}, {Screen(lsh,is)}, {delta(lsh,is}
read: rcls(izeta,lsh,is), from izeta = 1 to nzls(l,is)
read: { contrf(izeta,il,is) }, from izeta = 1 to nzls(l,is)

And here is the variable description:

- Label: Species label, this label determines the species index is according to the block
ChemicalSpeciesLabel
- l_shells(is): Number of shells of orbitals with different angular momentum for species
is
- type(is): Optional input. Kind of basis set generation procedure for species is. Same
options as PAO.BasisType
- ionic_charge(is): Optional input. Net charge of species is. This is only used for basis set
generation purposes. Default value: 0.0 (neutral atom). Note that if the pseudopotential
was generated in an ionic configuration, and no charge is specified in PAO.Basis, the ionic
charge setting will be that of pseudopotential generation.
- n: Principal quantum number of the shell. This is an optional input for normal atoms,
however it must be specified when there are semicore states (i.e. when states that usually
are not considered to belong to the valence shell have been included in the calculation)
- l: Angular momentum of basis orbitals of this shell

33
 - nzls(lsh,is): Number of “zetas” for this shell. For a filteret basis this number is ignored
since the number is controlled by the cutoff.
- PolOrb(l+1): Optional input. If set equal to P, a shell of polarization functions (with an-
gular momentum l+1) will be constructed from the first-zeta orbital of angular momentum
l. Default value: ’ ’ (blank = No polarization orbitals).
- NzetaPol(l+1): Optional input. Number of “zetas” for the polarization shell (generated
automatically in a split-valence fashion). For a filteret basis this number is ignored since
the number is controlled by the cutoff. Only active if PolOrb = P. Default value: 1
- SplitNormFlag(lsh,is): Optional input. If set equal to S, the following number sets the
split-norm parameter for that shell.
- SoftConfFlag(l,is): Optional input. If set equal to E, the soft confinement potential
proposed in equation (1) of the paper by J. Junquera et al., Phys. Rev. B 64, 235111
(2001), is used instead of the Sankey hard-well potential.
- PrefactorSoft(l,is): Optional input. Prefactor of the soft confinement potential (V0 in
the formula). Units in Ry. Default value: 0 Ry.
- InnerRadSoft(l,is): Optional input. Inner radius where the soft confinement potential
starts off (ri in the formula). If negative, the inner radius will be computed as the given
fraction of the PAO cutoff radius. Units in bohrs. Default value: 0 bohrs.
- FilteretFlag(l,is): Optional input. If set equal to F, then an individual filter cut-off
can be specified for the shell.
- FilteretCutoff(l,is): Optional input. Shell-specific value for the filteret basis cutoff.
Units in Ry. Default value: The same as the value given by FilterCutoff .
- ChargeConfFlag(lsh,is): Optional input. If set equal to Q, the charge confinement po-
tential in equation (2) above is added to the confining potential. If present it requires at
least one number after it (Z), but it can be followed by two or three numbers.
- Z(lhs,is): Optional input, needed if Q is set. Z charge in equation (2) above for charge
confinement (units of e).
- Screen(lhs,is): Optional input. Yukawa screening parameter λ in equation (2) above
for charge confinement (in Bohr−1 ).
- delta(lhs,is): Optional input. Singularity regularisation parameter δ in equation (2)
above for charge confinement (in Bohr).
- rcls(izeta,l,is): Cutoff radius (Bohr) of each ’zeta’ for this shell. For the second zeta
onwards, if this value is negative, the actual rc used will be the given fraction of the first
zeta’s rc.
- contrf(izeta,l,is): Optional input. Contraction factor of each “zeta” for this shell.
Default value: 1.0
Polarization orbitals are generated by solving the atomic problem in the presence of a polarizing
electric field. The orbitals are generated applying perturbation theory to the first-zeta orbital
of lower angular momentum. They have the same cutoff radius as the orbitals from which they
are constructed.
Note: The perturbative method has traditionally used the ’l’ component of the pseudopotential.
It can be argued that it should use the ’l+1’ component. By default, for backwards compatibility,

34
 the traditional method is used, but the alternative one can be activated by setting the logical
PAO.OldStylePolOrbs variable to false.
There is a different possibility for generating polarization orbitals: by introducing them ex-
plicitly in the PAO.Basis block. It has to be remembered, however, that they sometimes
correspond to unbound states of the atom, their shape depending very much on the cutoff ra-
dius, not converging by increasing it, similarly to the multiple-zeta orbitals generated with the
nodes option. Using PAO.EnergyShift makes no sense, and a cut off radius different from
zero must be explicitly given (the same cutoff radius as the orbitals they polarize is usually a
sensible choice).
A species with atomic number = -100 will be considered by SIESTA as a constant-
pseudopotential atom, i.e., the basis functions generated will be spherical Bessel functions with
the specified rc . In this case, rc has to be given, as EnergyShift will not calculate it.
Other negative atomic numbers will be interpreted by SIESTA as ghosts of the corresponding
positive value: the orbitals are generated and put in position as determined by the coordinates,
but neither pseudopotential nor electrons are considered for that ghost atom. Useful for BSSE
correction.
Use: This block is optional, except when Bessel functions or semicore states are present.
Default: Basis characteristics defined by global definitions given above.

6.3.9 Filtering

FilterCutoff 0 eV (energy)
Kinetic energy cutoff of plane waves used to filter all the atomic basis functions, the pseudo-
core densities for partial core corrections, and the neutral-atom potentials. The basis functions
(which must be squared to obtain the valence density) are really filtered with a cutoff reduced
by an empirical factor 0.72 ' 0.5. The FilterCutoff should be similar or lower than the
MeshCutoff to avoid the eggbox effect on the atomic forces. However, one should not try to
converge MeshCutoff while simultaneously changing FilterCutoff , since the latter in fact
changes the used basis functions. Rather, fix a sufficiently large FilterCutoff and converge
only MeshCutoff . If FilterCutoff is not explicitly set, its value is calculated from FilterTol.

FilterTol 0 eV (energy)
Residual kinetic-energy leaked by filtering each basis function. While FilterCutoff sets a
common reciprocal-space cutoff for all the basis functions, FilterTol sets a specific cutoff for
each basis function, much as the PAO.EnergyShift sets their real-space cutoff. Therefore,
it is reasonable to use similar values for both parameters. The maximum cutoff required to
meet the FilterTol, among all the basis functions, is used (multiplied by the empirical factor
1/0.72 ' 2) to filter the pseudo-core densities and the neutral-atom potentials. FilterTol is
ignored if FilterCutoff is present in the input file. If neither FilterCutoff nor FilterTol
are present, no filtering is performed. See Soler and Anglada [13] , for details of the filtering
procedure.
Warning: If the value of FilterCutoff is made too small (or FilterTol too large) some of the
filtered basis orbitals may be meaningless, leading to incorrect results or even a program crash.
To be implemented: If MeshCutoff is not present in the input file, it can be set using the
maximum filtering cutoff used for the given FilterTol (for the time being, you can use Atom-

35
 SetupOnly true to stop the program after basis generation, look at the maximum filtering
cutoff used, and set the mesh-cutoff manually in a later run.)

6.3.10 Saving and reading basis-set information

SIESTA (and the standalone program Gen-basis) always generate the files Atomlabel.ion, where
Atomlabel is the atomic label specified in block ChemicalSpeciesLabel. Optionally, if NetCDF
support is compiled in, the programs generate NetCDF files Atomlabel.ion.nc (except for ghost
atoms). See an Appendix for information on the optional NetCDF package.
These files can be used to read back information into SIESTA.

User.Basis false (logical)

If true, the basis, KB projector, and other information is read from files Atomlabel.ion, where
Atomlabel is the atomic species label specified in block ChemicalSpeciesLabel. These files can
be generated by a previous SIESTA run or (one by one) by the standalone program Gen-basis.
No pseudopotential files are necessary.

User.Basis.NetCDF false (logical)

If true, the basis, KB projector, and other information is read from NetCDF files Atom-
label.ion.nc, where Atomlabel is the atomic label specified in block ChemicalSpeciesLa-
bel. These files can be generated by a previous SIESTA run or by the standalone program
Gen-basis. No pseudopotential files are necessary. NetCDF support is needed. Note that ghost
atoms cannot yet be adequately treated with this option.

6.3.11 Tools to inspect the orbitals and KB projectors

The program ioncat in Util/Gen-basis can be used to extract orbital, KB projector, and other
information contained in the .ion files. The output can be easily plotted with a graphics program.
If the option WriteIonPlotFiles is enabled, SIESTA will generate and extra set of files that can
be plotted with the gnuplot scripts in Tutorials/Bases. The stand-alone program gen-basis sets
that option by default, and the script Tutorials/Bases/gen-basis.sh can be used to automate
the process. See also the NetCDF-based utilities in Util/PyAtom.

6.3.12 Basis optimization

There are quite a number of options for the input of the basis-set and KB projector specification, and
they are all optional! By default, SIESTA will use a DZP basis set with appropriate choices for the
determination of the range, etc. Of course, the more you experiment with the different options, the
better your basis set can get. To aid in this process we offer an auxiliary program for optimization
which can be used in particular to obtain variationally optimal basis sets (within a chosen basis size).
SeeÂăUtil/Optimizer for general information, and Util/Optimizer/Examples/Basis_Optim for
an example.

BasisPressure 0.2 GPa (pressure)

SIESTA will compute and print the value of the “effective basis enthalpy” constructed by
adding a term of the form pbasis Vorbs to the total energy. Here pbasis is a fictitious basis pressure

36
 and Vorbs is the volume of the system’s orbitals. This is a useful quantity for basis optimization
(See Anglada et al.). The total basis enthalpy is also written to the ASCII file BASIS_ENTHALPY.

6.3.13 Low-level options regarding the radial grid

For historical reasons, the basis-set and KB projector code in SIESTA uses a logarithmic radial
grid, which is taken from the pseudopotential file. Any “interesting” radii have to fall on a grid
point, which introduces a certain degree of coarseness that can limit the accuracy of the results and
the faithfulness of the mapping of input parameters to actual operating parameters. For example,
the same orbital will be produced by a finite range of PAO.EnergyShift values, and any user-
defined cutoffs will not be exactly reflected in the actual cutoffs. This is particularly troublesome for
automatic optimization procedures (such as those implemented in Util/Optimizer), as the engine
might be confused by the extra level of indirection. The following options can be used to fine-tune
the mapping. They are not enabled by default, as they change the numerical results apreciably (in
effect, they lead to different basis orbitals and projectors).

Reparametrize.Pseudos false (logical)

By changing the a and b parameters of the logarithmic grid, a new one with a more adequate
grid-point separation can be used for the generation of basis sets and projectors. For example,
by using a = 0.001 and b = 0.01, the grid point separations at r = 0 and 10 bohrs are 0.00001
and 0.01 bohrs, respectively. More points are needed to reach r’s of the order of a hundred bohrs,
but the extra computational effort is negligible. The net effect of this option (notably when
coupled to Restricted.Radial.Grid false) is a closer mapping of any user-specified cutoff radii
and of the radii implicitly resulting from other input parameters to the actual values used by
the program. (The small grid-point separation near r=0 is still needed to avoid instabilities for
s channels that occurred with the previous (reparametrized) default spacing of 0.005 bohr. This
effect is not yet completely understood. )

New.A.Parameter 0.001 (real)

New setting for the pseudopotential grid’s a parameter

New.B.Parameter 0.01 (real)

New setting for the pseudopotential grid’s b parameter

Rmax.Radial.Grid 50.0 (real)

New setting for the maximum value of the radial coordinate for integration of the atomic
Schrodinger equation.
If Reparametrize.Pseudos is false this will be the maximum radius in the pseudopotential
file.

Restricted.Radial.Grid true (logical)

In normal operation of the basis-set and projector generation code the various cutoff radii are
restricted to falling on an odd-numbered grid point, shifting then accordingly. This restriction
can be lifted by setting this parameter to false.

37
6.4 Structural information

There are many ways to give SIESTA structural information.

• Directly from the fdf file in traditional format.

• Directly from the fdf file in the newer Z-Matrix format, using a Zmatrix block.

• From an external data file

Note that, regardless of the way in which the structure is described, the ChemicalSpeciesLabel
block is mandatory.
In the following sections we document the different structure input methods, and provide a guide to
their precedence.

6.4.1 Traditional structure input in the fdf file

Firstly, the size of the cell itself should be specified, using some combination of the options Lat-
ticeConstant, LatticeParameters, and LatticeVectors, and SuperCell. If nothing is specified,
SIESTA will construct a cubic cell in which the atoms will reside as a cluster.
Secondly, the positions of the atoms within the cells must be specified, using either the traditional
SIESTA input format (a modified xyz format) which must be described within a AtomicCoordi-
natesAndAtomicSpecies block.

LatticeConstant 〈None〉 (length)

Lattice constant. This is just to define the scale of the lattice vectors.
Default value: Minimum size to include the system (assumed to be a molecule) without intercell
interactions, plus 10%.
NOTE: A LatticeConstant value, even if redundant, might be needed for other options, such as
the units of the k-points used for band-structure calculations. This mis-feature will be corrected
in future versions.

%block LatticeParameters 〈None〉 (block)

Crystallographic way of specifying the lattice vectors, by giving six real numbers: the three
vector modules, a, b, and c, and the three angles α (angle between ~b and ~c), β, and γ. The
three modules are in units of LatticeConstant, the three angles are in degrees.
This defaults to a square cell with side-lengths equal to LatticeConstant.
1.0 1.0 1.0 90. 90. 90.

%block LatticeVectors 〈None〉 (block)

The cell vectors are read in units of the lattice constant defined above. They are read as a
matrix CELL(ixyz,ivector), each vector being one line.
This defaults to a square cell with side-lengths equal to LatticeConstant.
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0

38
 If the LatticeConstant default is used, the default of LatticeVectors is still diagonal but not
necessarily cubic.

%block SuperCell 〈None〉 (block)

Integer 3x3 matrix defining a supercell in terms of the unit cell. Any values larger than 1 will
expand the unitcell (plus atoms) along that lattice vector direction (if possible).
%block SuperCell
M(1,1) M(2,1) M(3,1)
M(1,2) M(2,2) M(3,2)
M(1,3) M(2,3) M(3,3)
%endblock SuperCell

and the supercell is defined as SuperCell(ix, i) = j CELL(ix, j) ∗ M (j, i). Notice that the
P

matrix indexes are inverted: each input line specifies one supercell vector.
Warning: SuperCell is disregarded if the geometry is read from the XV file, which can happen
inadvertently.
Use: The atomic positions must be given only for the unit cell, and they are ’cloned’ automat-
ically in the rest of the supercell. The NumberOfAtoms given must also be that in a single
unit cell. However, all values in the output are given for the entire supercell. In fact, CELL is
immediately redefined as the whole supercell and the program no longer knows the existence of
an underlying unit cell. All other input (apart from NumberOfAtoms and atomic positions),
including kgrid.MonkhorstPack must refer to the supercell (this is a change over previous
versions). Therefore, to avoid confusions, we recommend to use SuperCell only to generate
atomic positions, and then to copy them from the output to a new input file with all the atoms
specified explicitly and with the supercell given as a normal unit cell.

AtomicCoordinatesFormat Bohr (string)

Character string to specify the format of the atomic positions in input. These can be expressed
in four forms:
Bohr|NotScaledCartesianBohr atomic positions are given directly in Bohr, in Cartesian co-
ordinates
Ang|NotScaledCartesianAng atomic positions are given directly in Ångström, in Cartesian
coordinates
ScaledCartesian atomic positions are given in Cartesian coordinates, in units of the lattice
constant
Fractional|ScaledByLatticeVectors atomic positions are given referred to the lattice vectors

AtomCoorFormatOut 〈AtomicCoordinatesFormat〉 (string)

Character string to specify the format of the atomic positions in output.
Same possibilities as for input AtomicCoordinatesFormat.

%block AtomicCoordinatesOrigin 〈None〉 (block)

Vector specifying a rigid shift to apply to the atomic coordinates, given in the same format and
units as these. Notice that the atomic positions (shifted or not) need not be within the cell
formed by LatticeVectors, since periodic boundary conditions are always assumed.
This defaults to the origo:

39
 0.0 0.0 0.0

%block AtomicCoordinatesAndAtomicSpecies 〈None〉 (block)

Block specifying the position and species of each atom. One line per atom, the reading is done
this way:
From ia = 1 to natoms
read: xa(ix,ia), isa(ia)

where xa(ix,ia) is the ix coordinate of atom iai in the format (units) specified by Atomic-
CoordinatesFormat, and isa(ia) is the species index of atom ia.
NOTE: This block must be present in the fdf file. If NumberOfAtoms is not specified,
NumberOfAtoms will be defaulted to the number of atoms in this block.
NOTE: Zmatrix has precedence if specified.

6.4.2 Z-matrix format and constraints

The advantage of the traditional format is that it is much easier to set up a system. However, when
working on systems with constraints, there are only a limited number of (very simple) constraints
that may be expressed within this format, and recompilation is needed for each new constraint.
For any more involved set of constraints, a full Zmatrix formulation should be used - this offers
much more control, and may be specified fully at run time (thus not requiring recompilation) - but
it is more work to generate the input files for this form.

%block Zmatrix 〈None〉 (block)

This block provides a means for inputting the system geometry using a Z-matrix format, as
well as controlling the optimization variables. This is particularly useful when working with
molecular systems or restricted optimizations (such as locating transition states or rigid unit
movements). The format also allows for hybrid use of Z-matrices and Cartesian or fractional
blocks, as is convenient for the study of a molecule on a surface. As is always the case for a Z-
matrix, the responsibility falls to the user to chose a sensible relationship between the variables
to avoid triads of atoms that become linear.
Below is an example of a Z-matrix input for a water molecule:
%block Zmatrix
molecule fractional
1 0 0 0 0.0 0.0 0.0 0 0 0
2 1 0 0 HO1 90.0 37.743919 1 0 0
2 1 2 0 HO2 HOH 90.0 1 1 0
variables
HO1 0.956997
HO2 0.956997
HOH 104.4
%endblock Zmatrix

The sections that can be used within the Zmatrix block are as follows:
Firstly, all atomic positions must be specified within either a “molecule” block or a “cartesian”
block. Any atoms subject to constraints more complicated than “do not change this coordinate
of this atom” must be specified within a “molecule” block.

40
molecule There must be one of these blocks for each independent set of constrained atoms
within the simulation.
This specifies the atoms that make up each molecule and their geometry. In addition, an
option of “fractional” or “scaled” may be passed, which indicates that distances are spec-
ified in scaled or fractional units. In the absence of such an option, the distance units are
taken to be the value of “ZM.UnitsLength”.
A line is needed for each atom in the molecule; the format of each line should be:
Nspecies i j k r a t ifr ifa ift
Here the values Nspecies, i, j, k, ifr, ifa, and ift are integers and r, a, and t are double
precision reals.
For most atoms, Nspecies is the species number of the atom, r is distance to atom number
i, a is the angle made by the present atom with atoms j and i, while t is the torsional
angle made by the present atom with atoms k, j, and i. The values ifr, ifa and ift are
integer flags that indicate whether r, a, and t, respectively, should be varied; 0 for fixed, 1
for varying.
The first three atoms in a molecule are a special case. Because there are insufficient atoms
defined to specify a distance/angle/torsion, the values are set differently. For atom 1, r, a,
and t, are the Cartesian coordinates of the atom. For the second atom, r, a, and t are the
coordinates in spherical form of the second atom relative to the first: first the radius, then the
polar angle (angle between the z-axis and the displacement vector) and then the azimuthal
angle (angle between the x-axis and the projection of the displacement vector on the x-y
plane). Finally, for the third atom, the numbers take their normal form, but the torsional
angle is defined relative to a notional atom 1 unit in the z-direction above the atom j.
Secondly. blocks of atoms all of which are subject to the simplest of constraints may be
specified in one of the following three ways, according to the units used to specify their
coordinates:
cartesian This section specifies a block of atoms whose coordinates are to be specified in Carte-
sian coordinates. Again, an option of “fractional” or “scaled” may be added, to specify
the units used; and again, in their absence, the value of “ZM.UnitsLength” is taken.
The format of each atom in the block will look like:
Nspecies x y z ix iy iz
Here Nspecies, ix, iy, and iz are integers and x, y, z are reals. Nspecies is the species
number of the atom being specified, while x, y, and z are the Cartesian coordinates of the
atom in whichever units are being used. The values ix, iy and iz are integer flags that
indicate whether the x, y, and z coordinates, respectively, should be varied or not. A value of
0 implies that the coordinate is fixed, while 1 implies that it should be varied. NOTE: When
performing “variable cell” optimization while using a Zmatrix format for input, the algorithm
will not work if some of the coordinates of an atom in a cartesian block are variables and
others are not (i.e., ix iy iz above must all be 0 or 1). This will be fixed in future versions
of the program.
A Zmatrix block may also contain the following, additional, sections, which are designed to
make it easier to read.
constants Instead of specifying a numerical value, it is possible to specify a symbol within the
above geometry definitions. This section allows the user to define the value of the symbol as

41
 a constant. The format is just a symbol followed by the value:
HOH 104.4
variables Instead of specifying a numerical value, it is possible to specify a symbol within the
above geometry definitions. This section allows the user to define the value of the symbol as
a variable. The format is just a symbol followed by the value:
HO1 0.956997
Finally, constraints must be specified in a constraints block.
constraint This sub-section allows the user to create constraints between symbols used in a
Z-matrix:
constraint
var1 var2 A B
Here var1 and var2 are text symbols for two quantities in the Z-matrix definition, and AandB
are real numbers. The variables are related by var1 = A ∗ var2 + B.
An example of a Z-matrix input for a benzene molecule over a metal surface is:
%block Zmatrix
molecule
2 0 0 0 xm1 ym1 zm1 0 0 0
2 1 0 0 CC 90.0 60.0 0 0 0
2 2 1 0 CC CCC 90.0 0 0 0
2 3 2 1 CC CCC 0.0 0 0 0
2 4 3 2 CC CCC 0.0 0 0 0
2 5 4 3 CC CCC 0.0 0 0 0
1 1 2 3 CH CCH 180.0 0 0 0
1 2 1 7 CH CCH 0.0 0 0 0
1 3 2 8 CH CCH 0.0 0 0 0
1 4 3 9 CH CCH 0.0 0 0 0
1 5 4 10 CH CCH 0.0 0 0 0
1 6 5 11 CH CCH 0.0 0 0 0
fractional
3 0.000000 0.000000 0.000000 0 0 0
3 0.333333 0.000000 0.000000 0 0 0
3 0.666666 0.000000 0.000000 0 0 0
3 0.000000 0.500000 0.000000 0 0 0
3 0.333333 0.500000 0.000000 0 0 0
3 0.666666 0.500000 0.000000 0 0 0
3 0.166667 0.250000 0.050000 0 0 0
3 0.500000 0.250000 0.050000 0 0 0
3 0.833333 0.250000 0.050000 0 0 0
3 0.166667 0.750000 0.050000 0 0 0
3 0.500000 0.750000 0.050000 0 0 0
3 0.833333 0.750000 0.050000 0 0 0
3 0.000000 0.000000 0.100000 0 0 0
3 0.333333 0.000000 0.100000 0 0 0
3 0.666666 0.000000 0.100000 0 0 0
3 0.000000 0.500000 0.100000 0 0 0
3 0.333333 0.500000 0.100000 0 0 0
3 0.666666 0.500000 0.100000 0 0 0
3 0.166667 0.250000 0.150000 0 0 0

42
 3 0.500000 0.250000 0.150000 0 0 0
3 0.833333 0.250000 0.150000 0 0 0
3 0.166667 0.750000 0.150000 0 0 0
3 0.500000 0.750000 0.150000 0 0 0
3 0.833333 0.750000 0.150000 0 0 0
constants
ym1 3.68
variables
zm1 6.9032294
CC 1.417
CH 1.112
CCH 120.0
CCC 120.0
constraints
xm1 CC -1.0 3.903229
%endblock Zmatrix
Here the species 1, 2 and 3 represent H, C, and the metal of the surface, respectively.
(Note: the above example shows the usefulness of symbolic names for the relevant coordinates,
in particular for those which are allowed to vary. The current output options for Zmatrix
information work best when this approach is taken. By using a “fixed” symbolic Zmatrix block
and specifying the actual coordinates in a “variables” section, one can monitor the progress
of the optimization and easily reconstruct the coordinates of intermediate steps in the original
format.)

ZM.UnitsLength Bohr (string)

Parameter that specifies the units of length used during Z-matrix input.
Specify Bohr or Ang for the corresponding unit of length.

ZM.UnitsAngle rad (string)

Parameter that specifies the units of angles used during Z-matrix input.
Specify rad or deg for the corresponding unit of angle.

6.4.3 Output of structural information

SIESTA is able to generate several kinds of files containing structural information (maybe too
many).

• SystemLabel.STRUCT_OUT:Siesta always produces a .STRUCT_OUT file with cell vectors in Å

and atomic positions in fractional coordinates. This file, renamed to .STRUCT_IN can be used
for crystal-structure input. Note that the geometry reported is the last one for which forces
and stresses were computed. See UseStructFile

• SystemLabel.STRUCT_NEXT_ITER:This file is always written, in the same format as

.STRUCT_OUT file. The only difference is that it contains the structural information after
it has been updated by the relaxation or the molecular-dynamics algorithms, and thus it could
be used as input (renamed as .STRUCT_IN) for a continuation run, in the same way as the .XV
file.
See UseStructFile

43
• SystemLabel.XV:The coordinates are always written in the .XV file, and overriden at every
step.

• OUT.UCELL.ZMATRIX:This file is produced if the Zmatrix format is being used for input. (Please
note that SystemLabel is not used as a prefix.) It contains the structural information in fdf
form, with blocks for unit-cell vectors and for Zmatrix coordinates. The Zmatrix block is in a
“canonical” form with the following characteristics:

1. No symbolic variables or constants are used.

2. The position coordinates of the first atom in each molecule
are absolute Cartesian coordinates.
3. Any coordinates in ‘‘cartesian’’ blocks are also absolute Cartesians.
4. There is no provision for output of constraints.
5. The units used are those initially specified by the user, and are
noted also in fdf form.

Note that the geometry reported is the last one for which forces and stresses were computed.

• NEXT_ITER.UCELL.ZMATRIX:A file with the same format as OUT.UCELL.ZMATRIX but with a

possibly updated geometry.

• The coordinates can be also accumulated in the SystemLabel.MD or SystemLabel.MDX files

depending on WriteMDHistory.

• Additionally, several optional formats are supported:

WriteCoorXmol false (logical)

If true it originates the writing of an extra file named SystemLabel.xyz containing the
final atomic coordinates in a format directly readable by XMol.4 Coordinates come
out in Ångström independently of what specified in AtomicCoordinatesFormat and
in AtomCoorFormatOut. There is a present Java implementation of XMol called
JMol.

WriteCoorCerius false (logical)

If trueit originates the writing of an extra file named SystemLabel.xtl containing the
final atomic coordinates in a format directly readable by Cerius.5 Coordinates come out
in Fractional format (the same as ScaledByLatticeVectors) independently of what
specified in AtomicCoordinatesFormat and in AtomCoorFormatOut. If negative
coordinates are to be avoided, it has to be done from the start by shifting all the co-
ordinates rigidly to have them positive, by using AtomicCoordinatesOrigin. See the
Sies2arc utility in the Util/ directory for generating ..arc files for CERIUS animation.

WriteMDXmol false (logical)

If true it causes the writing of an extra file named SystemLabel.ANI containing all
the atomic coordinates of the simulation in a format directly readable by XMol for
animation. Coordinates come out in Ångström independently of what is specified in
4
XMol is under © copyright of Research Equipment Inc., dba Minnesota Supercomputer Center Inc.
5
Cerius is under © copyright of Molecular Simulations Inc.

44
 AtomicCoordinatesFormat and in AtomCoorFormatOut. This file is accumulative
even for different runs.
There is an alternative for animation by generating a .arc file for CERIUS. It is through
the Sies2arc postprocessing utility in the Util/ directory, and it requires the coordinates
to be accumulated in the output file, i.e., WriteCoorStep true.

6.4.4 Input of structural information from external files

The structural information can be also read from external files. Note that ChemicalSpeciesLabel
is mandatory in the fdf file.

MD.UseSaveXV false (logical)

Logical variable which instructs SIESTA to read the atomic positions and velocities stored in
file SystemLabel.XV by a previous run.
If the file does not exist, a warning is printed but the program does not stop. Overrides
UseSaveData, but can be implicitly set by it.

UseStructFile false (logical)

Controls whether the structural information is read from an external file of name
SystemLabel.STRUCT_IN. If true, all other structural information in the fdf file will be ig-
nored.
The format of the file is implied by the following code:
read(*,*) ((cell(ixyz,ivec),ixyz=1,3),ivec=1,3) ! Cell vectors, in Angstroms
read(*,*) na
do ia = 1,na
read(iu,*) isa(ia), dummy, xfrac(1:3,ia) ! Species number
! Dummy numerical column
! Fractional coordinates
enddo
Warning: Note that the resulting geometry could be clobbered if an .XV file is read after this
file. It is up to the user to remove any .XV files.

MD.UseSaveZM false (logical)

Instructs to read the Zmatrix information stored in file .ZM by a previous run.
If the required file does not exist, a warning is printed but the program does not stop. Overrides
UseSaveData, but can be implicitly set by it.
Warning: Note that the resulting geometry could be clobbered if an .XV file is read after this
file. It is up to the user to remove any .XV files.

6.4.5 Input from a FIFO file

See the “Forces” option in MD.TypeOfRun. Note that ChemicalSpeciesLabel is still mandatory
in the fdf file.

45
6.4.6 Precedence issues in structural input

• If the “Forces” option is active, it takes precedence over everything (it will overwrite all other
input with the information it gets from the FIFO file).

• If MD.UseSaveXV is active, it takes precedence over the options below.

• If UseStructFile (or MD.UseStructFile) is active, it takes precedence over the options

below.

• For atomic coordinates, the traditional and Zmatrix formats in the fdf file are mutually exclu-
sive. If MD.UseSaveZM is active, the contents of the ZM file, if found, take precedence over
the Zmatrix information in the fdf file.

6.4.7 Interatomic distances

WarningMinimumAtomicDistance 1 Bohr (length)
Fixes a threshold interatomic distance below which a warning message is printed.

MaxBondDistance 6 Bohr (length)

SIESTA prints the interatomic distances, up to a range of MaxBondDistance,
to file SystemLabel.BONDS upon first reading the structural information, and to file
SystemLabel.BONDS_FINAL after the last geometry iteration. The reference atoms are all the
atoms in the unit cell. The routine now prints the real location of the neighbor atoms in space,
and not, as in earlier versions, the location of the equivalent representative in the unit cell.

6.5 k-point sampling

These are options for the k-point grid used in the SCF cycle. For other specialized grids, see the
Macroscopic Polarization and Density of States sections.

kgrid.Cutoff 0. Bohr (length)

Parameter which determines the fineness of the k-grid used for Brillouin zone sampling. It is half
the length of the smallest lattice vector of the supercell required to obtain the same sampling
precision with a single k point. Ref: Moreno and Soler, PRB 45, 13891 (1992).
Use: If it is zero, only the gamma point is used. The resulting k-grid is chosen in an optimal way,
according to the method of Moreno and Soler (using an effective supercell which is as spherical as
possible, thus minimizing the number of k-points for a given precision). The grid is displaced for
even numbers of effective mesh divisions. This parameter is not used if kgrid.MonkhorstPack
is specified. If the unit cell changes during the calculation (for example, in a cell-optimization
run, the k-point grid will change accordingly (see ChangeKgridInMD for the case of variable-
cell molecular-dynamics runs, such as Parrinello-Rahman). This is analogous to the changes in
the real-space grid, whose fineness is specified by an energy cutoff. If sudden changes in the
number of k-points are not desired, then the Monkhorst-Pack data block should be used instead.
In this case there will be an implicit change in the quality of the sampling as the cell changes.
Both methods should be equivalent for a well-converged sampling.

%block kgrid.MonkhorstPack Γ-point (block)

46
 Real-space supercell, whose reciprocal unit cell is that of the k-sampling grid, and grid displace-
ment for each grid coordinate. Specified as an integer matrix and a real vector:
%block kgrid.MonkhorstPack
Mk(1,1) Mk(2,1) Mk(3,1) dk(1)
Mk(1,2) Mk(2,2) Mk(3,2) dk(2)
Mk(1,3) Mk(2,3) Mk(3,3) dk(3)
%endblock

where Mk(j,i) are integers and dk(i) are usually either 0.0 or 0.5 (the program will warn the
user if the displacements chosen are not optimal). The k-grid supercell is defined from Mk as in
block SuperCell above, i.e.: KgridSuperCell(ix, i) = j CELL(ix, j) ∗ M k(j, i). Note again
P

that the matrix indexes are inverted: each input line gives the decomposition of a supercell
vector in terms of the unit cell vectors.
Use: Used only if SolutionMethod diagon. The k-grid supercell is compatible and unrelated
(except for the default value, see below) with the SuperCell specifier. Both supercells are
given in terms of the CELL specified by the LatticeVectors block. If Mk is the identity matrix
and dk is zero, only the Γ point of the unit cell is used. Overrides kgrid.Cutoff

ChangeKgridInMD false (logical)

If true, the k-point grid is recomputed at every iteration during MD runs that potentially
change the unit cell: Parrinello-Rahman, Nose-Parrinello-Rahman, and Anneal. Regardless of
the setting of this flag, the k-point grid is always updated at every iteration of a variable-cell
optimization and after each step in a “siesta-as-server” run.
It is defaulted to false for historical reasons. The rationale was to avoid sudden jumps in some
properties when the sampling changes, but if the calculation is well-converged there should be
no problems if the update is enabled.

TimeReversalSymmetryForKpoints true (logical)

If true, the k-points in the BZ generated by the methods above are paired as (k,-k) and only
one member of the pair is retained. This symmetry is valid in the absence of external magnetic
fields or non-collinear/spin-orbit interaction.
This flag should be used with care, as the code will produce wrong results if there is no support
for the appropriate symmetrization.
The default value is trueunless: a) the option Spin.Spiral is used. In this case time-reversal-
symmetry is broken explicitly. b) non-collinear spin calculations. This case is less clear cut, but
the time-reversal symmetry is not used to avoid possible breakings due to subtle implementation
details, and to make the set of wavefunctions compatible with spin-orbit case in analysis tools.

6.5.1 Output of k-point information

The coordinates of the ~k points used in the sampling are always stored in the file SystemLabel.KP.

WriteKpoints false (logical)

If true it writes the coordinates of the ~k vectors used in the grid for k-sampling, into the main
output file.
Default depends on LongOutput.

47
6.6 Exchange-correlation functionals
XC.Functional LDA (string)
Exchange-correlation functional type. May be LDA (local density approximation, equivalent
to LSD), GGA (Generalized Gradient Approximation), or VDW (van der Waals).

XC.Authors PZ (string)
Particular parametrization of the exchange-correlation functional. Options are:
• CA (equivalent to PZ): (Spin) local density approximation (LDA/LSD). Quantum Monte
Carlo calculation of the homogeneous electron gas by D. M. Ceperley and B. J. Alder, Phys.
Rev. Lett. 45,566 (1980), as parametrized by J. P. Perdew and A. Zunger, Phys. Rev B
23, 5075 (1981)
• PW92: LDA/LSD, as parametrized by J. P. Perdew and Y. Wang, Phys. Rev B, 45,
13244 (1992)
• PW91: Generalized gradients approximation (GGA) of Perdew and Wang. Ref: P&W,
J. Chem. Phys., 100, 1290 (1994)
• PBE: GGA of J. P. Perdew, K. Burke and M. Ernzerhof, Phys. Rev. Lett. 77, 3865
(1996)
• revPBE: Modified GGA-PBE functional of Y. Zhang and W. Yang, Phys. Rev. Lett. 80,
890 (1998)
• RPBE: Modified GGA-PBE functional of B. Hammer, L. B. Hansen and J. K. Norskov
Phys. Rev. B 59, 7413 (1999)
• WC: Modified GGA-PBE functional of Z. Wu and R. E. Cohen, Phys. Rev. B 73, 235116
(2006)
• AM05: Modified GGA-PBE functional of R. Armiento and A. E. Mattsson, Phys. Rev.
B 72, 085108 (2005)
• PBEsol: Modified GGA-PBE functional of J. P. Perdew et al, Phys. Rev. Lett. 100,
136406 (2008)
• PBEJsJrLO: GGA-PBE functional with parameters β, µ, and κ fixed by the jellium
surface (Js), jellium response (Jr), and Lieb-Oxford bound (LO) criteria, respectively, as
described by L. S. Pedroza, A. J. R. da Silva, and K. Capelle, Phys. Rev. B 79, 201106(R)
(2009), and by M. M. Odashima, K. Capelle, and S. B. Trickey, J. Chem. Theory Comput.
5, 798 (2009)
• PBEJsJrHEG: Same as PBEJsJrLO, with parameter κ fixed by the Lieb-Oxford bound
for the low density limit of the homogeneous electron gas (HEG)
• PBEGcGxLO: Same as PBEJsJrLO, with parameters β and µ fixed by the gradient
expansion of correlation (Gc) and exchange (Gx), respectively
• PBEGcGxHEG: Same as previous ones, with parameters β, µ, and κ fixed by the Gc,
Gx, and HEG criteria, respectively.
• BLYP (equivalent to LYP): GGA with Becke exchange (A. D. Becke, Phys. Rev. A 38,
3098 (1988)) and Lee-Yang-Parr correlation (C. Lee, W. Yang, R. G. Parr, Phys. Rev.
B 37, 785 (1988)), as modified by B. Miehlich, A. Savin, H. Stoll, and H. Preuss, Chem.
Phys. Lett. 157, 200 (1989). See also B. G. Johnson, P. M. W. Gill and J. A. Pople, J.
Chem. Phys. 98, 5612 (1993). (Some errors were detected in this last paper, so not all of
their expressions correspond exactly to those implemented in SIESTA)

48
 • DRSLL (equivalent to DF1): van der Waals density functional (vdW-DF) of M. Dion, H.
Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401
(2004), with the efficient implementation of G. Román-Pérez and J. M. Soler, Phys. Rev.
Lett. 103, 096102 (2009)
• LMKLL (equivalent to DF2): vdW-DF functional of Dion et al (same as DRSLL)
reparametrized by K. Lee, E. Murray, L. Kong, B. I. Lundqvist and D. C. Langreth,
Phys. Rev. B 82, 081101 (2010)
• KBM: vdW-DF functional of Dion et al (same as DRSLL) with exchange modified by J.
Klimes, D. R. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 022201 (2010)
(optB88-vdW version)
• C09: vdW-DF functional of Dion et al (same as DRSLL) with exchange modified by V.
R. Cooper, Phys. Rev. B 81, 161104 (2010)
• BH: vdW-DF functional of Dion et al (same as DRSLL) with exchange modified by K.
Berland and P. Hyldgaard, Phys. Rev. B 89, 035412 (2014)
• VV: vdW-DF functional of O. A. Vydrov and T. Van Voorhis, J. Chem. Phys. 133,
244103 (2010)

%block XC.Hybrid 〈None〉 (block)

This data block allows the user to create a “cocktail” functional by mixing the desired amounts
of exchange and correlation from each of the functionals described under XC.authors. Note that
these “mixed” functionals do not have the exact Hartree-Fock exchange which is a key ingredient
of the true “hybrid” functionals. The use of the word “hybrid” in the label is unfortunate in
this regard, and might be deprecated in a future version.
The first line of the block must contain the number of functionals to be mixed. On the subse-
quent lines the values of XC.functl and XC.authors must be given and then the weights for the
exchange and correlation, in that order. If only one number is given then the same weight is
applied to both exchange and correlation.
The following is an example in which a 75:25 mixture of Ceperley-Alder and PBE correlation
is made, with an equal split of the exchange energy:
%block XC.hybrid
2
LDA CA 0.5 0.75
GGA PBE 0.5 0.25
%endblock XC.hybrid

6.7 Spin polarization

Spin non-polarized (string)
Choose the spin-components in the simulation.
NOTE: This flag has precedence over SpinOrbit, NonCollinearSpin and SpinPolarized
while these deprecated flags may still be used.
non-polarized Perform a calculation with spin-degeneracy (only one component).
polarized Perform a calculation with colinear spin (two spin components).

49
 non-colinear Perform a calculation with non-colinear spin (4 spin components), up-down and
angles.
Refs: T. Oda et al, PRL, 80, 3622 (1998); V. M. García-Suárez et al, Eur. Phys. Jour. B
40, 371 (2004); V. M. García-Suárez et al, Journal of Phys: Cond. Matt 16, 5453 (2004).
spin-orbit Perform a calculation with spin-orbit coupling. This requires the pseudopotentials
to be relativistic.
See Sect. 6.8.
SIESTA can read a .DM with different spin structure by adapting the information to the cur-
rently selected spin multiplicity, averaging or splitting the spin components equally, as needed.
This may be used to greatly increase convergence.
Certain options may not be used together with specific parallelization routines. For instance
only a spin-polarized calculation may use the Diag.ParallelOverK option.

Spin.Fix false (logical)

If true, the calculation is done with a fixed value of the spin of the system, defined by variable
Spin.Total. This option can only be used for colinear spin polarized calculations.

Spin.Total 0 (real)
Value of the imposed total spin polarization of the system (in units of the electron spin, 1/2).
It is only used if Spin.Fix true.

SingleExcitation false (logical)

If true, SIESTA calculates a very rough approximation to the lowest excited state by swapping
the populations of the HOMO and the LUMO. If there is no spin polarisation, it is half swap
only. It is done for the first spin component (up) and first k vector.

6.8 Spin–Orbit coupling

SIESTA includes the posibility to perform fully relativistic calculations by means of the inclusion
in the total Hamiltonian not only the Darwin and velocity correction terms (Scalar–Relativistic
calculations), but also the spin-orbit (SO) contribution. The implementation is based on the on-site
SO approximation, where only the intra-SO contribution of each atom is taken into account. See
Spin on how to turn on the spin-orbit coupling.
The current implementation in SIESTA has been implemented by Dr. Ramón Cuadrado based on
the original on-site SO formalism and implementation developed by Prof. Jaime Ferrer, et al (L
Fernández–Seivane, M Oliveira, S Sanvito, and J Ferrer, Journal of Physics: Condensed Matter,
2006 vol. 18 pp. 7999; L Fernández–Seivane and Jaime Ferrer, Phys. Rev. Lett. 99, 2007, 183401).
The inclusion of the SO term in the Hamiltonian (and in the Density Matrix) will involve the
0 σσ 0
increase of non-zero elements in their off-diagonal parts, i.e., for some µν orbitals, Hσσ µν (DMµν )
[σ, σ 0 =↑, ↓] will be 6=0. This is mainly due to the fact that the L · S operator will promote the mixing
between different spin-up/down components. The terms responsible of this matrices expansion are
the exchange-correlation potential and the SO. The remaining terms such as the kinetic energy or
Hartree contribution do not depend of the spin orientations and hence will be only added to the
total Hamiltonian (and DM) to their diagonal parts.
The current SO formalism enables the possibility of several types of calculations:

50
 • Selfconsistent calculations for gamma point as well as for bulks (Not yet implemented for
optimizations).

• Magnetic Anisotropy Energy (MAE) can be easily calculated. From first principles calcula-
tions, MAE is obtained after subtract the total selfconsistent energy in two different orienta-
tions, usually the total energy associated with easy axis from the hard axis. In SIESTA it is
possible to perform several self-consistent calculations for different magnetization orientations
using the specific block DM.InitSpin in the fdf file. In doing so one will be able to include
the initial orientation angles of the magnetization for each atom, as well as an initial value of
their net magnetic moments.

• By means of Mulliken analysis, after the self-consistent procedure, local spin and orbital mo-
ments can be calculated by means of the flags WriteMullikenPop and WriteOrbMom.

Note: Due to the small SO energy value contribution to the total energy, the level of precision
requiered to perform a proper fully relativistic calculation during the selfconsistent process is quite
demanding. The following values must be carefully converged and checked for each specific system to
assure that the results are accurate enough: SCF.H.Tolerance during the selfconsistency (typically
<10−5 eV), ElectronicTemperature, k-point sampling and high values of MeshCutoff (specifi-
cally for extended solids). In general, one can say that a good calculation will have high number
of k–points, low ElectronicTemperature, extremely small SCF.H.Tolerance and high values of
MeshCutoff . We encourage the user to test carefully these options for each system. An addi-
tional point to take into account when the spin–orbit contribution is included is the mixing scheme
employed. You are encouraged to use SCF.Mix hamiltonian instead of the density matrix, due
to the fact that the convergence speed increases considerably for the first case. In addition, the
pseudopotentials have to be well generated and tested for each specific system and they have to be
generated in their fully relativistic form and use the non-linear core corrections.

Spin.OrbitStrength 1.0 (real)

It allows to vary the strength of the spin-orbit interaction from zero to any positive value,
including the physical value. This flag is only active when Spin is set to spin-orbit.

WriteOrbMom false (logical)

If true, a table is provided in the main output file, which includes an estimation of the vector
orbital magnetic moments, in units of the Bohr magneton, projected onto each orbital and also
onto each atom. The estimation for the orbital moments is based on a two-center approximation,
and makes use of the Mulliken population analysis.
If MullikenInScf is true, this information is printed at every scf step.

6.9 The self-consistent-field loop

IMPORTANT NOTE: Convergence of the Kohn-Sham energy and forces

In versions prior to 4.0 of the program, the Kohn-Sham energy was computed using the “in” DM.
The typical DM used as input for the calculation of H was not directly computed from a set of
wave-functions (it was either the product of mixing or of the initialization from atomic values). In
this case, the “kinetic energy” term in the total energy computed in the way stated in the Siesta
paper had an error which decreased with the approach to self-consistency, but was non-zero. The

51
net result was that the Kohn-Sham energy converged more slowly than the “Harris” energy (which
is correctly computed).
When mixing H (see below under “Mixing Options”), the KS energy is in effect computed from
DM(out), so this error vanishes.
As a related issue, the forces and stress computed after SCF convergence were calculated using the
DM coming out of the cycle, which by default was the product of a final mixing. This also introduced
errors which grew with the degree of non-selfconsistency.
The current version introduces several changes:

• When mixing the DM, the Kohn-Sham energy may be corrected to make it variational. This
involves an extra call to dhscf (although with neither forces nor matrix elements being cal-
culated, i.e. only calls to rhoofd, poison, and cellxc), and is turned on by the option
SCF.Want.Variational.EKS.

• The program now prints a new column labeled “dHmax” for the self-consistent cycle. The
value represents the maximum absolute value of the changes in the entries of H, but its actual
meaning depends on whether DM or H mixing is in effect: if mixing the DM, dHmax refers to
the change in H(in) with respect to the previous step; if mixing H, dHmax refers to H(out)-
H(in) in the previous(?) step.

• When achieving convergence, the loop might be exited without a further mixing of the DM,
thus preserving DM(out) for further processing (including the calculation of forces and the
analysis of the electronic structure) (see the SCF.Mix.AfterConvergence option).

• It remains to be seen whether the forces, being computed “right” on the basis of DM(out),
exhibit somehow better convergence as a function of the scf step. In order to gain some
more data and heuristics on this we have implemented a force-monitoring option, activated by
setting to true the variable SCF.MonitorForces. The program will then print the maximum
absolute value of the change in forces from one step to the next. Other statistics could be
implemented.

• While the (mixed) DM is saved at every SCF step, as was standard practice, the final DM(out)
overwrites the .DM file at the end of the SCF cycle. Thus it is still possible to use a “mixed” DM
for restarting an interrupted loop, but a “good” DM will be used for any other post-processing.

MinSCFIterations 0 (integer)
Minimum number of SCF iterations per time step. In MD simulations this can with benefit be
set to 3.

MaxSCFIterations 1000 (integer)

Maximum number of SCF iterations per time step.

SCF.MustConverge true (logical)

Defines the behaviour if convergence is not reached in the maximum number of SCF iterations.
The default is to stop on the first SCF convergence failure. Increasing MaxSCFIterations to
a large number may be advantageous when this is true.

52
6.9.1 Harris functional
Harris.Functional false (logical)
Logical variable to choose between self-consistent Kohn-Sham functional or non self-consistent
Harris functional to calculate energies and forces.
• false: Fully self-consistent Kohn-Sham functional.
• true: Non self consistent Harris functional. Cheap but pretty crude for some systems. The
forces are computed within the Harris functional in the first SCF step. Only implemented
for LDA in the Perdew-Zunger parametrization. It really only applies to starting densities
which are superpositions of atomic charge densities.
When this option is choosen, the values of DM.UseSaveDM, SCF.MustConverge and
SCF.Mix.First are automatically set falseand MaxSCFIterations is set to 1, no matter
whatever other specification are in the INPUT file.

6.9.2 Mixing options

Whether a calculation reaches self-consistency in a moderate number of steps depends strongly on

the mixing parameters used. The available mixing options should be carefully tested for a given
calculation type. This search for optimal parameters can repay itself handsomely by potentially
saving many self-consistency steps in production runs.

SCF.Mix Hamiltonian|density|charge (string)

Control what physical quantity to mix in the self-consistent cycle.
The default is mixing the Hamiltonian, which may typically perform better than density matrix
mixing.
Hamiltonian Mix the Hamiltonian matrix (default).
density Mix the density matrix.
charge Mix the real-space charge density. Note this is an experimental feature.
NOTE: Real-space charge density does not follow the regular options that adhere to density-
matrix or Hamiltonian mixing. Also it is not recommended to use real-space charge density
mixing with TranSIESTA.

SCF.Mix.Spin all|spinor|sum|sum+diff (string)

Controls how the mixing is performed when carrying out spin-polarized calculations.
all Use all spin-components in the mixing
spinor Estimate mixing coefficients using the spinor components
sum Estimate mixing coefficients using the sum of the spinor components
sum+diff Estimate mixing coefficients using the sum and the difference between the spinor
components
NOTE: This option only influences density-matrix (ρ) or Hamiltonian (H) mixing when using
anything but the linear mixing scheme. And it does not influence not charge (ρ) mixing.

SCF.Mix.First true (logical)

53
 Whether the first SCF should be mixed or it uses the output as input in the next SCF step. It
is generally advised to set this to true, at least when restarting calculations.

In the following the density matrix (ρ) will be used in the equations, while for Hamiltonian mixing,
ρ, should be replaced by the Hamiltonian matrix. Also we define R[i] = ρiout − ρiin and ∆R[i] =
R[i] − R[i − 1].

SCF.Mixer.Method Pulay|Broyden|Linear (string)

Choose the mixing algorithm between different methods. Each method may have different
variants, see SCF.Mixer.Variant.
Linear A simple linear extrapolation of the input matrix as

ρn+1
in = ρnin + w R[n]. (3)

Pulay Using the Pulay mixing method corresponds using the Kresse and Furthmüller [5] variant.
It relies on the previous N steps and uses those for estimating an optimal input ρn+1
in for the
following iteration. The equation can be written as
N −1
ρn+1
X
in = ρnin + G R[n] + αi (R[i] + G ∆R[i]), (4)
i=n−N +1

where G is the damping factor of the Pulay mixing (also known as the mixing weight). The
values αi are calculated using this formula
N −1
A−1
X
αi = − ji h∆R[j]| R[N ]i, (5)
j=1

with Aji = h∆R[j]| ∆R[i]i.

In SIESTA G is a constant, and not a matrix.
NOTE: Pulay mixing is a special case of Broyden mixing, see the Broyden method.
Broyden The Broyden mixing is mixing method relying on the previous N steps in the history
for calculating an optimum input ρn+1
in for the following iteration. The equation can be
written as
N −1 N −1
ρn+1
X X
in = ρnin + G R[n] − wi wj cj βij (R[i] + G ∆R[i]), (6)
i=n−N +1 j=n−N +1

where G is the damping factor (also known as the mixing weight). The values weights may
be expressed by
wi = 1 , for i > 0 (7)
ci = h∆R[i]| R[n]i, (8)
h
−1 i
βij = w02 I + A (9)
ij
Aij = wi wj h∆R[i]| ∆R[j]i. (10)
It should be noted that wi for i > 0 may be chosen arbitrarily. Comparing with the Pulay
mixing scheme it is obvious that Broyden and Pulay are equivalent for a suitable set of
parameters.

54
SCF.Mixer.Variant original (string)
Choose the variant of the mixing method.
Pulay This is implemented in two variants:
original|kresse The original6 Pulay mixing scheme, as implemented in Kresse and Furth-
müller [5] .
GR The “guaranteed-reduction” variant of Pulay [3] . This variant has a special convergence
path. It interchanges between linear and Pulay mixing thus using the exact gradient at
each ρnin . For relatively simple systems this may be advantageous to use. However, for
complex systems it may be worse until it reaches a convergence basin.
To obtain the
original guaranteed-reduction variant one should set SCF.Mixer.<>.weight.linear to
1.

SCF.Mixer.Weight 0.25 (real)

The mixing weight used to mix the quantity. In the linear mixing case this refers to

ρn+1
in = ρnin + w R[n]. (11)

For details regarding the other methods please see SCF.Mixer.Method.

SCF.Mixer.History 2 (integer)
Number of previous SCF steps used in estimating the following input. Increasing this number,
typically, increases stability and a number of around 6 or above may be advised.

SCF.Mixer.Kick 0 (integer)
After every N SCF steps a linear mix is inserted to kick the SCF cycle out of a possible local
minimum.
The mixing weight for this linear kick is determined by SCF.Mixer.Kick.Weight.

SCF.Mixer.Kick.Weight 〈SCF.Mixer.Weight〉 (real)

The mixing weight for the linear kick (if used).

SCF.Mixer.Restart 0 (integer)
When using advanced mixers (Pulay/Broyden) the mixing scheme may periodically restart the
history. This may greatly improve the convergence path as local constraints in the minimiza-
tion process are periodically removed. This method has similarity to the method proposed in
Banerjee et al. [2] and is a special case of the SCF.Mixer.Kick method.
Please see SCF.Mixer.Restart.Save which is advised to be set simultaneously.

SCF.Mixer.Restart.Save 1 (integer)
When restarting the history of saved SCF steps one may choose to save a subset of the latest
history steps. When using SCF.Mixer.Restart it is encouraged to also save a couple of
previous history steps.

SCF.Mixer.Linear.After -1 (integer)
6
As such the “original” version is a variant it-self. But this is more stable in the far majority of cases.

55
 After reaching convergence one may run additional SCF cycles using a linear mixing scheme. If
this has a value ≥ 0 SIESTA will perform linear mixing after it has converged using the regular
mixing method (SCF.Mixer.Method).
The mixing weight for this linear mixing is controlled by SCF.Mixer.Linear.After.Weight.

SCF.Mixer.Linear.After.Weight 〈SCF.Mixer.Weight〉 (real)

After reaching convergence one may run additional SCF cycles using a linear mixing scheme. If
this has a value ≥ 0 SIESTA will perform linear mixing after it has converged using the regular
mixing method (SCF.Mixer.Method).
The mixing weight for this linear mixing is controlled by SCF.Mixer.Linear.After.Weight.

In conjunction with the above simple settings controlling the SCF cycle SIESTA employs a very
configurable mixing scheme. In essence one may switch mixing methods, arbitrarily, during the SCF
cycle via control commands. This can greatly speed up convergence.

%block SCF.Mixers 〈None〉 (block)

Each line in this block defines a separate mixer that is defined in a subsequent SCF.Mixer.<>
block.
The first line is the initial mixer used.
See the following options for controlling individual mixing methods.
NOTE: If this block is defined you must define all mixing parameters individually.

%block SCF.Mixer.<> 〈None〉 (block)

This block controls the mixer named <>.
method Define the method for the mixer, see SCF.Mixer.Method for possible values.
variant Define the variant of the method, see SCF.Mixer.Variant for possible values.
weight|w Define the mixing weight for the mixing scheme, see SCF.Mixer.Weight.
history Define number of previous history steps used in the minimization process, see
SCF.Mixer.History.
weight.linear|w.linear Define the linear mixing weight for the mixing scheme. This only has
meaning for Pulay or Broyden mixing. It defines the initial linear mixing weight.
To obtain the original Pulay Guarenteed-Reduction variant one should set this to 1.
restart Define the periodic restart of the saved history, see SCF.Mixer.Restart.
restart.save Define number of latest history steps retained when restarting the history, see
SCF.Mixer.Restart.Save.
iterations Define the maximum number of iterations this mixer should run before changing to
another mixing method.
NOTE: This must be used in conjunction with the next setting.
next <> Specify the name of the next mixing scheme after having conducted iterations SCF
cycles using this mixing method.
next.conv <> If SCF convergence is reached using this mixer, switch to the mixing scheme
via <>. Then proceed with the SCF cycle.

56
 next.p If the relative difference between the latest two residuals is below this quantity, the mixer
will switch to the method given in next. Thus if

hR[i]| R[i]i − hR[i − 1]| R[i − 1]i

< next.p (12)
hR[i − 1]| R[i − 1]i

is fulfilled it will skip to the next mixer.

restart.p If the relative difference between the latest two residuals is below this quantity, the
mixer will restart the history. Thus if

hR[i]| R[i]i − hR[i − 1]| R[i − 1]i

< restart.p (13)
hR[i − 1]| R[i − 1]i

is fulfilled it will reset the history.

The options covered now may be exemplified in these examples. If the input file contains:

SCF.Mixer.Method pulay
SCF.Mixer.Weight 0.05
SCF.Mixer.History 10
SCF.Mixer.Restart 25
SCF.Mixer.Restart.Save 4
SCF.Mixer.Linear.After 0
SCF.Mixer.Linear.After.Weight 0.1

This may be equivalently setup using the more advanced input blocks:

%block SCF.Mixers
init
final
%endblock

%block SCF.Mixer.init
method pulay
weight 0.05
history 10
restart 25
restart.save 4
next.conv final
%endblock

%block SCF.Mixer.final
method linear
weight 0.1
%endblock

This advanced setup may be used to change mixers during the SCF to change certain parameters
of the mixing method, or fully change the method for mixing. For instance it may be advantageous
to increase the mixing weight once a certain degree of self-consistency has been reached. In the
following example we change the mixing method to a different scheme by increasing the weight and
decreasing the history steps:

57
 %block SCF.Mixers
init
final
%endblock

%block SCF.Mixer.init
method pulay
weight 0.05
history 10
next final
# Switch when the relative residual goes below 5%
next.p 0.05
%endblock

%block SCF.Mixer.final
method pulay
weight 0.1
history 6
%endblock

In essence, very complicated schemes of convergence may be created using the block’s input.
The following options refer to the global treatment of how/when mixing should be performed.

Compat.Pre-v4-DM-H false (logical)

This
controls the default values of SCF.Mix.AfterConvergence, SCF.RecomputeHAfterScf
and SCF.Mix.First.
In versions prior to v4 the two former options where defaulted to true while the latter option
was defaulted to false.

SCF.Mix.AfterConvergence false (logical)

Indicate whether mixing is done in the last SCF cycle (after convergence has been achieved) or
not. Not mixing after convergence improves the quality of the final Kohn-Sham energy and of
the forces when mixing the DM.
NOTE: See Compat.Pre-v4-DM-H.

SCF.RecomputeHAfterSCF false (logical)

Indicate whether the Hamiltonian is updated after the scf cycle, while computing the final
energy, forces, and stresses. Not recomputing H makes further analysis tasks (such as the
computation of band structures) more consistent, as they will be able to use the same H used
to generate the last density matrix.
NOTE: See Compat.Pre-v4-DM-H.

6.9.3 Mixing of the Charge Density

See SCF.Mix on how to enable charge density mixing. If charge density mixing is enabled the
fourier components of the charge density are mixed, as done in some plane-wave codes. (See for
example Kresse and Furthmüller, Comp. Mat. Sci. 6, 15-50 (1996), KF in what follows.)

58
The charge mixing is implemented roughly as follows:

• The charge density computed in dhscf is fourier-transformed and stored in a new module. This
is done both for “ρ(G)(in)” and “ρ(G)(out)” (the “out” charge is computed during the extra
call to dhscf for correction of the variational character of the Kohn-Sham energy)

• The “in” and “out” charges are mixed (see below), and the resulting “in” fourier components
are used by dhscf in successive iterations to reconstruct the charge density.

• The new arrays needed and the processing of most new options is done in the new module
m_rhog.F90. The fourier-transforms are carried out by code in rhofft.F.

• Following standard practice, two options for mixing are offered:

– A simple Kerker mixing, with an optional Thomas-Fermi wavevector to damp the contri-
butions for small G’s. The overall mixing weight is the same as for other kinds of mixing,
read from DM.MixingWeight.
– A DIIS (Pulay) procedure that takes into account a sub-set of the G vectors (those within
a smaller cutoff). Optionally, the scalar product used for the construction of the DIIS
matrix from the residuals uses a weight factor.
The DIIS extrapolation is followed by a Kerker mixing step.
The code is m_diis.F90. The DIIS history is kept in a circular stack, implemented using
the new framework for reference-counted types. This might be overkill for this particular
use, and there are a few rough edges, but it works well.

The default convergence criteria remains based on the differences in the density matrix, but in this
case the differences are from step to step, not the more fundamental DM_out-DM_in. Perhaps some
other criterion should be made the default (max |∆rho(G)|, convergence of the free-energy...)
Note that with charge mixing the Harris energy as it is currently computed in Siesta loses its meaning,
since there is no DM_in. The program prints zeroes in the Harris energy field.
Note that the KS energy is correctly computed throughout the scf cycle, as there is an extra step for
the calculation of the charge stemming from DM_out, which also updates the energies. Forces and
final energies are correctly computed with the final DM_out, regardless of the setting of the option
for mixing after scf convergence.
Initial tests suggest that charge mixing has some desirable properties and could be a drop-in re-
placement for density-matrix mixing, but many more tests are needed to calibrate its efficiency for
different kinds of systems, and the heuristics for the (perhaps too many) parameters:

SCF.Kerker.q0sq 0 Ry (energy)
2
Determines the parameter q0 featuring in the Kerker preconditioning, which is always performed
on all components of ρ(G), even those treated with the DIIS scheme.

SCF.RhoGMixingCutoff 9 Ry (energy)
Determines the sub-set of G vectors which will undergo the DIIS procedure. Only those with
kinetic energies below this cutoff will be considered. The optimal extrapolation of the ρ(G)
elements will be replaced in the fourier series before performing the Kerker mixing.

59
 SCF.RhoG.DIIS.Depth 0 (integer)
Determines the maximum number of previous steps considered in the DIIS procedure.

NOTE: The information from the first scf step is not included in the DIIS history. There is no
provision yet for any other kind of “kick-starting” procedure. The logic is in m_rhog (rhog_mixing
routine).

SCF.RhoG.Metric.Preconditioner.Cutoff 〈None〉 (energy)

2
Determines the value of q1 in the weighing of the different G components in the scalar products
among residuals in the DIIS procedure. Following the KF ansatz, this parameter is chosen so
that the smallest (non-zero) G has a weight 20 times larger than that of the smallest G vector
in the DIIS set.
The default is the result of the KF prescription.

SCF.DebugRhoGMixing false (logical)

Controls the level of debugging output in the mixing procedure (basically whether the first few
stars worth of Fourier components are printed). Note that this feature will only display the
components in the master node.

Debug.DIIS false (logical)

Controls the level of debugging output in the DIIS procedure. If set, the program prints the
DIIS matrix and the extrapolation coefficients.

SCF.MixCharge.SCF1 false (logical)

Logical variable to indicate whether or not the charge is mixed in the first SCF cycle. Anecdotal
evidence indicates that it might be advantageous, at least for calculations started from scratch,
to avoid that first mixing, and retain the “out” charge density as “in” for the next step.

6.9.4 Initialization of the density-matrix

NOTE: The conditions and options for density-matrix re-use are quite varied and not completely
orthogonal at this point. For further information, see routine Src/m_new_dm.F. What follows is a
summary.
The Density matrix can be:

1. Synthesized directly from atomic occupations.

(See the options below for spin considerations)
2. Read from a .DM file (if the appropriate options are set)
3. Extrapolated from previous geometry steps
(this includes as a special case the re-use of the DM
of the previous geometry iteration)

In cases 2 and 3, the structure of the read or extrapolated DM

is automatically adjusted to the current sparsity pattern.

In what follows, "Initialization" of the DM means that the DM is

either read from file (if available) or synthesized from atomic

60
 data. This is confusing, and better terminology should be used.

Special cases:

Harris functional: The matrix is always initialized

Force calculation: The DM should be written to disk

at the time of the "no displacement"
calculation and read from file at
every subsequent step.

Variable-cell calculation:

If the auxiliary cell changes, the DM is forced to be

synthesized (conceivably one could rescue some important
information from an old DM, but it is too much trouble
for now). NOTE that this is a change in policy with respect
to previous versions of the program, in which a (blind?)
re-use was allowed, except if ’ReInitialiseDM’ was ’true’.
Now ’ReInitialiseDM’ is ’true’ by default. Setting it to
’false’ is not recommended.

In all other cases (including "server operation"), the

default is to allow DM re-use (with possible extrapolation)
from previous geometry steps.

For "CG" calculations, the default is not to extrapolate the

DM (unless requested by setting ’DM.AllowExtrapolation’ to
"true"). The previous step’s DM is reused.

The fdf variables ’DM.AllowReuse’ and ’DM.AllowExtrapolation’

can be used to turn off DM re-use and extrapolation.

DM.UseSaveDM false (logical)

Instructs to read the density matrix stored in file SystemLabel..DM by a previous run.
SIESTA will continue even if .DM is not found.
NOTE: That if the spin settings has changed SIESTA allows reading a .DM from a similar cal-
culation with different Spin option. This may be advantageous when going from non-polarized
calculations to polarized, and beyond, see Spin for details.

DM.Init.Unfold true (logical)

depends on: DM.UseSaveDM
When reading the DM from a previous calculation there may be inconsistencies in the auxiliary
supercell. E.g. if the previous calculation did not use an auxiliary supercell and the current
calculation does (adding k-point sampling). SIESTA will automatically unfold the Γ-only DM

61
 to the auxiliary supercell elements (if true).
For false the DM elements are assumed to originate from an auxiliary supercell calculation and
the sparse elements are not unfolded but directly copied.
NOTE: Generally this shouldn’t not be touched, however, if the initial DM is generated using
sisl [11] and only on-site DM elements are set, this should be set to false.

DM.FormattedFiles false (logical)

Setting this alters the default for DM.FormattedInput and DM.FormattedOutput. In-
structs to use formatted files for reading and writing the density matrix. In this case, the files
are labelled SystemLabel.DMF.
Only usable if one has problems transferring files from one computer to another.

DM.FormattedInput false (logical)

Instructs to use formatted files for reading the density matrix.

DM.FormattedOutput false (logical)

Instructs to use formatted files for writing the density matrix.

DM.InitSpin.AF false (logical)

It defines the initial spin density for a spin polarized calculation. The spin density is initially
constructed with the maximum possible spin polarization for each atom in its atomic configu-
ration. This variable defines the relative orientation of the atomic spins:
If false the initial spin-configuration is a ferromagnetic order (all spins up). If true all odd
atoms are initialized to spin-up, all even atoms are initialized to spin-down.

%block DM.InitSpin 〈None〉 (block)

Define the initial spin density for a spin polarized calculation atom by atom. In the block
there is one line per atom to be spin-polarized, containing the atom index (integer, ordinal in
the block AtomicCoordinatesAndAtomicSpecies) and the desired initial spin-polarization
(real, positive for spin up, negative for spin down). A value larger than possible will be reduced
to the maximum possible polarization, keeping its sign. Maximum polarization can also be
given by introducing the symbol + or - instead of the polarization value. There is no need to
include a line for every atom, only for those to be polarized. The atoms not contemplated in
the block will be given non-polarized initialization.
For non-colinear spin, the spin direction may be specified for each atom by the polar angle θ and
the azimuthal angle φ (using the physics ISO convention), given as the last two arguments in
degrees. If not specified, θ = 0 is assumed (z-polarized). Spin must be set to use non-colinear
or spin-orbit for the directions to have effect.
Example:
%block DM.InitSpin
5 -1. 90. 0. # Atom index, spin, theta, phi (deg)
3 + 45. -90.
7 -
%endblock DM.InitSpin

In the above example, atom 5 is polarized in the x-direction.

If this block is defined, but empty, all atoms are not polarized. This block has precedence over

62
 DM.InitSpin.AF.

DM.AllowReuse true (logical)

Controls whether density matrix information from previous geometry iterations is re-used to
start the new geometry’s SCF cycle.

DM.AllowExtrapolation true (logical)

Controls whether the density matrix information from several previous geometry iterations
is extrapolated to start the new geometry’s SCF cycle. This feature is useful for molecular
dynamics simulations and possibly also for geometry relaxations. The number of geometry
steps saved is controlled by the variable DM.History.Depth.
This is default true for molecular-dynamics simulations, but false, for now, for geometry-
relaxations (pending further tests which users are kindly requested to perform).

DM.History.Depth 1 (integer)
Sets the number of geometry steps for which density-matrix information is saved for extrapola-
tion.

6.9.5 Initialization of the SCF cycle with charge densities

SCF.Read.Charge.NetCDF false (logical)
Instructs SIESTA to read the charge density stored in the netCDF file Rho.IN.grid.nc. This
feature allows the easier re-use of electronic-structure information from a previous run. It is not
necessary that the basis sets are “similar” (a requirement if density-matrices are to be read in).
NOTE: This is an experimental feature. Until robust checks are implemented, care must be
taken to make sure that the FFT grids in the .grid.nc file and in SIESTA are the same.

SCF.Read.Deformation.Charge.NetCDF false (logical)

Instructs Siesta to read the deformation charge density stored in the netCDF file
DeltaRho.IN.grid.nc. This feature allows the easier re-use of electronic-structure informa-
tion from a previous run. It is not necessary that the basis sets are “similar” (a requirement
if density-matrices are to be read in). The deformation charge is particularly useful to give a
good starting point for slightly different geometries.
NOTE: This is an experimental feature. Until robust checks are implemented, care must be
taken to make sure that the FFT grids in the .grid.nc file and in Siesta are the same.

6.9.6 Output of density matrix and Hamiltonian

Performance Note: For large-scale calculations, writing the DM at every scf step can have a severe
impact on performance. The sparse-matrix I/O is undergoing a re-design, to facilitate the analysis
of data and to increase the efficiency.

Use.Blocked.WriteMat false (logical)

By using blocks of orbitals (according to the underlying default block-cyclic distribution), the
sparse-matrix I/O can be speeded-up significantly, both by saving MPI communication and by
reducing the number of file accesses. This is essential for large systems, for which the I/O could
take a significant fraction of the total computation time.

63
 To enable this “blocked format” (recommended for large-scale calculations) use the option
Use.Blocked.WriteMat true. Note that it is off by default.
The new format is not backwards compatible. A
converter program (Util/DensityMatrix/dmUnblock.F90) has been written to post-process
those files intended for further analysis or re-use in Siesta. This is the best option for now, since
it allows liberal checkpointing with a much smaller time consumption, and only incurs costs
when re-using or analyzing files.
Note that TranSIESTA will continue to produce SystemLabel.DM files, in the old format (See
save_density_matrix.F)
To test the new features, the option S.Only true can be used. It will produce three files: a
standard one, another one with optimized MPI communications, and a third, blocked one.

Write.DM true (logical)

Control the creation of the current iterations density matrix to a file for restart purposes and
post-processing. If false nothing will be written.
If Use.Blocked.WriteMat is false the SystemLabel.DM file will be written. Otherwise these
density matrix files will be created; DM_MIXED.blocked and DM_OUT.blocked which are the
mixed and the diagonalization output, respectively.

Write.DM.end.of.cycle 〈Write.DM〉 (logical)

Equivalent to Write.DM, but will only write at the end of each SCF loop.
NOTE: The file generated depends on SCF.Mix.AfterConvergence.

Write.H false (logical)

Whether restart Hamiltonians should be written (not intrinsically supported in 4.1).
If true these files will be created; H_MIXED or H_DMGEN which is the mixed or the generated
Hamiltonian from the current density matrix, respectively. If Use.Blocked.WriteMat the
just mentioned files will have the additional suffix .blocked.

Write.H.end.of.cycle 〈Write.H〉 (logical)

Equivalent to Write.H, but will only write at the end of each SCF loop.
NOTE: The file generated depends on SCF.Mix.AfterConvergence.

The following options control the creation of netCDF files. The relevant routines have not been
optimized yet for large-scale calculations, so in this case the options should not be turned on (they
are off by default).

Write.DM.NetCDF true (logical)

It determines whether the density matrix (after the mixing step) is output as a DM.nc netCDF
file or not.
The file is overwritten at every SCF step. Use the Write.DM.History.NetCDF option if a
complete history is desired.
The DM.nc and standard DM file formats can be converted at will with the programs in
Util/DensityMatrix directory. Note that the DM values in the DM.nc file are in single preci-
sion.

Write.DMHS.NetCDF true (logical)

64
 If true, the input density matrix, Hamiltonian, and output density matrix, are stored in a
netCDF file named DMHS.nc. The file also contains the overlap matrix S.
The file is overwritten at every SCF step. Use the Write.DMHS.History.NetCDF option if
a complete history is desired.

Write.DM.History.NetCDF false (logical)

If true, a series of netCDF files with names of the form DM-NNNN.nc is created to hold the
complete history of the density matrix (after mixing). (See also Write.DM.NetCDF). Each
file corresponds to a geometry step.

Write.DMHS.History.NetCDF false (logical)

If true, a series of netCDF files with names of the form DMHS-NNNN.nc is created to hold
the complete history of the input and output density matrix, and the Hamiltonian. (See also
Write.DMHS.NetCDF). Each file corresponds to a geometry step. The overlap matrix is
stored only once per SCF cycle.

Write.TSHS.History false (logical)

If true, a series of TSHS files with names of the form SystemLabel.N.TSHS is created to hold the
complete history of the Hamiltonian and overlap matrix. Each file corresponds to a geometry
step. The overlap matrix is stored only once per SCF cycle. This option only works with
TranSIESTA.

6.9.7 Convergence criteria

NOTE: The older options with a DM prefix is still working for backwards compatibility. However,
the following flags has precedence.
Note that all convergence criteria are additive and may thus be used simultaneously for complete
control.

SCF.DM.Converge true (logical)

Logical variable to use the density matrix elements as monitor of self-consistency.

SCF.DM.Tolerance 10−4 (real)

depends on: SCF.DM.Converge
Tolerance of Density Matrix. When the maximum difference between the output and the input
on each element of the DM in a SCF cycle is smaller than SCF.DM.Tolerance, the self-
consistency has been achieved.
NOTE: DM.Tolerance is the actual default for this flag.

DM.Normalization.Tolerance 10−5 (real)

Tolerance for unnormalized density matrices (typically the product of solvers such as PEXSI
which have a built-in electron-count tolerance). If this tolerance is exceeded, the program stops.
It is understood as a fractional tolerance. For example, the default will allow an excess or shorfall
of 0.01 electrons in a 1000-electron system.

SCF.H.Converge true (logical)

Logical variable to use the Hamiltonian matrix elements as monitor of self-consistency: this is

65
 considered achieved when the maximum absolute change (dHmax) in the H matrix elements is
below SCF.H.Tolerance. The actual meaning of dHmax depends on whether DM or H mixing
is in effect: if mixing the DM, dHmax refers to the change in H(in) with respect to the previous
step; if mixing H, dHmax refers to H(out)-H(in) in the previous(?) step.

SCF.H.Tolerance 10−3 eV (energy)

depends on: SCF.H.Converge
If SCF.H.Converge is true, then self-consistency is achieved when the maximum absolute
change in the Hamiltonian matrix elements is below this value.

SCF.EDM.Converge true (logical)

Logical variable to use the energy density matrix elements as monitor of self-consistency: this is
considered achieved when the maximum absolute change (dEmax) in the energy density matrix
elements is below SCF.EDM.Tolerance. The meaning of dEmax is equivalent to that of
SCF.DM.Tolerance.

SCF.EDM.Tolerance 10−3 eV (energy)

depends on: SCF.EDM.Converge
If SCF.EDM.Converge is true, then self-consistency is achieved when the maximum absolute
change in the energy density matrix elements is below this value.

SCF.FreeE.Converge false (logical)

Logical variable to request an additional requirement for self-consistency: it is considered
achieved when the change in the total (free) energy between cycles of the SCF procedure is
below SCF.FreeE.Tolerance and the density matrix change criterion is also satisfied.

SCF.FreeE.Tolerance 10−4 eV (energy)

depends on: SCF.FreeE.Converge
If SCF.FreeE.Converge is true, then self-consistency is achieved when the change in the total
(free) energy between cycles of the SCF procedure is below this value and the density matrix
change criterion is also satisfied.

SCF.Harris.Converge false (logical)

Logical variable to use the Harris energy as monitor of self-consistency: this is considered
achieved when the change in the Harris energy between cycles of the SCF procedure is below
SCF.Harris.Tolerance. This is useful if only energies are needed, as the Harris energy tends
to converge faster than the Kohn-Sham energy. The user is responsible for using the correct
energies in further processing, e.g., the Harris energy if the Harris criterion is used.
To help in basis-optimization tasks, a new file BASIS_HARRIS_ENTHALPY is provided, holding the
same information as BASIS_ENTHALPY but using the Harris energy instead of the Kohn-Sham
energy.
NOTE: Setting this to true makes SCF.DM.Converge SCF.H.Converge default to false.

SCF.Harris.Tolerance 10−4 eV (energy)

depends on: SCF.Harris.Converge
If SCF.Harris.Converge is true, then self-consistency is achieved when the change in the
Harris energy between cycles of the SCF procedure is below this value. This is useful if only
energies are needed, as the Harris energy tends to converge faster than the Kohn-Sham energy.

66
6.10 The real-space grid and the eggbox-effect

SIESTA uses a finite 3D grid for the calculation of some integrals and the representation of charge
densities and potentials. Its fineness is determined by its plane-wave cutoff, as given by the Mesh-
Cutoff option. It means that all periodic plane waves with kinetic energy lower than this cutoff can
be represented in the grid without aliasing. In turn, this implies that if a function (e.g. the density
or the effective potential) is an expansion of only these plane waves, it can be Fourier transformed
back and forth without any approximation.
The existence of the grid causes the breaking of translational symmetry (the egg-box effect, due to
the fact that the density and potential do have plane wave components above the mesh cutoff). This
symmetry breaking is clear when moving one single atom in an otherwise empty simulation cell.
The total energy and the forces oscillate with the grid periodicity when the atom is moved, as if the
atom were moving on an eggbox. In the limit of infinitely fine grid (infinite mesh cutoff) this effect
disappears.
For reasonable values of the mesh cutoff, the effect of the eggbox on the total energy or on the relaxed
structure is normally unimportant. However, it can affect substantially the process of relaxation, by
increasing the number of steps considerably, and can also spoil the calculation of vibrations, usually
much more demanding than relaxations.
The Util/Scripting/eggbox_checker.py script can be used to diagnose the eggbox effect to be
expected for a particular pseudopotential/basis-set combination.
Apart from increasing the mesh cutoff (see the MeshCutoff option), the following options might
help in lessening a given eggbox problem. But note also that a filtering of the orbitals and the
relevant parts of the pseudopotential and the pseudocore charge might be enough to solve the issue
(see Sec. 6.3.9).

MeshCutoff 300 Ry (energy)

Defines the plane wave cutoff for the grid.

MeshSubDivisions 2 (integer)
Defines the number of sub-mesh points in each direction used to save index storage on the mesh.
It affects the memory requirements and the CPU time, but not the results.
NOTE: The default value might be a bit conservative. Users might experiment with higher
values, 4 or 6, to lower the memory and cputime usage.

%block Grid.CellSampling 〈None〉 (block)

It specifies points within the grid cell for a symmetrization sampling.
For a given grid the grid-cutoff convergence can be improved (and the eggbox lessened) by
recovering the lost symmetry: by symmetrizing the sensitive quantities. The full symmetrization
implies an integration (averaging) over the grid cell. Instead, a finite sampling can be performed.
It is a sampling of rigid displacements of the system with respect to the grid. The original
grid-system setup (one point of the grid at the origin) is always calculated. It is the (0,0,0)
displacement. The block Grid.CellSampling gives the additional displacements wanted for
the sampling. They are given relative to the grid-cell vectors, i.e., (1,1,1) would displace to the
next grid point across the body diagonal, giving an equivalent grid-system situation (a useless
displacement for a sampling).

67
Examples: Assume a cubic cell, and therefore a (smaller) cubic grid cell. If there is no block or
the block is empty, then the original (0,0,0) will be used only. The block:
%block Grid.CellSampling
0.5 0.5 0.5
%endblock Grid.CellSampling

would use the body center as a second point in the sampling. Or:
%block Grid.CellSampling
0.5 0.5 0.0
0.5 0.0 0.5
0.0 0.5 0.5
%endblock Grid.CellSampling

gives an fcc kind of sampling, and

%block Grid.CellSampling
0.5 0.0 0.0
0.0 0.5 0.0
0.0 0.0 0.5
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
0.5 0.5 0.5
%endblock Grid.CellSampling

gives again a cubic sampling with half the original side length. It is not trivial to choose a
right set of displacements so as to maximize the new ’effective’ cutoff. It depends on the kind
of cell. It may be automatized in the future, but it is now left to the user, who introduces the
displacements manually through this block.
The quantities which are symmetrized are: (i) energy terms that depend on the grid, (ii) forces,
(iii) stress tensor, and (iv) electric dipole.
The symmetrization is performed at the end of every SCF cycle. The whole cycle is done for the
(0,0,0) displacement, and, when the density matrix is converged, the same (now fixed) density
matrix is used to obtain the desired quantities at the other displacements (the density matrix
itself is not symmetrized as it gives a much smaller egg-box effect). The CPU time needed for
each displacement in the Grid.CellSampling block is of the order of one extra SCF iteration.
This may be required in systems where very precise forces are needed, and/or if partial cores
are used. It is advantageous to test whether the forces are sampled sufficiently by sampling one
point.
Additionally this may be given as a list of 3 integers which corresponds to a “Monkhorst-Pack”
like grid sampling. I.e.
Grid.CellSampling [2 2 2]

is equivalent to
%block Grid.CellSampling
0.5 0.0 0.0
0.0 0.5 0.0
0.5 0.5 0.0
0.0 0.0 0.5
0.5 0.0 0.5

68
 0.0 0.5 0.5
0.5 0.5 0.5
%endblock Grid.CellSampling

This is an easy method to see if the flag is important for your system or not.

%block EggboxRemove 〈None〉 (block)

For recovering translational invariance in an approximate way.
It works by substracting from Kohn-Sham’s total energy (and forces) an approximation to
the eggbox energy, sum of atomic contributions. Each atom has a predefined eggbox energy
depending on where it sits on the cell. This atomic contribution is species dependent and is
obviously invariant under grid-cell translations. Each species contribution is thus expanded in
the appropriate Fourier series. It is important to have a smooth eggbox, for it to be represented
by a few Fourier components. A jagged egg-box (unless very small, which is then unimportant)
is often an indication of a problem with the pseudo.
In the block there is one line per Fourier component. The first integer is for the atomic species
it is associated with. The other three represent the reciprocal lattice vector of the grid cell (in
units of the basis vectors of the reciprocal cell). The real number is the Fourier coefficient in
units of the energy scale given in EggboxScale (see below), normally 1 eV.
The number and choice of Fourier components is free, as well as their order in the block. One
can choose to correct only some species and not others if, for instance, there is a substantial
difference in hardness of the cores. The 0 0 0 components will add a species-dependent constant
energy per atom. It is thus irrelevant except if comparing total energies of different calculations,
in which case they have to be considered with care (for instance by putting them all to zero,
i.e. by not introducing them in the list). The other components average to zero representing
no bias in the total energy comparisons.
If the total energies of the free atoms are put as 0 0 0 coefficients (with spin polarisation if
adequate etc.) the corrected total energy will be the cohesive energy of the system (per unit
cell).
Example: For a two species system, this example would give a quite sufficent set in many
instances (the actual values of the Fourier coefficients are not realistic).
%block EggBoxRemove
1 0 0 0 -143.86904
1 0 0 1 0.00031
1 0 1 0 0.00016
1 0 1 1 -0.00015
1 1 0 0 0.00035
1 1 0 1 -0.00017
2 0 0 0 -270.81903
2 0 0 1 0.00015
2 0 1 0 0.00024
2 1 0 0 0.00035
2 1 0 1 -0.00077
2 1 1 0 -0.00075
2 1 1 1 -0.00002
%endblock EggBoxRemove

It represents an alternative to grid-cell sampling (above). It is only approximate, but once the
Fourier components for each species are given, it does not represent any computational effort

69
 (neither memory nor time), while the grid-cell sampling requires CPU time (roughly one extra
SCF step per point every MD step).
It will be particularly helpful in atoms with substantial partial core or semicore electrons.
NOTE: This should only be used for fixed cell calculations, i.e. not with MD.VariableCell.
For the time being, it is up to the user to obtain the Fourier components to be introduced. They
can be obtained by moving one isolated atom through the cell to be used in the calculation (for
a give cell size, shape and mesh), once for each species. The Util/Scripting/eggbox_checker.py
script can be used as a starting point for this.

EggboxScale 1 eV (energy)
Defines the scale in which the Fourier components of the egg-box energy are given in the
EggboxRemove block.

6.11 Matrix elements of the Hamiltonian and overlap

NeglNonOverlapInt false (logical)
Logical variable to neglect or compute interactions between orbitals which do not overlap. These
come from the KB projectors. Neglecting them makes the Hamiltonian more sparse, and the
calculation faster.
NOTE: Use with care!

SaveHS false (logical)

Instructs to write the Hamiltonian and overlap matrices, as well as other data required to
generate bands and density of states, in file SystemLabel.HSX. The .HSX format is more compact
than the traditional .HS, and the Hamiltonian, overlap matrix, and relative-positions array
(which is always output, even for gamma-point only calculations) are in single precision.
The program hsx2hs in Util/HSX can be used to generate an old-style .HS file if needed.
SIESTA produces also an .HSX file if the COOP.Write option is active.
See also the Write.DMHS.NetCDF and Write.DMHS.History.NetCDF options.

Compat.Matel.NRTAB false (logical)

Internally the two-center integrals involved in some matrix element calculations are tabulated
with a preset number of elements. In versions 4.0.1 and prior this was 128. Since 4.0.2 the
number of table elements has been increased to 1024, which translates to more accurate matrix
element calculations.
This compatibility option should only be used when preservation of the (lower accuracy) nu-
merical results of 4.0.1 or prior versions is required for reproducibility purposes.

6.11.1 The auxiliary supercell

When using k-points, this auxiliary supercell is needed to compute properly the matrix elements
involving orbitals in different unit cells. It is computed automatically by the program at every
geometry step.
Note that for gamma-point-only calculations there is an implicit “folding” of matrix elements corre-
sponding to the images of orbitals outside the unit cell. If information about the specific values of

70
these matrix elements is needed (as for COOP/COHP analysis), one has to make sure that the unit
cell is large enough, or force the use of an aunxiliary supercell.

ForceAuxCell false (logical)

If true, the program uses an auxiliary cell even for gamma-point-only calculations. This might
be needed for COOP/COHP calculations, as noted above, or in degenerate cases, such as
when the cell is so small that a given orbital “self-interacts” with its own images (via direct
overlap or through a KB projector). In this case, the diagonal value of the overlap matrix
S for this orbital is different from 1, and an initialization of the DM via atomic data would
be faulty. The program corrects the problem to zeroth-order by dividing the DM value by the
corresponding overlap matrix entry, but the initial charge density would exhibit distortions from
a true atomic superposition (See routine m_new_dm.F). The distortion of the charge density is
a serious problem for Harris functional calculations, so this option must be enabled for them if
self-folding is present. (Note that this should not happen in any serious calculation...)

6.12 Calculation of the electronic structure

SIESTA can use three qualitatively different methods to determine the electronic structure of the
system. The first is standard diagonalization, which works for all systems and has a cubic scaling
with the size. The second is based on the direct minimization of a special functional over a set of
trial orbitals. These orbitals can either extend over the entire system, resulting in a cubic scaling
algorithm, or be constrained within a localization radius, resulting in a linear scaling algorithm. The
former is a recent implementation (described in 6.12.4), that can be viewed as an equivalent approach
to diagonalization in terms of the accuracy of the solution; the latter is the historical O(N) method
used by SIESTA (described in 6.12.5); it scales in principle linearly with the size of the system (only
if the size is larger than the radial cutoff for the local solution wave-functions), but is quite fragile
and substantially more difficult to use, and only works for systems with clearly separated occupied
and empty states. The default is to use diagonalization. The third method (PEXSI) is based on the
pole expansion of the Fermi-Dirac function and the direct computation of the density matrix via an
efficient scheme of selected inversion (see Sec 6.13).
The calculation of the H and S matrix elements is always done with an O(N) method. The actual
scaling is not linear for small systems, but it becomes O(N) when the system dimensions are larger
than the scale of orbital rc ’s.
The relative importance of both parts of the computation (matrix elements and solution) depends on
the size and quality of the calculation. The mesh cutoff affects only the matrix-element calculation;
orbital cutoff radii affect the matrix elements and all solvers except diagonalization; the need for
k-point sampling affects the solvers only, and the number of basis orbitals affects them all.
In practice, the vast majority of users employ diagonalization (or the OMM method) for the cal-
culation of the electronic structure. This is so because the vast majority of calculations (done for
intermediate system sizes) would not benefit from the O(N) or PEXSI solvers.

SolutionMethod diagon (string)

Character string to choose among diagonalization (diagon), cubic-scaling minimization
(OMM), Order-N (OrderN) solution of the Kohn-Sham Hamiltonian, transiesta, or the
PEXSI method (PEXSI).

71
6.12.1 Diagonalization options
NumberOfEigenStates 〈all orbitals〉 (integer)
depends on: Diag.Algorithm
This parameter allows the user to reduce the number of eigenstates that are calculated from
the maximum possible. The benefit is that, for any calculation, the cost of the diagonalization
is reduced by finding fewer eigenvalues/eigenvectors. For example, during a geometry optimisa-
tion, only the occupied states are required rather than the full set of virtual orbitals. Note, that
if the electronic temperature is greater than zero then the number of partially occupied states
increases, depending on the band gap. The value specified must be greater than the number of
occupied states and less than the number of basis functions.
If a negative number is passed it corresponds to the number of orbitals above the total charge
of the system. In effect it corresponds to the number of orbitals above the Fermi level for zero
temperature. I.e. if −2 is specified for a system with 20 orbitals and 10 electrons it is equivalent
to 12.
Using this option can greatly speed up your calculations if used correctly.
NOTE: If experiencing PDORMTR errors in Γ calculations with MRRR algorithm, it is because
of a buggy ScaLAPACK implementation, simply use another algorithm.
NOTE: This only affects the MRRR, ELPA and Expert diagonalization routines.

Diag.UseNewDiagk false (logical)

Selects whether a more efficient diagonalization routine (with intermediate storage of eigenvec-
tors in NetCDF format) is used for the case of k-point sampling.
In order to use the new routine, netCDF support should be compiled in. Specifying a number
of eigenvectors to store is possible through the symbol NumberOfEigenStates (see above).
Note that for now, for safety, all eigenvectors for a given k-point and spin are computed by
the diagonalization routine, but only that number specified by the user are stored. If they are
insufficient, the program stops. A rule of thumb to select the number of eigenvectors to store is
to count the number of electrons and divide by two, and then apply a “safety factor” of around
1.1-1.2 to take into account fractional occupations and band overlaps.
A new file OCCS is produced with information about the number of states occupied.
This is an experimental feature.
NOTE: It is not compatible with the Diag.ParallelOverK option.

Diag.Use2D true (logical)

Determine whether a 1D or 2D data decomposition should be used when calling ScaLAPACK.
The use of 2D leads to superior scaling on large numbers of processors and is therefore the
default. This option only influences the parallel performance.
If Diag.BlockSize is different from BlockSize this flag defaults to true, else if
Diag.ProcessorY is 1 or the total number of processors, then this flag will default to false.
√
Diag.ProcessorY ∼ N (integer)
depends on: Diag.Use2D
Set the number of processors in the 2D distribution√along the rows. Its default is equal to the
lowest multiple of N (number of MPI cores) below N such that, ideally, the distribution will
be a square grid.

72
 The input is required to be a multiple of the total number of MPI cores but SIESTA will reduce
the input value such that it coincides with this.
√
Once the lowest multiple closest to N, or the input, is determined the 2D distribution will be
ProcessorY × N/ProcessorY, rows × columns.
NOTE: If the automatic correction (lowest multiple of MPI cores) is 1 the default of
Diag.Use2D will be false.

Diag.BlockSize 〈BlockSize〉 (integer)

depends on: Diag.Use2D
The block-size used for the 2D distribution in the ScaLAPACK calls. This number greatly
affects the performance of ScaLAPACK.
If the ScaLAPACK library is threaded this parameter should not be too small. In any case it
may be advantageous to run a few tests to find a suitable value.
NOTE: If Diag.Use2D is set to false this flag is not used.

Diag.Algorithm Divide-and-Conquer|... (string)

Select the algorithm when calculating the eigenvalues and/or eigenvectors.
The fastest routines are typically MRRR or ELPA which may be significantly faster by specifying
a suitable NumberOfEigenStates value.
Currently the implemented solvers are:
divide-and-Conquer Use the divide-and-conquer algorithm.
divide-and-Conquer-2stage Use the divide-and-conquer 2stage algorithm (fall-back to the
divide-and-conquer if not available).
MRRR depends on: NumberOfEigenStates
Use the multiple relatively robust algorithm.
NOTE: The MRRR method is defaulted not to be compiled in, however, if your ScaLAPACK
library does contain the relevant sources one may add this pre-processor flag -DSIESTA__MRRR.

MRRR-2stage depends on: NumberOfEigenStates

Use the 2-stage multiple relatively robust algorithm.
expert depends on: NumberOfEigenStates
Use the expert algorithm which allows calculating a subset of the eigenvalues/eigenvectors.
expert-2stage depends on: NumberOfEigenStates
Use the 2-stage expert algorithm which allows calculating a subset of the eigenval-
ues/eigenvectors.
noexpert|QR Use the QR algorithm.
noexpert-2stage|QR-2stage Use the 2-stage QR algorithm.
ELPA-1stage depends on: NumberOfEigenStates

Use the ELPA [1;7]

1-stage solver. Requires compilation of SIESTA with ELPA, see Sec. 2.4.
Not compatible with Diag.ParallelOverK.
ELPA|ELPA-2stage depends on: NumberOfEigenStates

73
 Use the ELPA [1;7] 2-stage solver. Requires compilation of SIESTA with ELPA, see Sec. 2.4.
Not compatible with Diag.ParallelOverK.
NOTE: All the 2-stage solvers are (as of July 2017) only implemented in the LAPACK library,
so they will only be usable in serial or when using Diag.ParallelOverK.
To enable the 2-stage solvers add this flag to the arch.make
FPPFLAGS += -DSIESTA__DIAG_2STAGE

If one uses the shipped LAPACK library the 2-stage solvers are added automatically.
NOTE: This flag has precedence over the deprecated flags: Diag.DivideAndConquer,
Diag.MRRR, Diag.ELPA and Diag.NoExpert. However, the default is taking from the
deprecated flags.

Diag.ParallelOverK false (logical)

For the diagonalization there is a choice in strategy about whether to parallelise over the k
points (true) or over the orbitals (false). k point diagonalization is close to perfectly parallel
but is only useful where the number of k points is much larger than the number of processors
and therefore orbital parallelisation is generally preferred. The exception is for metals where
the unit cell is small, but the number of k points to be sampled is very large. In this last case
it is recommend that this option be used.
NOTE: This scheme is not used for the diagonalizations involved in the generation of the band-
structure (as specified with BandLines or BandPoints) or in the generation of wave-function
information (as specified with WaveFuncKPoints). In these cases the program falls back to
using parallelization over orbitals.

Diag.AbsTol 10−16 (real)

The absolute tolerance for the orthogonality of the eigenvectors. This tolerance is only applicable
for the solvers:
expert for both the serial and parallel solvers.
mrrr for the serial solver.

Diag.OrFac 10−3 (real)

Re-orthogonalization factor to determine when the eigenvectors should be re-orthogonalized.
Only applicable for the expert serial and parallel solvers.

Diag.Memory 1 (real)
Whether the parallel diagonalization of a matrix is successful or not can depend on how much
workspace is available to the routine when there are clusters of eigenvalues. Diag.Memory
allows the user to increase the memory available, when necessary, to achieve successful diago-
nalization and is a scale factor relative to the minimum amount of memory that ScaLAPACK
might need.

Diag.UpperLower lower|upper (string)

Which part of the symmetric triangular part should be used in the solvers.
NOTE: Do not change this variable unless you are performing benchmarks. It should be fastest
with the lower part.

74
Deprecated diagonalization options

Diag.MRRR false (logical)

depends on: NumberOfEigenStates
Use the MRRR method in ScaLAPACK for diagonalization. Specifying a number of eigenvectors
to store is possible through the symbol NumberOfEigenStates (see above).
NOTE: The MRRR method is defaulted not to be compiled in, however, if your ScaLAPACK
library does contain the relevant sources one may add this pre-processor flag -DSIESTA__MRRR.
NOTE: Use Diag.Algorithm instead.

Diag.DivideAndConquer true (logical)

Logical to select whether the normal or Divide and Conquer algorithms are used within the
ScaLAPACK/LAPACK diagonalization routines.
NOTE: Use Diag.Algorithm instead.

Diag.ELPA false (logical)

depends on: NumberOfEigenStates
See the ELPA articles [1;7] for additional information.
NOTE: It is not compatible with the Diag.ParallelOverK option.
NOTE: Use Diag.Algorithm instead.

Diag.NoExpert false (logical)

Logical to select whether the simple or expert versions of the ScaLAPACK/LAPACK routines
are used. Usually the expert routines are faster, but may require slightly more memory.
NOTE: Use Diag.Algorithm instead.

6.12.2 Output of eigenvalues and wavefunctions

This section focuses on the output of eigenvalues and wavefunctions produced during the (last)
iteration of the self-consistent cycle, and associated to the appropriate k-point sampling.
For band-structure calculations (which typically use a different set of k-points) and specific requests
for wavefunctions, see Secs. 6.14 and 6.15, respectively.
The complete set of wavefunctions obtained during the last iteration of the SCF loop will be written
to a NetCDF file WFS.nc if the Diag.UseNewDiagk option is in effect.
The complete set of wavefunctions obtained during the last iteration of the SCF loop will be written
to SystemLabel.fullBZ.WFSX if the COOP.Write option is in effect.

WriteEigenvalues false (logical)

If true it writes the Hamiltonian eigenvalues for the sampling ~k points, in the main output
file. If false, it writes them in the file SystemLabel.EIG, which can be used by the Eig2DOS
postprocessing utility (in the Util/Eig2DOS directory) for obtaining the density of states.
NOTE: this option only works for SolutionMethod which calculates the eigenvalues.

75
6.12.3 Occupation of electronic states and Fermi level

OccupationFunction FD (string)
String variable to select the function that determines the occupation of the electronic states.
Two options are available:
FD The usual Fermi-Dirac occupation function is used.
MP The occupation function proposed by Methfessel and Paxton (Phys. Rev. B, 40, 3616
(1989)), is used.
The smearing of the electronic occupations is done, in both cases, using an energy width defined
by the ElectronicTemperature variable. Note that, while in the case of Fermi-Dirac, the
occupations correspond to the physical ones if the electronic temperature is set to the physical
temperature of the system, this is not the case in the Methfessel-Paxton function. In this
case, the tempeature is just a mathematical artifact to obtain a more accurate integration of
the physical quantities at a lower cost. In particular, the Methfessel-Paxton scheme has the
advantage that, even for quite large smearing temperatures, the obtained energy is very close
to the physical energy at T = 0. Also, it allows a much faster convergence with respect to
k-points, specially for metals. Finally, the convergence to selfconsistency is very much improved
(allowing the use of larger mixing coefficients).
For the Methfessel-Paxton case, one can use relatively large values for the ElectronicTem-
perature parameter. How large depends on the specific system. A guide can be found in the
article by J. Kresse and J. Furthmüller, Comp. Mat. Sci. 6, 15 (1996).
If Methfessel-Paxton smearing is used, the order of the corresponding Hermite polynomial ex-
pansion must also be chosen (see description of variable OccupationMPOrder).
We finally note that, in both cases (FD and MP), once a finite temperature has been chosen,
the relevant energy is not the Kohn-Sham energy, but the Free energy. In particular, the atomic
forces are derivatives of the Free energy, not the KS energy. See R. Wentzcovitch et al., Phys.
Rev. B 45, 11372 (1992); S. de Gironcoli, Phys. Rev. B 51, 6773 (1995); J. Kresse and J.
Furthmüller, Comp. Mat. Sci. 6, 15 (1996), for details.

OccupationMPOrder 1 (integer)
Order of the Hermite-Gauss polynomial expansion for the electronic occupation functions in
the Methfessel-Paxton scheme (see Phys. Rev. B 40, 3616 (1989)). Specially for metals,
higher order expansions provide better convergence to the ground state result, even with larger
smearing temperatures, and provide also better convergence with k-points.
NOTE: only used if OccupationFunction is MP.

ElectronicTemperature 300 K (temperature/energy)

Temperature for Fermi-Dirac or Methfessel-Paxton distribution. Useful specially for metals,
and to accelerate selfconsistency in some cases.

6.12.4 Orbital minimization method (OMM)

The OMM is an alternative cubic-scaling solver that uses a minimization algorithm instead of direct
diagonalization to find the occupied subspace. The main advantage over diagonalization is the
possibility of iteratively reusing the solution from each SCF/MD step as the starting guess of the

76
following one, thus greatly reducing the time to solution. Typically, therefore, the first few SCF
cycles of the first MD step of a simulation will be slower than diagonalization, but the rest will be
faster. The main disadvantages are that individual Kohn-Sham eigenvalues are not computed, and
that only a fixed, integer number of electrons at each k point/spin is allowed. Therefore, only spin-
polarized calculations with Spin.Fix are allowed, and Spin.Total must be chosen appropriately.
For non-Γ point calculations, the number of electrons is set to be equal at all k points. Non-colinear
calculations (see Spin) are not supported at present. The OMM implementation was initially
developed by Fabiano Corsetti.
It is important to note that the OMM requires all occupied Kohn-Sham eigenvalues to be negative;
this can be achieved by applying a shift to the eigenspectrum, controlled by ON.eta (in this case,
ON.eta simply needs to be higher than the HOMO level). If the OMM exhibits a pathologically slow
or unstable convergence, this is almost certainly due to the fact that the default value of ON.eta
(0.0 eV) is too low, and should be raised by a few eV.

OMM.UseCholesky true (logical)

Select whether to perform a Cholesky factorization of the generalized eigenvalue problem; this
removes the overlap matrix from the problem but also destroys the sparsity of the Hamiltonian
matrix.

OMM.Use2D true (logical)

Select whether to use a 2D data decomposition of the matrices for parallel calculations. This
generally leads to superior scaling for large numbers of MPI processes.

OMM.UseSparse false (logical)

Select whether to make use of the sparsity of the Hamiltonian and overlap matrices where
possible when performing matrix-matrix multiplications (these operations are thus reduced from
O(N 3 ) to O(N 2 ) without loss of accuracy).
NOTE: not compatible with OMM.UseCholesky, OMM.Use2D, or non-Γ point calcula-
tions

OMM.Precon -1 (integer)
Number of SCF steps for all MD steps for which to apply a preconditioning scheme based on the
overlap and kinetic energy matrices; for negative values the preconditioning is always applied.
Preconditioning is usually essential for fast and accurate convergence (note, however, that it
is not needed if a Cholesky factorization is performed; in such cases this variable will have no
effect on the calculation).
NOTE: cannot be used with OMM.UseCholesky.

OMM.PreconFirstStep 〈OMM.Precon〉 (integer)

Number of SCF steps in the first MD step for which to apply the preconditioning scheme; if
present, this will overwrite the value given in OMM.Precon for the first MD step only.

OMM.Diagon 0 (integer)
Number of SCF steps for all MD steps for which to use a standard diagonalization before
switching to the OMM; for negative values diagonalization is always used, and so the calculation
is effectively equivalent to SolutionMethod diagon. In general, selecting the first few SCF
steps can speed up the calculation by removing the costly initial minimization (at present this

77
 works best for Γ point calculations).

OMM.DiagonFirstStep 〈OMM.Diagon〉 (integer)

Number of SCF steps in the first MD step for which to use a standard diagonalization before
switching to the OMM; if present, this will overwrite the value given in OMM.Diagon for the
first MD step only.

OMM.BlockSize 〈BlockSize〉 (integer)

Blocksize used for distributing the elements of the matrix over MPI processes. Specifically, this
variable controls the dimension relating to the trial orbitals used in the minimization (equal to
the number of occupied states at each k point/spin); the equivalent variable for the dimension
relating to the underlying basis orbitals is controlled by BlockSize.

OMM.TPreconScale 10 Ry (energy)
Scale of the kinetic energy preconditioning (see C. K. Gan et al., Comput. Phys. Commun.
134, 33 (2001)). A smaller value indicates more aggressive kinetic energy preconditioning,
while an infinite value indicates no kinetic energy preconditioning. In general, the kinetic
energy preconditioning is much less important than the tensorial correction brought about by
the overlap matrix, and so this value will have fairly little impact on the overall performace of the
preconditioner; however, too aggressive kinetic energy preconditioning can have a detrimental
effect on performance and accuracy.

OMM.RelTol 10−9 (real)

Relative tolerance in the conjugate gradients minimization of the Kohn-Sham band energy (see
ON.Etol).

OMM.Eigenvalues false (logical)

Select whether to perform a diagonalization at the end of each MD step to obtain the Kohn-
Sham eigenvalues.

OMM.WriteCoeffs false (logical)

Select whether to write the coefficients of the solution orbitals to file at the end of each MD
step.

OMM.ReadCoeffs false (logical)

Select whether to read the coefficients of the solution orbitals from file at the beginning of
a new calculation. Useful for restarting an interrupted calculation, especially when used in
conjuction with DM.UseSaveDM. Note that the same number of MPI processes and values
of OMM.Use2D, OMM.BlockSize, and BlockSize must be used when restarting.

OMM.LongOutput false (logical)

Select whether to output detailed information of the conjugate gradients minimization for each
SCF step.

6.12.5 Order(N) calculations

The Ordern(N) subsystem is quite fragile and only works for systems with clearly separated occupied
and empty states. Note also that the option to compute the chemical potential automatically does

78
not yet work in parallel.
NOTE: Since it is used less often, bugs creeping into the O(N) solver have been more resilient than
in more popular bits of the code. Work is ongoing to clean and automate the O(N) process, to make
the solver more user-friendly and robust.

ON.functional Kim (string)

Choice of order-N minimization functionals:
Kim Functional of Kim, Mauri and Galli, PRB 52, 1640 (1995).
Ordejon-Mauri Functional of Ordejón et al, or Mauri et al, see PRB 51, 1456 (1995). The num-
ber of localized wave functions (LWFs) used must coincide with Nel /2 (unless spin polarized).
For the initial assignment of LWF centers to atoms, atoms with even number of electrons, n,
get n/2 LWFs. Odd atoms get (n + 1)/2 and (n − 1)/2 in an alternating sequence, ir order
of appearance (controlled by the input in the atomic coordinates block).
files Reads localized-function information from a file and chooses automatically the functional
to be used.

ON.MaxNumIter 1000 (integer)

Maximum number of iterations in the conjugate minimization of the electronic energy, in each
SCF cycle.

ON.Etol 10−8 (real)

Relative-energy tolerance in the conjugate minimization of the electronic energy. The mini-
mization finishes if 2(En − En−1 )/(En + En−1 ) ≤ ON.Etol.

ON.eta 0 eV (energy)
Fermi level parameter of Kim et al.. This should be in the energy gap, and tuned to obtain the
correct number of electrons. If the calculation is spin polarised, then separate Fermi levels for
each spin can be specified.

ON.eta.alpha 0 eV (energy)
Fermi level parameter of Kim et al. for alpha spin electrons. This should be in the energy gap,
and tuned to obtain the correct number of electrons. Note that if the Fermi level is not specified
individually for each spin then the same global eta will be used.

ON.eta.beta 0 eV (energy)
Fermi level parameter of Kim et al. for beta spin electrons. This should be in the energy gap,
and tuned to obtain the correct number of electrons. Note that if the Fermi level is not specified
individually for each spin then the same global eta will be used.

ON.RcLWF 9.5 Bohr (length)

Localization redius for the Localized Wave Functions (LWF’s).

ON.ChemicalPotential false (logical)

Specifies whether to calculate an order-N estimate of the Chemical Potential, by the projection
method (Goedecker and Teter, PRB 51, 9455 (1995); Stephan, Drabold and Martin, PRB 58,
13472 (1998)). This is done by expanding the Fermi function (or density matrix) at a given
temperature, by means of Chebyshev polynomials, and imposing a real space truncation on

79
 the density matrix. To obtain a realistic estimate, the temperature should be small enough
(typically, smaller than the energy gap), the localization range large enough (of the order of
the one you would use for the Localized Wannier Functions), and the order of the polynomial
expansion sufficiently large (how large depends on the temperature; typically, 50-100).
NOTE: this option does not work in parallel. An alternative is to obtain the approximate value
of the chemical potential using an initial diagonalization.

ON.ChemicalPotential.Use false (logical)

Specifies whether to use the calculated estimate of the Chemical Potential, instead of the pa-
rameter ON.eta for the order-N energy functional minimization. This is useful if you do not
know the position of the Fermi level, typically in the beginning of an order-N run.
NOTE: this overrides the value of ON.eta and ON.ChemicalPotential. Also, this option
does not work in parallel. An alternative is to obtain the approximate value of the chemical
potential using an initial diagonalization.

ON.ChemicalPotential.Rc 9.5 Bohr (length)

Defines the cutoff radius for the density matrix or Fermi operator in the calculation of the
estimate of the Chemical Potential.

ON.ChemicalPotential.Temperature 0.05 Ry (temperature/energy)

Defines the temperature to be used in the Fermi function expansion in the calculation of the
estimate of the Chemical Potential. To have an accurate results, this temperature should be
smaller than the gap of the system.

ON.ChemicalPotential.Order 100 (integer)

Order of the Chebishev expansion to calculate the estimate of the Chemical Potential.

ON.LowerMemory false (logical)

If true, then a slightly reduced memory algorithm is used in the 3-point line search during the
order N minimisation. Only affects parallel runs.

Output of localized wavefunctions At the end of each conjugate gradient minimization of

the energy functional, the LWF’s are stored on disk. These can be used as an input for the same
system in a restart, or in case something goes wrong. The LWF’s are stored in sparse form in file
SystemLabel.LWF
It is important to keep very good care of this file, since the first minimizations can take MANY
steps. Loosing them will mean performing the whole minimization again. It is also a good practice
to save it periodically during the simulation, in case a mid-run restart is necessary.

ON.UseSaveLWF false (logical)

Instructs to read the localized wave functions stored in file SystemLabel.LWF by a previous run.

6.13 The PEXSI solver

The PEXSI solver is based on the combination of the pole expansion of the Fermi-Dirac function
and the computation of only a selected (sparse) subset of the elements of the matrices (H − zl S)−1

80
at each pole zl .
This solver can efficiently use the sparsity pattern of the Hamiltonian and overlap matrices generated
in SIESTA, and for large systems has a much lower computational complexity than that associated
with the matrix diagonalization procedure. It is also highly scalable.
The PEXSI technique can be used to evaluate the electron density, free energy, atomic forces,
density of states and local density of states without computing any eigenvalue or eigenvector of the
Kohn-Sham Hamiltonian. It can achieve accuracy fully comparable to that obtained from a matrix
diagonalization procedure for general systems, including metallic systems at low temperature.
The current implementation of the PEXSI solver in SIESTA makes use of the full fine-grained-level
interface in the PEXSI library (http://pexsi.org), and can deal with spin-polarization, but it is
still restricted to Γ-point calculations.
The following is a brief description of the input-file parameters relevant to the workings of the
PEXSI solver. For more background, including a discussion of the conditions under which this
solver is competitive, the user is referred to the paper Lin et al. [6] , and references therein.
The technology involved in the PEXSI solver can also be used to compute densities of states and
“local densities of states”. These features are documented in this section and also linked to in the
relevant general sections.

6.13.1 Pole handling

Note that the temperature for the Fermi-Dirac distribution which is pole-expanded is taken directly
from the ElectronicTemperature parameter (see Sec. 6.12.3).

PEXSI.NumPoles 40 (integer)
Effective number of poles used to expand the Fermi-Dirac function.

PEXSI.deltaE 3 Ry (energy)
In principle PEXSI.deltaE should be Emax −µ, where Emax is the largest eigenvalue for (H,S),
and µ is the chemical potential. However, due to the fast decay of the Fermi-Dirac function,
PEXSI.deltaE can often be chosen to be much lower. In practice we set the default to be 3
Ryd. This number should be set to be larger if the difference between Tr[H·DM] and Tr[S∗EDM]
(displayed in the output if PEXSI.Verbosity is at least 2) does not decrease with the increase
of the number of poles.

PEXSI.Gap 0 Ry (energy)
Spectral gap. This can be set to be 0 in most cases.

6.13.2 Parallel environment and control options

MPI.Nprocs.SIESTA 〈total processors〉 (integer)
Specifies the number of MPI processes to be used in those parts of the program (such as
Hamiltonian setup and computation of forces) which are outside of the PEXSI solver itself.
This is needed in large-scale calculations, for which the number of processors that can be used
by the PEXSI solver is much higher than those needed by other parts of the code.
Note that when the PEXSI solver is not used, this parameter will simply reduce the number

81
 of processors actually used by all parts of the program, leaving the rest idle for the whole
calculation. This will adversely affect the computing budget, so take care not to use this option
in that case.

PEXSI.NP-per-pole 4 (integer)
Number of MPI processes used to perform the PEXSI computations in one pole. If the total
number of MPI processes is smaller than this number times the number of poles (times the spin
multiplicity), the PEXSI library will compute appropriate groups of poles in sequence. The
minimum time to solution is achieved by increasing this parameter as much as it is reasonable
for parallel efficiency, and using enough MPI processes to allow complete parallelization over
poles. On the other hand, the minimum computational cost (in the sense of computing budget)
is obtained by using the minimum value of this parameter which is compatible with the mem-
ory footprint. The additional parallelization over poles will be irrelevant for cost, but it will
obviously affect the time to solution.
Internally, SIESTA computes the processor grid parameters nprow and npcol for the PEXSI
library, with nprow >= npcol, and as similar as possible. So it is best to choose PEXSI.NP-
per-pole as the product of two similar numbers.
NOTE: The total number of MPI processes must be divisible by PEXSI.NP-per-pole. In
case of spin-polarized calculations, the total number of MPI processes must be divisible by
PEXSI.NP-per-pole times 2.

PEXSI.Ordering 1 (integer)
For large matrices, symbolic factorization should be performed in parallel to reduce the wall
clock time. This can be done using ParMETIS/PT-Scotch by setting PEXSI.Ordering to
0. However, we have been experiencing some instability problem of the symbolic factorization
phase when ParMETIS/PT-Scotch is used. In such case, for relatively small matrices one can
either use the sequential METIS (PEXSI.Ordering = 1) or set PEXSI.NP-symbfact to 1.

PEXSI.NP-symbfact 1 (integer)
Number of MPI processes used to perform the symbolic factorizations needed in the PEXSI
procedure. A default value should be given to reduce the instability problem. From experience
so far setting this to be 1 is most stable, but going beyond 64 does not usually improve much.

PEXSI.Verbosity 1 (integer)
It determines the amount of information logged by the solver in different places. A value of zero
gives minimal information.
• In the files logPEXSI[0-9]+, the verbosity level is interpreted by the PEXSI library itself.
In the latest version, when PEXSI is compiled in RELEASE mode, only logPEXSI0 is
given in the output. This is because we have observed that simultaneous output for all
processors can have very significant cost for a large number of processors (>10000).
• In the SIESTA output file, a verbosity level of 1 and above will print lines (prefixed by &o)
indicating the various heuristics used at each scf step. A verbosity level of 2 and above
will print extra information.
The design of the output logging is still in flux.

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6.13.3 Electron tolerance and the PEXSI solver
PEXSI.num-electron-tolerance 10−4 (real)
Tolerance in the number of electrons for the PEXSI solver. At each iteration of the solver, the
number of electrons is computed as the trace of the density matrix times the overlap matrix,
and compared with the total number of electrons in the system. This tolerance can be fixed,
or dynamically determined as a function of the degree of convergence of the self-consistent-field
loop.

PEXSI.num-electron-tolerance-lower-bound 10−2 (real)

See PEXSI.num-electron-tolerance-upper-bound.

PEXSI.num-electron-tolerance-upper-bound 0.5 (real)

The upper and lower bounds for the electron tolerance are used to dynamically change the
tolerance in the PEXSI solver, following the simple algorithm:
tolerance = Max(lower_bound,Min(dDmax, upper_bound))
The first scf step uses the upper bound of the tolerance range, and subsequent steps use pro-
gressively lower values, in correspondence with the convergence-monitoring variable dDmax.
NOTE: This simple update schedule tends to work quite well. There is an experimental
algorithm, documented only in the code itself, which allows a finer degree of control of the
tolerance update.

PEXSI.mu-max-iter 10 (integer)
Maximum number of iterations of the PEXSI solver. Note that in this implementation there is no
fallback procedure if the solver fails to converge in this number of iterations to the prescribed
tolerance. In this case, the resulting density matrix might still be re-normalized, and the
calculation able to continue, if the tolerance for non normalized DMs is not set too tight. For
example,
# (true_no_electrons/no_electrons) - 1.0
DM.NormalizationTolerance 1.0e-3
will allow a 0.1% error in the number of electrons. For obvious reasons, this feature, which is
also useful in connection with the dynamic tolerance update, should not be abused.
If the parameters of the PEXSI solver are adjusted correctly (including a judicious use of
inertia-counting to refine the µ bracket), we should expect that the maximum number of solver
iterations needed is around 3

PEXSI.mu −0.6 Ry (energy)

The starting guess for the chemical potential for the PEXSI solver. Note that this value does not
affect the initial µ bracket for the inertia-count refinement, which is controlled by PEXSI.mu-
min and PEXSI.mu-max. After an inertia-count phase, µ will be reset, and further iterations
inherit this estimate, so this parameter is only relevant if there is no inertia-counting phase.

PEXSI.mu-pexsi-safeguard 0.05 Ry (energy)

NOTE: This feature has been deactivated for now. The condition for starting a new phase of
inertia-counting is that the Newton estimation falls outside the current bracket. The bracket is
expanded accordingly.

83
 The PEXSI solver uses Newton’s method to update the estimate of µ. If the attempted change
in µ is larger than PEXSI.mu-pexsi-safeguard, the solver cycle is stopped and a fresh phase
of inertia-counting is started.

6.13.4 Inertia-counting
PEXSI.Inertia-Counts 3 (integer)
In a given scf step, the PEXSI procedure can optionally employ a µ bracket-refinement proce-
dure based on inertia-counting. Typically, this is used only in the first few scf steps, and this
parameter determines how many. If positive, inertia-counting will be performed for exactly that
number of scf steps. If negative, inertia-counting will be performed for at least that number of
scf steps, and then for as long as the scf cycle is not yet deemed to be near convergence (as
determined by the PEXSI.safe-dDmax-no-inertia parameter).
NOTE: Since it is cheaper to perform an inertia-count phase than to execute one iteration of
the solver, it pays to call the solver only when the µ bracket is sufficiently refined.

PEXSI.mu-min −1 Ry (energy)
The lower bound of the initial range for µ used in the inertia-count refinement. In runs with
multiple geometry iterations, it is used only for the very first scf iteration at the first geometry
step. Further iterations inherit possibly refined values of this parameter.

PEXSI.mu-max 0 Ry (energy)
The upper bound of the initial range for µ used in the inertia-count refinement. In runs with
multiple geometry iterations, it is used only for the very first scf iteration at the first geometry
step. Further iterations inherit possibly refined values of this parameter.

PEXSI.safe-dDmax-no-inertia 0.05 (real)

During the scf cycle, the variable conventionally called dDmax monitors how far the cycle is
from convergence. If PEXSI.Inertia-Counts is negative, an inertia-counting phase will be
performed in a given scf step for as long as dDmax is greater than PEXSI.safe-dDmax-no-
inertia.
NOTE: Even though dDmax represents historically how far from convergence the density-
matrix is, the same mechanism applies to other forms of mixing in which other magnitudes are
monitored for convergence (Hamiltonian, charge density...).

PEXSI.lateral-expansion-inertia 3 eV (energy)
If the correct µ is outside the bracket provided to the inertia-counting phase, the bracket is
expanded in the appropriate direction(s) by this amoount.

PEXSI.Inertia-mu-tolerance 0.05 Ry (energy)

One of the criteria for early termination of the inertia-counting phase. The value of the estimated
µ (basically the center of the resulting brackets) is monitored, and the cycle stopped if its change
from one iteration to the next is below this parameter.

PEXSI.Inertia-max-iter 5 (integer)
Maximum number of inertia-count iterations per cycle.

PEXSI.Inertia-min-num-shifts 10 (integer)

84
 Minimum number of sampling points for inertia counts.

PEXSI.Inertia-energy-width-tolerance 〈PEXSI.Inertia-mu-tolerance〉 (energy)

One of the criteria for early termination of the inertia-counting phase. The cycle stops if the
width of the resulting bracket is below this parameter.

6.13.5 Re-use of µ information accross iterations

This is an important issue, as the efficiency of the PEXSI procedure depends on how close a guess
of µ we have at our disposal. There are two types of information re-use:

• Bracketing information used in the inertia-counting phase.

• The values of µ itself for the solver.

PEXSI.safe-width-ic-bracket 4 eV (energy)
By default, the µ bracket used for the inertia-counting phase in scf steps other than the first is
taken as an interval of width PEXSI.safe-width-ic-bracket around the latest estimate of µ.

PEXSI.safe-dDmax-ef-inertia 0.1 (real)

The change in µ from one scf iteration to the next can be crudely estimated by assuming that
the change in the band structure energy (estimated as Tr∆HDM) is due to a rigid shift. When
the scf cycle is near convergence, this ∆µ can be used to estimate the new initial bracket for
the inertia-counting phase, rigidly shifting the output bracket from the previous scf step. The
cycle is assumed to be near convergence when the monitoring variable dDmax is smaller than
PEXSI.safe-dDmax-ef-inertia.
NOTE: Even though dDmax represents historically how far from convergence the density-
matrix is, the same mechanism applies to other forms of mixing in which other magnitudes are
monitored for convergence (Hamiltonian, charge density...).
NOTE: This criterion will lead in general to tighter brackets than the previous one, but oscil-
lations in H in the first few iterations might make it more dangerous. More information from
real use cases is needed to refine the heuristics in this area.

PEXSI.safe-dDmax-ef-solver 0.05 (real)

When the scf cycle is near convergence, the ∆µ estimated as above can be used to shift the
initial guess for µ for the PEXSI solver. The cycle is assumed to be near convergence when the
monitoring variable dDmax is smaller than PEXSI.safe-dDmax-ef-solver.
NOTE: Even though dDmax represents historically how far from convergence the density-
matrix is, the same mechanism applies to other forms of mixing in which other magnitudes are
monitored for convergence (Hamiltonian, charge density...).

PEXSI.safe-width-solver-bracket 4 eV (energy)
In all cases, a “safe” bracket around µ is provided even in direct calls to the PEXSI solver,
in case a fallback to executing internally a cycle of inertia-counting is needed. The size of the
bracket is given by PEXSI.safe-width-solver-bracket

85
6.13.6 Calculation of the density of states by inertia-counting

The cumulative or integrated density of states (INTDOS) can be easily obtained by inertia-counting,
which involves a factorization of H − σS for varying σ (see SIESTA-PEXSI paper). Apart from the
DOS-specific options below, the “ordering”, “symbolic factorization”, and “pole group size” (re-
interpreted as the number of MPI processes dealing with a given σ) options are honored.
The current version of the code generates a file with the energy-INTDOS information, PEXSI_INTDOS,
which can be later processed to generate the DOS by direct numerical differentiation, or a SIESTA-
style SystemLabel.EIG file (using the Util/PEXSI/intdos2eig program).

PEXSI.DOS false (logical)

Whether to compute the DOS (actually, the INTDOS — see above) using the PEXSI technology.

PEXSI.DOS.Emin −1 Ry (energy)
Lower bound of energy window to compute the DOS in.
See PEXSI.DOS.Ef.Reference.

PEXSI.DOS.Emax 1 Ry (energy)
Upper bound of energy window to compute the DOS in.
See PEXSI.DOS.Ef.Reference.

PEXSI.DOS.Ef.Reference true (logical)

If this flag is true, the bounds of the energy window (PEXSI.DOS.Emin and
PEXSI.DOS.Emax) are with respect to the Fermi level.

PEXSI.DOS.NPoints 200 (integer)

The number of points in the energy interval at which the DOS is computed. It is rounded up
to the nearest multiple of the number of available factorization groups, as the operations are
perfectly parallel and there will be no extra cost involved.

6.13.7 Calculation of the LDOS by selected-inversion

The local-density-of-states (LDOS) around a given reference energy ε, representing the contribution
to the charge density of the states with eigenvalues in the vicinity of ε, can be obtained formally by
a “one-pole expansion” with suitable broadening (see SIESTA-PEXSI paper).
Apart from the LDOS-specific options below, the “ordering”, “verbosity”, and “symbolic factoriza-
tion” options are honored.
The current version of the code generates a real-space grid file with extension SystemLabel.LDSI,
and (if netCDF is compiled-in) a file Rho.grid.nc (which unfortunately will overwrite any other
charge-density files produced in the same run).
NOTE: The LDOS computed with this procedure is not exactly the same as the vanilla SIESTA
LDOS, which uses an explicit energy interval. Here the broadening acts around a single value of the
energy.

PEXSI.LDOS false (logical)

Whether to compute the LDOS using the PEXSI technology.

86
 PEXSI.LDOS.Energy 0 Ry (energy)
The (absolute) energy at which to compute the LDOS.

PEXSI.LDOS.Broadening 0.01 Ry (energy)

The broadening parameter for the LDOS.

PEXSI.LDOS.NP-per-pole 〈PEXSI.NP-per-pole〉 (integer)

The value of this parameter supersedes PEXSI.NP-per-pole for the calculation of the LDOS,
which otherwise would keep idle all but PEXSI.NP-per-pole MPI processes, as it essentially
consists of a “one-pole” procedure.

6.14 Band-structure analysis

This calculation of the band structure is performed optionally after the geometry loop finishes, and
the output information written to the SystemLabel.bands file (see below for the format).

BandLinesScale pi/a (string)

Specifies the scale of the k vectors given in BandLines and BandPoints below. The options
are:
pi/a k-vector coordinates are given in Cartesian coordinates, in units of π/a, where a is the
lattice constant
ReciprocalLatticeVectors k vectors are given in reciprocal-lattice-vector coordinates
NOTE: you might need to define explicitly a LatticeConstant tag in your fdf file if you do not
already have one, and make it consistent with the scale of the k-points and any unit-cell vectors
you might have already defined.

%block BandLines 〈None〉 (block)

Specifies the lines along which band energies are calculated (usually along high-symmetry di-
rections). An example for an FCC lattice is:
%block BandLines
1 1.000 1.000 1.000 L # Begin at L
20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma
25 2.000 0.000 0.000 X # 25 points from gamma to X
30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma
%endblock BandLines
where the last column is an optional LATEX label for use in the band plot. If only given points
(not lines) are required, simply specify 1 in the first column of each line. The first column of
the first line must be always 1.
NOTE: this block is not used if BandPoints is present.

%block BandPoints 〈None〉 (block)

Band energies are calculated for the list of arbitrary k points given in the block. Units defined
by BandLinesScale as for BandLines. The generated SystemLabel.bands file will contain
the k point coordinates (in a.u.) and the corresponding band energies (in eV). Example:
%block BandPoints
0.000 0.000 0.000 # This is a comment. eg this is gamma

87
 1.000 0.000 0.000
0.500 0.500 0.500
%endblock BandPoints

See also BandLines.

WriteKbands false (logical)

~
If true, it writes the coordinates of the k vectors defined for band plotting, to the main output
file.

WriteBands false (logical)

If true, it writes the Hamiltonian eigenvalues corresponding to the ~k vectors defined for band
plotting, in the main output file.

6.14.1 Format of the .bands file

FermiEnergy (all energies in eV) \\

kmin, kmax (along the k-lines path, i.e. range of k in the band plot) \\
Emin, Emax (range of all eigenvalues) \\
NumberOfBands, NumberOfSpins (1 or 2), NumberOfkPoints \\
k1, ((ek(iband,ispin,1),iband=1,NumberOfBands),ispin=1,NumberOfSpins) \\
k2, ek \\
. \\
. \\
. \\
klast, ek \\
NumberOfkLines \\
kAtBegOfLine1, kPointLabel \\
kAtEndOfLine1, kPointLabel \\
. \\
. \\
. \\
kAtEndOfLastLine, kPointLabel \\

The gnubands postprocessing utility program (found in the Util/Bands directory) reads the
SystemLabel.bands for plotting. See the BandLines data descriptor above for more information.

6.14.2 Output of wavefunctions associated to bands

The user can optionally request that the wavefunctions corresponding to the computed bands be
written to file. They are written to the SystemLabel.bands.WFSX file. The relevant options are:

WFS.Write.For.Bands false (logical)

Instructs the program to compute and write the wave functions associated to the bands specified
(by a BandLines or a BandPoints block) to the file SystemLabel.WFSX.
The information in this file might be useful, among other things, to generate “fatbands” plots,
in which both band eigenvalues and information about orbital projections is presented. See the

88
 fat program in the Util/COOP directory for details.

WFS.Band.Min 1 (integer)
Specifies the lowest band index of the wave-functions to be written to the file SystemLabel.WFSX
for each k-point (all k-points in the band set are affected).

WFS.Band.Max number of orbitals (integer)

Specifies the highest band index of the wave-functions to be written to the file
SystemLabel.WFSX for each k-point (all k-points in the band set are affected).

6.15 Output of selected wavefunctions

The user can optionally request that specific wavefunctions are written to file. These wavefunctions
are re-computed after the geometry loop (if any) finishes, using the last (presumably converged)
density matrix produced during the last self-consistent field loop (after a final mixing). They are
written to the SystemLabel.selected.WFSX file.
Note that the complete set of wavefunctions obtained during the last iteration of the SCF loop will
be written to SystemLabel.fullBZ.WFSX if the COOP.Write option is in effect.
Note that the complete set of wavefunctions obtained during the last iteration of the SCF loop will
be written to a NetCDF file WFS.nc if the Diag.UseNewDiagk option is in effect.

WaveFuncKPointsScale pi/a (string)

Specifies the scale of the k vectors given in WaveFuncKPoints below. The options are:
pi/a k-vector coordinates are given in Cartesian coordinates, in units of π/a, where a is the
lattice constant
ReciprocalLatticeVectors k vectors are given in reciprocal-lattice-vector coordinates

%block WaveFuncKPoints 〈None〉 (block)

Specifies the k-points at which the electronic wavefunction coefficients are written. An example
for an FCC lattice is:
%block WaveFuncKPoints
0.000 0.000 0.000 from 1 to 10 # Gamma wavefuncs 1 to 10
2.000 0.000 0.000 1 3 5 # X wavefuncs 1,3 and 5
1.500 1.500 1.500 # K wavefuncs, all
%endblock WaveFuncKPoints

The index of a wavefunction is defined by its energy, so that the first one has lowest energy.
The user can also narrow the energy-range used with the WFS.Energy.Min and
WFS.Energy.Max options (both take an energy (with units) as extra argument – see sec-
tion 6.17.3). Care should be taken to make sure that the actual values of the options make
sense.
The output of the wavefunctions in described in Section 6.15.

WriteWaveFunctions false (logical)

If true, it writes to the output file a list of the wavefunctions actually written to the
SystemLabel.selected.WFSX file, which is always produced.

89
The unformatted WFSX file contains the information of the k-points for which wavefunctions coeffi-
cients are written, and the energies and coefficients of each wavefunction which was specified in the
input file (see WaveFuncKPoints descriptor above). It also contains information on the atomic
species and the orbitals for postprocessing purposes.
NOTE: The SystemLabel.WFSX file is in a more compact form than the old WFS, and the wave-
functions are output in single precision. The Util/WFS/wfsx2wfs program can be used to convert
to the old format.
The readwf and readwfsx postprocessing utilities programs (found in the Util/WFS directory) read
the SystemLabel.WFS or SystemLabel.WFSX files, respectively, and generate a readable file.

6.16 Densities of states

6.16.1 Total density of states

There are several options to obtain the total density of states:

• The Hamiltonian eigenvalues for the SCF sampling ~k points can be dumped into SystemLa-
bel.EIG in a format analogous to SystemLabel.bands, but without the kmin, kmax, emin,
emax information, and without the abscissa. The Eig2DOS postprocessing utility can be then
used to obtain the density of states. See the WriteEigenvalues descriptor.

• As a side-product of a partial-density-of-states calculation (see below)

• As one of the files produced by the Util/COOP/mprop during the off-line analysis of the elec-
tronic structure. This method allows the flexibility of specifying energy ranges and resolutions
at will, without re-running SIESTA See Sec. 6.17.3.

• Using the inertia-counting routines in the PEXSI solver (see Sec. 6.13.6).

6.16.2 Partial (projected) density of states

There are two options to obtain the partial density of states

• Using the options below

• Using the Util/COOP/mprop program for the off-line analysis of the electronic structure in
PDOS mode. This method allows the flexibility of specifying energy ranges, orbitals, and
resolutions at will, without re-running SIESTA. See Sec. 6.17.3.

%block ProjectedDensityOfStates 〈None〉 (block)

Instructs to write the Total Density Of States (Total DOS) and the Projected Density Of
States (PDOS) on the basis orbitals, between two given energies, in files SystemLabel.DOS and
SystemLabel.PDOS, respectively. The block must be a single line with the energies of the range
for PDOS projection, (relative to the program’s zero, i.e. the same as the eigenvalues printed by
the program), the peak width (an energy) for broadening the eigenvalues, the number of points
in the energy window, and the energy units. An example is:

90
 %block ProjectedDensityOfStates
-20.00 10.00 0.200 500 eV
%endblock ProjectedDensityOfStates

By default the projected density of states is generated for the same grid of points in re-
ciprocal space as used for the SCF calculation. However, a separate set of K-points, usu-
ally on a finer grid, can be generated using one of the options PDOS.kgrid.Cutoff or
PDOS.kgrid.MonkhorstPack. The format of these options is exactly the same as for
kgrid.Cutoff and kgrid.MonkhorstPack, respectively. Note that if a gamma point cal-
culation is being used in the SCF part, especially as part of a geometry optimisation, and this
is then to be run with a grid of K-points for the PDOS calculation it is more efficient to run
the SCF phase first and then restart to perform the PDOS evaluation using the density matrix
saved from the SCF phase.
NOTE: the two energies of the range must be ordered, with lowest first.
The total DOS is stored in a file called SystemLabel.DOS. The format of this file is:
Energy value, Total DOS (spin up), Total DOS (spin down)

The Projected Density Of States for all the orbitals in the unit cell is dumped sequentially into
a file called SystemLabel.PDOS. This file is structured using spacing and xml tags. A machine-
readable (but not very human readable) xml file SystemLabel.PDOS.xml is also produced.
Both can be processed by the program in Util/pdosxml. The SystemLabel.PDOS file can be
processed by utilites in Util/Contrib/APostnikov.
In all cases, the units for the DOS are (number of states/eV), and the Total DOS, g(), is
normalized as follows:
Z ∞
g()d = number of basis orbitals in unit cell (14)
−∞

6.16.3 Local density of states

The LDOS is formally the DOS weighted by the amplitude of the corresponding wavefunctions at
different points in space, and is then a function of energy and position. SIESTA can output the
LDOS integrated over a range of energies. This information can be used to obtain simple STM
images in the Tersoff-Hamann approximation (See Util/STM/simple-stm).

%block LocalDensityOfStates 〈None〉 (block)

Instructs to write the LDOS, integrated between two given energies, at the mesh used by
DHSCF, in file SystemLabel.LDOS. This file can be read by routine IORHO, which may be
used by an application program in later versions. The block must be a single line with the
energies of the range for LDOS integration (relative to the program’s zero, i.e. the same as the
eigenvalues printed by the program) and their units. An example is:
%block LocalDensityOfStates
-3.50 0.00 eV
%endblock LocalDensityOfStates

NOTE: the two energies of the range must be ordered, with lowest first.

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6.17 Options for chemical analysis

6.17.1 Mulliken charges and overlap populations

WriteMullikenPop 0 (integer)
It determines the level of Mulliken population analysis printed:
0 none
1 atomic and orbital charges
2 atomic, orbital and atomic overlap populations
3 atomic, orbital, atomic overlap and orbital overlap populations
The order of the orbitals in the population lists is defined by the order of atoms. For each atom,
populations for PAO orbitals and double-z, triple-z, etc... derived from them are displayed
first for all the angular momenta. Then, populations for perturbative polarization orbitals are
written. Within a l-shell be aware that the order is not conventional, being y, z, x for p orbitals,
and xy, yz, z 2 , xz, and x2 − y 2 for d orbitals.

MullikenInSCF false (logical)

If true, the Mulliken populations will be written for every SCF step at the level of detail specified
in WriteMullikenPop. Useful when dealing with SCF problems, otherwise too verbose.

SpinInSCF true (logical)

If true, the size and components of the (total) spin polarization will be printed at every SCF
step. This is analogous to the MullikenInSCF feature. Enabled by default for calculations
involving spin.

6.17.2 Voronoi and Hirshfeld atomic population analysis

WriteHirshfeldPop false (logical)
If true, the program calculates and prints the Hirshfeld “net” atomic populations on each atom
in the system. For a definition of the Hirshfeld charges, see Hirshfeld, Theo Chem Acta 44, 129
(1977) and Fonseca et al, J. Comp. Chem. 25, 189 (2003). Hirshfeld charges are more reliable
than Mulliken charges, specially for large basis sets. The number printed is the total net charge
of the atom: the variation from the neutral charge, in units of |e|: positive (negative) values
indicate deficiency (excess) of electrons in the atom.

WriteVoronoiPop false (logical)

If true, the program calculates and prints the Voronoi “net” atomic populations on each atom
in the system. For a definition of the Voronoi charges, see Bickelhaupt et al, Organometallics
15, 2923 (1996) and Fonseca et al, J. Comp. Chem. 25, 189 (2003). Voronoi charges are more
reliable than Mulliken charges, specially for large basis sets. The number printed is the total
net charge of the atom: the variation from the neutral charge, in units of |e|: positive (negative)
values indicate deficiency (excess) of electrons in the atom.

The Hirshfeld and Voronoi populations (partial charges) are computed by default only at the end of
the program (i.e., for the final geometry, after self-consistency). The following options allow more
control:

92
 PartialChargesAtEveryGeometry false (logical)
The Hirshfeld and Voronoi populations are computed after self-consistency is achieved, for all
the geometry steps.

PartialChargesAtEverySCFStep false (logical)

The Hirshfeld and Voronoi populations are computed for every step of the self-consistency
process.

Performance note: The default behavior (computing at the end of the program) involves an extra
calculation of the charge density.

6.17.3 Crystal-Orbital overlap and hamilton populations (COOP/COHP)

These curves are quite useful to analyze the electronic structure to get insight about bonding charac-
teristics. See the Util/COOP directory for more details. The COOP.Write option must be activated
to get the information needed.
References:

• Original COOP reference: Hughbanks, T.; Hoffmann, R., J. Am. Chem. Soc., 1983, 105, 3528.

• Original COHP reference: Dronskowski, R.; BlÃűchl, P. E., J. Phys. Chem., 1993, 97, 8617.

• A tutorial introduction: Dronskowski, R. Computational Chemistry of Solid State Materials;

Wiley-VCH: Weinheim, 2005.

• Online material maintained by R. Dronskowski’s group: http://www.cohp.de/

COOP.Write false (logical)

Instructs the program to generate SystemLabel.fullBZ.WFSX (packed wavefunction file) and
SystemLabel.HSX (H, S and X_ ij file), to be processed by Util/COOP/mprop to generate
COOP/COHP curves, (projected) densities of states, etc.
The .WFSX file is in a more compact form than the usual .WFS, and the wavefunctions are output
in single precision. The Util/wfsx2wfs program can be used to convert to the old format. The
HSX file is in a more compact form than the usual HS, and the Hamiltonian, overlap matrix,
and relative-positions array (which is always output, even for gamma-point only calculations)
are in single precision.
The user can narrow the energy-range used (and save some file space) by using the
WFS.Energy.Min and WFS.Energy.Max options (both take an energy (with units) as
extra argument), and/or the WFS.Band.Min and WFS.Band.Max options. Care should
be taken to make sure that the actual values of the options make sense.
Note that the band range options could also affect the output of wave-functions associated to
bands (see section 6.14.2), and that the energy range options could also affect the output of
user-selected wave-functions with the WaveFuncKPoints block (see section 6.15).

WFS.Energy.Min −∞ (energy)
Specifies the lowest value of the energy (eigenvalue) of the wave-functions to be written to the
file SystemLabel.fullBZ.WFSX for each k-point (all k-points in the BZ sampling are affected).

93
 WFS.Energy.Max ∞ (energy)
Specifies the highest value of the energy (eigenvalue) of the wave-functions to be written to the
file SystemLabel.fullBZ.WFSX for each k-point (all k-points in the BZ sampling are affected).

6.18 Optical properties

OpticalCalculation false (logical)
If specified, the imaginary part of the dielectric function will be calculated and stored in a file
called SystemLabel.EPSIMG. The calculation is performed using the simplest approach based
on the dipolar transition matrix elements between different eigenfunctions of the self-consistent
Hamiltonian. For molecules the calculation is performed using the position operator matrix
elements, while for solids the calculation is carried out in the momentum space formulation.
Corrections due to the non-locality of the pseudopotentials are introduced in the usual way.

Optical.Energy.Minimum 0 Ry (energy)
This specifies the minimum of the energy range in which the frequency spectrum will be calcu-
lated.

Optical.Energy.Maximum 10 Ry (energy)
This specifies the maximum of the energy range in which the frequency spectrum will be calcu-
lated.

Optical.Broaden 0 Ry (energy)
If this is value is set then a Gaussian broadening will be applied to the frequency values.

Optical.Scissor 0 Ry (energy)
Because of the tendency of DFT calculations to under estimate the band gap, a rigid shift of the
unoccupied states, known as the scissor operator, can be added to correct the gap and thereby
improve the calculated results. This shift is only applied to the optical calculation and no where
else within the calculation.

Optical.NumberOfBands all bands (integer)

This option controls the number of bands that are included in the optical property calculation.
Clearly this number must be larger than the number of occupied bands and less than or equal
to the number of basis functions (which determines the number of unoccupied bands available).
Note, while including all the bands may be the most accurate choice this will also be the most
expensive!

%block Optical.Mesh 〈None〉 (block)

This block contains 3 numbers that determine the mesh size used for the integration across the
Brillouin zone. For example:
%block Optical.Mesh
5 5 5
%endblock Optical.Mesh
The three values represent the number of mesh points in the direction of each reciprocal lattice
vector.

Optical.OffsetMesh false (logical)

94
 If set to true, then the mesh is offset away from the gamma point for odd numbers of points.

Optical.PolarizationType polycrystal (string)

This option has three possible values that represent the type of polarization to be used in the
calculation. The options are
polarized implies the application of an electric field in a given direction
unpolarized implies the propagation of light in a given direction
polycrystal In the case of the first two options a direction in space must be specified for the
electric field or propagation using the Optical.Vector data block.

%block Optical.Vector 〈None〉 (block)

This block contains 3 numbers that specify the vector direction for either the electric field or
light propagation, for a polarized or unpolarized calculation, respectively. A typical block might
look like:
%block Optical.Vector
1.0 0.0 0.5
%endblock Optical.Vector

6.19 Macroscopic polarization

%block PolarizationGrids 〈None〉 (block)
If specified, the macroscopic polarization will be calculated using the geometric Berry phase
approach (R.D. King-Smith, and D. Vanderbilt, PRB 47, 1651 (1993)). In this method the
electronic contribution to the macroscopic polarization, along a given direction, is calculated
using a discretized version of the formula
M Z |Gk |
if qe δ
Z X
Pe,k = dk⊥ dkk hukn | |ukn i (15)
8π 3 A n=1 0
δkk

where f is the occupation (2 for a non-magnetic system), qe the electron charge, M is the
number of occupied bands (the system must be an insulator), and ukn are the periodic Bloch
functions. Gk is the shortest reciprocal vector along the chosen direction.
As it can be seen in formula (15), to compute each component of the polarization we must
perform a surface integration of the result of a 1-D integral in the selected direction. The grids
for the calculation along the direction of each of the three lattice vectors are specified in the
block PolarizationGrids.
%block PolarizationGrids
10 3 4 yes
2 20 2 no
4 4 15
%endblock PolarizationGrids
All three grids must be specified, therefore a 3 × 3 matrix of integer numbers must be given:
the first row specifies the grid that will be used to calculate the polarization along the direction
of the first lattice vector, the second row will be used for the calculation along the the direction
of the second lattice vector, and the third row for the third lattice vector. The numbers in
the diagonal of the matrix specifie the number of points to be used in the one dimensional

95
 line integrals along the different directions. The other numbers specifie the mesh used in the
surface integrals. The last column specifies if the bidimensional grids are going to be diplaced
from the origin or not, as in the Monkhorst-Pack algorithm (PRB 13, 5188 (1976)). This last
column is optional. If the number of points in one of the grids is zero, the calculation will not
be performed for this particular direction.
For example, in the given example, for the computation in the direction of the first lattice
vector, 15 points will be used for the line integrals, while a 3 × 4 mesh will be used for the
surface integration. This last grid will be displaced from the origin, so Γ will not be included
in the bidimensional integral. For the directions of the second and third lattice vectors, the
number of points will be 20 and 2 × 2, and 15 and 4 × 4, respectively.
It has to be stressed that the macroscopic polarization can only be meaningfully calculated
using this approach for insulators. Therefore, the presence of an energy gap is necessary, and
no band can cross the Fermi level. The program performs a simple check of this condition, just
by counting the electrons in the unit cell ( the number must be even for a non-magnetic system,
and the total spin polarization must have an integer value for spin polarized systems), however
is the responsability of the user to check that the system under study is actually an insulator
(for both spin components if spin polarized).
The total macroscopic polarization, given in the output of the program, is the sum of the
electronic contribution (calculated as the Berry phase of the valence bands), and the ionic con-
tribution, which is simply defined as the sum of the atomic positions within the unit cell multiply
by the ionic charges ( N
P a
i Zi ri ). In the case of the magnetic systems, the bulk polarization for
each spin component has been defined as
Na
1X
Pσ = Pσe + Zi ri (16)
2 i
Na is the number of atoms in the unit cell, and ri and Zi are the positions and charges of the
ions.
It is also worth noting, that the macroscopic polarization given by formula (15) is only defined
modulo a “quantum” of polarization (the bulk polarization per unit cell is only well defined
modulo f qe R, being R an arbitrary lattice vector). However, the experimentally observable
quantities are associated to changes in the polarization induced by changes on the atomic
positions (dynamical charges), strains (piezoelectric tensor), etc... The calculation of those
changes, between different configurations of the solid, will be well defined as long as they are
smaller than the “quantum”, i.e. the perturbations are small enough to create small changes in
the polarization.

BornCharge false (logical)

If true, the Born effective charge tensor is calculated for each atom by finite differences, by
calculating the change in electric polarization (see PolarizationGrids) induced by the small
displacements generated for the force constants calculation (see MD.TypeOfRun FC):

∗ Ω0 ∂Pα 
Zi,α,β =  (17)
e ∂ui,β q=0

where e is the charge of an electron and Ω0 is the unit cell volume.

To calculate the Born charges it is necessary to specify both the Born charge flag and the mesh
used to calculate the polarization, for example:

96
 %block PolarizationGrids
7 3 3
3 7 3
3 3 7
%endblock PolarizationGrids
BornCharge True

The Born effective charge matrix is then written to the file SystemLabel.BC.
The method by which the polarization is calculated may introduce an arbitrary phase (polar-
ization quantum), which in general is far larger than the change in polarization which results
from the atomic displacement. It is removed during the calculation of the Born effective charge
tensor.
The Born effective charges allow the calculation of LO-TO splittings and infrared activities. The
version of the Vibra utility code in which these magnitudes are calculated is not yet distributed
with SIESTA, but can be obtained form Tom Archer ([email protected]).

6.20 Maximally Localized Wannier Functions.

Interface with the wannier90 code

wannier90 (http://www.wannier.org) is a code to generate maximally localized wannier functions

according to the original Marzari and Vanderbilt recipe.
It is strongly recommended to read the original papers on which this method is based and the
documentation of wannier90 code. Here we shall focus only on those internal SIESTA variables
required to produce the files that will be processed by wannier90.
A complete list of examples and tests (including molecules, metals, semiconductors, insulators,
magnetic systems, plotting of Fermi surfaces or interpolation of bands), can be downloaded from
http://personales.unican.es/junqueraj/Wannier-examples.tar.gz
NOTE: The Bloch functions produced by a first-principles code have arbitrary phases that depend
on the number of processors used and other possibly non-reproducible details of the calculation. In
what follows it is essential to maintain consistency in the handling of the overlap and Bloch-funcion
files produced and fed to wannier90.

Siesta2Wannier90.WriteMmn false (logical)

This flag determines whether the overlaps between the periodic part of the Bloch states at
neighbour k-points are computed and dumped into a file in the format required by wannier90.
These overlaps are defined in Eq. (27) in the paper by N. Marzari et al., Review of Modern
Physics 84, 1419 (2012), or Eq. (1.7) of the Wannier90 User Guide, Version 2.0.1.
The k-points for which the overlaps will be computed are read from a .nnkp file produced by
wannier90. It is strongly recommended for the user to read the corresponding user guide.
The overlap matrices are written in a file with extension .mmn.

Siesta2Wannier90.WriteAmn false (logical)

This flag determines whether the overlaps between Bloch states and trial localized orbitals are
computed and dumped into a file in the format required by wannier90. These projections are
defined in Eq. (16) in the paper by N. Marzari et al., Review of Modern Physics 84, 1419
(2012), or Eq. (1.8) of the Wannier90 User Guide, Version 2.0.1.

97
 The localized trial functions to use are taken from the .nnkp file produced by wannier90. It is
strongly recommended for the user to read the corresponding user guide.
The overlap matrices are written in a file with extension .amn.

Siesta2Wannier90.WriteEig false (logical)

Flag that determines whether the Kohn-Sham eigenvalues (in eV) at each point in the
Monkhorst-Pack mesh required by wannier90 are written to file. This file is mandatory in
wannier90 if any of disentanglement, plot_bands, plot_fermi_surface or hr_plot options are
set to true in the wannier90 input file.
The eigenvalues are written in a file with extension .eigW. This extension is chosen to avoid
name clashes with SIESTA’s standard eigenvalue file in case-insensitive filesystems.

Siesta2Wannier90.WriteUnk false (logical)

Produces UNKXXXXX.Y files which contain the periodic part of a Bloch function in the unit cell
on a grid given by global unk_nx, unk_ny, unk_nz variables. The name of the output files is
assumed to have the previous form, where the XXXXXX refer to the k-point index (from 00001 to
the total number of k-points considered), and the Y refers to the spin component (1 or 2)
The periodic part of the Bloch functions is defined by
~ ~
cnµ (~k)eik·(~rµ +RÂă−~r) φµ (~r − ~rµ − R),
~
X
un~k (~r) = (18)
~
RÂăµ

~ is a basis set atomic orbital centered on atom µ in the unit cell R,

where φµ (~r − ~rµ − R) ~ and
~
cnµ (k) are the coefficients of the wave function. The latter must be identical to the ones used
for wannierization in Mmn . (See the above comment about arbitrary phases.)

Siesta2Wannier90.UnkGrid1 〈mesh points along A〉 (integer)

Number of points along the first lattice vector in the grid where the periodic part of the wave
functions will be plotted.

Siesta2Wannier90.UnkGrid2 〈mesh points along B〉 (integer)

Number of points along the second lattice vector in the grid where the periodic part of the wave
functions will be plotted.

Siesta2Wannier90.UnkGrid3 〈mesh points along C〉 (integer)

Number of points along the third lattice vector in the grid where the periodic part of the wave
functions will be plotted.

Siesta2Wannier90.UnkGridBinary true (logical)

Flag that determines whether the periodic part of the wave function in the real space grid is
written in binary format (default) or in ASCII format.

Siesta2Wannier90.NumberOfBands occupied bands (integer)

In spin unpolarized calculations, number of bands that will be initially considered by SIESTA
to generate the information required by wannier90. Note that it should be at least as large
as the index of the highest-lying band in the wannier90 post-processing. For example, if the
wannierization is going to involve bands 3 to 5, the SIESTA number of bands should be at
least 5. Bands 1 and 2 should appear in a “excluded” list.

98
 NOTE: you are highly encouraged to explicitly specify the number of bands.

Siesta2Wannier90.NumberOfBandsUp 〈Siesta2Wannier90.NumberOfBands〉
(integer)
In spin-polarized calculations, number of bands with spin up that will be initially considered
by SIESTA to generate the information required by wannier90.

Siesta2Wannier90.NumberOfBandsDown 〈Siesta2Wannier90.NumberOfBands〉
(integer)
In spin-polarized calculations, number of bands with spin down that will be initially considered
by SIESTA to generate the information required by wannier90.

6.21 Systems with net charge or dipole, and electric fields

NetCharge 0 (real)
Specify the net charge of the system (in units of |e|). For charged systems, the energy converges
very slowly versus cell size. For molecules or atoms, a Madelung correction term is applied to
the energy to make it converge much faster with cell size (this is done only if the cell is SC, FCC
or BCC). For other cells, or for periodic systems (chains, slabs or bulk), this energy correction
term can not be applied, and the user is warned by the program. It is not advised to do charged
systems other than atoms and molecules in SC, FCC or BCC cells, unless you know what you
are doing.
Use: For example, the F− ion would have NetCharge -1 , and the Na+ ion would have
NetCharge 1. Fractional charges can also be used.

SimulateDoping false (logical)

This option instructs the program to add a background charge density to simulate doping.
The new “doping” routine calculates the net charge of the system, and adds a compensating
background charge that makes the system neutral. This background charge is constant at points
of the mesh near the atoms, and zero at points far from the atoms. This simulates situations
like doped slabs, where the extra electrons (holes) are compensated by oposite charges at the
material (the ionized dopant impurities), but not at the vacuum. This serves to simulate
properly doped systems in which there are large portions of vacuum, such as doped slabs.
See Tests/sic-slab.

%block ExternalElectricField 〈None〉 (block)

It specifies an external electric field for molecules, chains and slabs. The electric field should be
orthogonal to ‘bulk directions’, like those parallel to a slab (bulk electric fields, like in dielectrics
or ferroelectrics, are not allowed). If it is not, an error message is issued and the components
of the field in bulk directions are suppressed automatically. The input is a vector in Cartesian
coordinates, in the specified units. Example:
%block ExternalElectricField
0.000 0.000 0.500 V/Ang
%endblock ExternalElectricField
Starting with version 4.0, applying an electric field perpendicular to a slab will by default enable
the slab dipole correction, see SlabDipoleCorrection. To reproduce older calculations, set
this correction option explicitly to false in the input file.

99
SlabDipoleCorrection false (logical)
If true, SIESTA calculates the electric field required to compensate the dipole of the system
at every iteration of the self-consistent cycle. The potential added to the grid corresponds to
that of a dipole layer at the middle of the vacuum layer. For slabs, this exactly compensates the
electric field at the vacuum created by the dipole moment of the system, thus allowing to treat
asymmetric slabs (including systems with an adsorbate on one surface) and compute properties
such as the work funcion of each of the surfaces.
NOTE: If the program is fed a starting density matrix from an uncorrected calculation (i.e.,
with an exagerated dipole), the first iteration might use a compensating field that is too big,
with the risk of taking the system out of the convergence basin. In that case, it is advisable to
use the SCF.Mix.First option to request a mix of the input and output density matrices after
that first iteration.
See Tests/sic-slab.
This will default to true if an external field is applied to a slab calculation, otherwise it will
default to false.
For TranSIESTA calculations an additional step is added. For more than 1 electrode, the
dipole moments along the semi-infinite directions are removed. Otherwise, for 1 electrode, the
dipole is only allowed along the semi-infinite direction.

%block Geometry.Hartree 〈None〉 (block)

Allows introduction of regions with changed Hartree potential. Introducing a potential can act
as a repulsion (positive value) or attraction (negative value) region.
The regions are defined as geometrical objects and there are no limits to the number of defined
geometries.
Details regarding this implementation may be found in Papior et al. [9] .
Currently 4 different kinds of geometries are allowed:
Infinite plane Define a geometry by an infinite plane which cuts the unit-cell.
This geometry is defined by a single point which is in the plane and a vector normal to the
plane.
This geometry has 3 different settings:
delta An infinite plane with δ-height.
gauss An infinite plane with a Gaussian distributed height profile.
exp An infinite plane with an exponentially distributed height profile.
Bounded plane Define a geometric plane which is bounded, i.e. not infinite.
This geometry is defined by an origo of the bounded plane and two vectors which span the
plane, both originating in the respective origo.
This geometry has 3 different settings:
delta A plane with δ-height.
gauss A plane with a Gaussian distributed height profile.
exp A plane with an exponentially distributed height profile.
Box This geometry is defined by an origo of the box and three vectors which span the box, all
originating from the respective origo.

100
 This geometry has 1 setting:
delta No decay-region outside the box.
Spheres This geometry is defined by a list of spheres and a common radii.
This geometry has 2 settings:
gauss All spheres have an gaussian distribution about their centre.
exp All spheres have an exponential decay.
Here is a list of all options combined in one block:
%block Geometry.Hartree
plane 1. eV # The lifting potential on the geometry
delta
1.0 1.0 1.0 Ang # An intersection point, in the plane
1.0 0.5 0.2 # The normal vector to the plane
plane -1. eV # The lifting potential on the geometry
gauss 1. 2. Ang # the std. and the cut-off length
1.0 1.0 1.0 Ang # An intersection point, in the plane
1.0 0.5 0.2 # The normal vector to the plane
plane 1. eV # The lifting potential on the geometry
exp 1. 2. Ang # the half-length and the cut-off length
1.0 1.0 1.0 Ang # An intersection point, in the plane
1.0 0.5 0.2 # The normal vector to the plane
square 1. eV # The lifting potential on the geometry
delta
1.0 1.0 1.0 Ang # The starting point of the square
2.0 0.5 0.2 Ang # The first spanning vector
0.0 2.5 0.2 Ang # The second spanning vector
square 1. eV # The lifting potential on the geometry
gauss 1. 2. Ang # the std. and the cut-off length
1.0 1.0 1.0 Ang # The starting point of the square
2.0 0.5 0.2 Ang # The first spanning vector
0.0 2.5 0.2 Ang # The second spanning vector
square 1. eV # The lifting potential on the geometry
exp 1. 2. Ang # the half-length and the cut-off length
1.0 1.0 1.0 Ang # The starting point of the square
2.0 0.5 0.2 Ang # The first spanning vector
0.0 2.5 0.2 Ang # The second spanning vector
box 1. eV # The lifting potential on the geometry
delta
1.0 1.0 1.0 Ang # Origo of the box
2.0 0.5 0.2 Ang # The first spanning vector
0.0 2.5 0.2 Ang # The second spanning vector
0.0 0.5 3.2 Ang # The third spanning vector
coords 1. eV # The lifting potential on the geometry
gauss 2. 4. Ang # First is std. deviation, second is cut-off radii
2 spheres # How many spheres in the following lines
0.0 4. 2. Ang # The centre coordinate of 1. sphere
1.3 4. 2. Ang # The centre coordinate of 2. sphere
coords 1. eV # The lifting potential on the geometry
exp 2. 4. Ang # First is half-length, second is cut-off radii
2 spheres # How many spheres in the following lines
0.0 4. 2. Ang # The centre coordinate of 1. sphere

101
 1.3 4. 2. Ang # The centre coordinate of 2. sphere
%endblock Geometry.Hartree

%block Geometry.Charge 〈None〉 (block)

This is similar to the Geometry.Hartree block. However, instead of specifying a potential,
one defines the total charge that is spread on the geometry.
To see how the input should be formatted, see Geometry.Hartree and remove the unit-
specification. Note that the input value is number of electrons (similar to NetCharge).
Details regarding this implementation may be found in Papior et al. [9] .

6.22 Output of charge densities and potentials on the grid

SIESTA represents these magnitudes on the real-space grid. The following options control the gen-
eration of the appropriate files, which can be processed by the programs in the Util/Grid directory,
and also by Andrei Postnikov’s utilities in Util/Contrib/APostnikov. See also Util/Denchar for
an alternative way to plot the charge density (and wavefunctions).

SaveRho false (logical)

Instructs to write the valence pseudocharge density at the mesh used by DHSCF, in file
SystemLabel.RHO.
NOTE: file .RHO is only written, not read, by siesta. This file can be read by routine IORHO,
which may be used by other application programs.
If netCDF support is compiled in, the file Rho.grid.nc is produced.

SaveDeltaRho false (logical)

Instructs to write δρ(~r) = ρ(~r) − ρatm (~r), i.e., the valence pseudocharge density minus the sum
of atomic valence pseudocharge densities. It is done for the mesh points used by DHSCF and it
comes in file SystemLabel.DRHO. This file can be read by routine IORHO, which may be used
by an application program in later versions.
NOTE: file .DRHO is only written, not read, by siesta.
If netCDF support is compiled in, the file DeltaRho.grid.nc is produced.

SaveRhoXC false (logical)

Instructs to write the valence pseudocharge density at the mesh, including the nonlocal core
corrections used to calculate the exchange-correlation energy, in file SystemLabel.RHOXC.
Use: File .RHOXC is only written, not read, by siesta.
If netCDF support is compiled in, the file RhoXC.grid.nc is produced.

SaveElectrostaticPotential false (logical)

Instructs to write the total electrostatic potential, defined as the sum of the hartree potential
plus the local pseudopotential, at the mesh used by DHSCF, in file SystemLabel.VH. This file
can be read by routine IORHO, which may be used by an application program in later versions.
Use: File .VH is only written, not read, by siesta.
If netCDF support is compiled in, the file ElectrostaticPotential.grid.nc is produced.

SaveNeutralAtomPotential false (logical)

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 Instructs to write the neutral-atom potential, defined as the sum of the hartree potential of a
“pseudo atomic valence charge” plus the local pseudopotential, at the mesh used by DHSCF,
in file SystemLabel.VNA. It is written at the start of the self-consistency cycle, as this potential
does not change.
Use: File .VNA is only written, not read, by siesta.
If netCDF support is compiled in, the file Vna.grid.nc is produced.

SaveTotalPotential false (logical)

Instructs to write the valence total effective local potential (local pseudopotential + Hartree +
Vxc), at the mesh used by DHSCF, in file SystemLabel.VT. This file can be read by routine
IORHO, which may be used by an application program in later versions.
Use: File .VT is only written, not read, by siesta.
If netCDF support is compiled in, the file TotalPotential.grid.nc is produced.
NOTE: a side effect; the vacuum level, defined as the effective potential at grid points with
zero density, is printed in the standard output whenever such points exist (molecules, slabs) and
either SaveElectrostaticPotential or SaveTotalPotential are true. In a symetric (nonpo-
lar) slab, the work function can be computed as the difference between the vacuum level and
the Fermi energy.

SaveIonicCharge false (logical)

Instructs to write the soft diffuse ionic charge at the mesh used by DHSCF, in file
SystemLabel.IOCH. This file can be read by routine IORHO, which may be used by an ap-
plication program in later versions. Remember that, within the SIESTA sign convention, the
electron charge density is positive and the ionic charge density is negative.
Use: File .IOCH is only written, not read, by siesta.
If netCDF support is compiled in, the file Chlocal.grid.nc is produced.

SaveTotalCharge false (logical)

Instructs to write the total charge density (ionic+electronic) at the mesh used by DHSCF, in
file SystemLabel.TOCH. This file can be read by routine IORHO, which may be used by an
application program in later versions. Remember that, within the SIESTA sign convention,
the electron charge density is positive and the ionic charge density is negative.
Use: File .TOCH is only written, not read, by siesta.
If netCDF support is compiled in, the file TotalCharge.grid.nc is produced.

SaveBaderCharge false (logical)

Instructs the program to save the charge density for further post-processing by a Bader-analysis
program. This “Bader charge” is the sum of the electronic valence charge density and a set of
“model core charges” placed at the atomic sites. For a given atom, the model core charge is
a generalized Gaussian, but confined to a radius of 1.0 Bohr (by default), and integrating to
the total core charge (Z-Zval ). These core charges are needed to provide local maxima for the
charge density at the atomic sites, which are not guaranteed in a pseudopotential calculation.
For hydrogen, an artificial core of 1 electron is added, with a confinement radius of 0.6 Bohr by
default. The Bader charge is projected on the grid points of the mesh used by DHSCF, and saved
in file SystemLabel.BADER. This file can be post-processed by the program Util/grid2cube
to convert it to the “cube” format, accepted by several Bader-analysis programs (for example,

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 see http://theory.cm.utexas.edu/bader/). Due to the need to represent a localized core
charge, it is advisable to use a moderately high MeshCutoff when invoking this option (300-500
Ry). The size of the “basin of attraction” around each atom in the Bader analysis should be
monitored to check that the model core charge is contained in it.
The radii for the model core charges can be specified in the input fdf file. For example:
bader-core-radius-standard 1.3 Bohr
bader-core-radius-hydrogen 0.4 Bohr

The suggested way to run the Bader analysis with the Univ. of Texas code is to use both the
RHO and BADER files (both in “cube” format), with the BADER file providing the “reference”
and the RHO file the actual significant valence charge data which is important in bonding. (See
the notes for pseudopotential codes in the above web page.) For example, for the h2o-pop
example:
bader h2o-pop.RHO.cube -ref h2o-pop.BADER.cube

If netCDF support is compiled in, the file BaderCharge.grid.nc is produced.

AnalyzeChargeDensityOnly false (logical)

If true, the program optionally generates charge density files and computes partial atomic
charges (Hirshfeld, Voronoi, Bader) from the information in the input density matrix, and
stops. This is useful to analyze the properties of the charge density without a diagonalization
step, and with a user-selectable mesh cutoff. Note that the DM.UseSaveDM option should
be active. Note also that if an initial density matrix (DM file) is used, it is not normalized. All
the relevant fdf options for charge-density file production and partial charge calculation can be
used with this option.

SaveInitialChargeDensity false (logical)

If true, the program generates a SystemLabel.RHOINIT file (and a RhoInit.grid.nc file if
netCDF support is compiled in) containing the charge density used to start the first self-
consistency step, and it stops. Note that if an initial density matrix (DM file) is used, it is
not normalized. This is useful to generate the charge density associated to “partial” DMs, as
created by progras such as dm_creator and dm_filter.
(This option is to be deprecated in favor of AnalyzeChargeDensityOnly).

6.23 Auxiliary Force field

It is possible to supplement the DFT interactions with a limited set of force-field options, typically
useful to simulate dispersion interactions. It is not yet possible to turn off DFT and base the
dynamics only on the force field. The GULP program should be used for that.

%block MM.Potentials 〈None〉 (block)

This block allows the input of molecular mechanics potentials between species. The following
potentials are currently implemented:
• C6, C8, C10 powers of the Tang-Toennes damped dispersion potential.
• A harmonic interaction.
• A dispersion potential of the Grimme type (similar to the C6 type but with a different

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 damping function). (See S. Grimme, J. Comput. Chem. Vol 27, 1787-1799 (2006)). See
also MM.Grimme.D and MM.Grimme.S6 below.
The format of the input is the two species numbers that are to interact, the potential name (C6,
C8, C10, harm, or Grimme), followed by the potential parameters. For the damped dispersion
potentials the first number is the coefficient and the second is the exponent of the damping
term (i.e., a reciprocal length). A value of zero for the latter term implies no damping. For the
harmonic potential the force constant is given first, followed by r0. For the Grimme potential
C6 is given first, followed by the (corrected) sum of the van der Waals radii for the interacting
species (a real length). Positive values of the C6, C8, and C10 coefficients imply attractive
potentials.
%block MM.Potentials
1 1 C6 32.0 2.0
1 2 harm 3.0 1.4
2 3 Grimme 6.0 3.2
%endblock MM.Potentials

To automatically create input for Grimme’s method, please see the utility: Util/Grimme which
can read an fdf file and create the correct input for Grimme’s method.

MM.Cutoff 30 Bohr (length)

Specifies the distance out to which molecular mechanics potential will act before being treated
as going to zero.

MM.UnitsEnergy eV (unit)
Specifies the units to be used for energy in the molecular mechanics potentials.

MM.UnitsDistance Ang (unit)

Specifies the units to be used for distance in the molecular mechanics potentials.

MM.Grimme.D 20.0 (real)

Specifies the scale factor d for the scaling function in the Grimme dispersion potential (see
above).

MM.Grimme.S6 1.66 (real)

Specifies the overall fitting factor s6 for the Grimme dispersion potential (see above). This
number depends on the quality of the basis set, the exchange-correlation functional, and the
fitting set.

6.24 Parallel options

BlockSize 〈automatic〉 (integer)
The orbitals are distributed over the processors when running in parallel using a 1-D block-
cyclic algorithm. BlockSize is the number of consecutive orbitals which are located on a given
processor before moving to the next one. Large values of this parameter lead to poor load
balancing, while small values can lead to inefficient execution. The performance of the parallel
code can be optimised by varying this parameter until a suitable value is found.

ProcessorY 〈automatic〉 (integer)

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 The mesh points are divided in the Y and Z directions (more precisely, along the second and
third lattice vectors) over the processors in a 2-D grid. ProcessorY specifies the dimension of
the processor grid in the Y-direction and must be a factor of the total number of processors.
Ideally the processors should be divided so that the number of mesh points per processor along
each axis is as similar as possible.
Defaults to a multiple of number of processors.

6.24.1 Parallel decompositions for O(N)

Apart from the default block-cyclic decomposition of the orbital data, O(N) calculations can use
other schemes which should be more efficient: spatial decomposition (based on atom proximity),
and domain decomposition (based on the most efficient abstract partition of the interaction graph
of the Hamiltonian).

UseDomainDecomposition false (logical)

This option instructs the program to employ a graph-partitioning algorithm (using the METIS
library (See www.cs.umn.edu/~metis) to find an efficient distribution of the orbital data over
processors. To use this option (meaningful only in parallel) the program has to be compiled
with the preprocessor option SIESTA__METIS (or the deprecated ON_DOMAIN_DECOMP) and the
METIS library has to be linked in.

UseSpatialDecomposition false (logical)

When performing a parallel order N calculation, this option instructs the program to execute
a spatial decomposition algorithm in which the system is divided into cells, which are then
assigned, together with the orbitals centered in them, to the different processors. The size
of the cells is, by default, equal to the maximum distance at which there is a non-zero matrix
element in the Hamiltonian between two orbitals, or the radius of the Localized Wannier function
- which ever is the larger. If this is the case, then an orbital will only interact with other orbitals
in the same or neighbouring cells. However, by decreasing the cell size and searching over more
cells it is possible to achieve better load balance in some cases. This is controlled by the variable
RcSpatial.
NOTE: the distribution algorithm is quite fragile and a careful tuning of RcSpatial might be
needed. This option is therefore not enabled by default.

RcSpatial 〈maximum orbital range〉 (length)

Controls the cell size during the spatial decomposition.

6.25 Efficiency options

DirectPhi false (logical)
The calculation of the matrix elements on the mesh requires the value of the orbitals on the
mesh points. This array represents one of the largest uses of memory within the code. If set to
true this option allows the code to generate the orbital values when needed rather than storing
the values. This obviously costs more computer time but will make it possible to run larger
jobs where memory is the limiting factor.
This controls whether the values of the orbitals at the mesh points are stored or calculated on

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 the fly.

6.26 Memory, CPU-time, and Wall time accounting options

AllocReportLevel 0 (integer)
Sets the level of the allocation report, printed in file SystemLabel.alloc. However, not all
the allocated arrays are included in the report (this will be corrected in future versions). The
allowed values are:
• level 0 : no report at all (the default)
• level 1 : only total memory peak and where it occurred
• level 2 : detailed report printed only at normal program termination
• level 3 : detailed report printed at every new memory peak
• level 4 : print every individual (re)allocation or deallocation
NOTE: In MPI runs, only node-0 peak reports are produced.

AllocReportThreshold 0. (real)
Sets the minimum size (in bytes) of the arrays whose memory use is individually printed in the
detailed allocation reports (levels 2 and 3). It does not affect the reported memory sums and
peaks, which always include all arrays.

TimerReportThreshold 0. (real)
Sets the minimum fraction, of total CPU time, of the subroutines or code sections whose CPU
time is individually printed in the detailed timer reports. To obtain the accounting of MPI
communication times in parallel executions, you must compile with option -DMPI_TIMING. In
serial execution, the CPU times are printed at the end of the output file. In parallel execution,
they are reported in a separated file named SystemLabel.times.

UseTreeTimer false (logical)

Enable an experimental timer which is based on wall time on the master node and is aware of
the tree-structure of the timed sections. At the end of the program, a report is generated in
the output file, and a time.json file in JSON format is also written. This file can be used by
third-party scripts to process timing data.
NOTE: , if used with the PEXSI solver (see Sec. 6.13) this defaults to true.

UseParallelTimer true (logical)

Determine whether timings are performed in parallel. This may introduce slight overhead.
NOTE: , if used with the PEXSI solver (see Sec. 6.13) this defaults to false.

MaxWalltime Infinity (real time)

Set an internal limit to the wall time allotted to the program’s execution. Typically this is related
to the external limit imposed by queuing systems. The code checks its wall time periodically
and will abort if nearing the limit, with some slack left for clean-up operations (proper closing
of files, emergency output...), as determined by MaxWalltime.Slack. See Sec. 16 for available
units of time (s, mins, hours, days).

MaxWalltime.Slack 5s (real time)

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 The code checks its wall time Twall periodically and will abort if Twall > Tmax − Tslack , so that
some slack is left for any clean-up operations.

6.27 The catch-all option UseSaveData

This is a dangerous feature, and is deprecated, but retained for historical compatibility. Use the
individual options instead.

UseSaveData false (logical)

Instructs to use as much information as possible stored from previous runs in files
SystemLabel.XV, SystemLabel.DM and SystemLabel.LWF,
NOTE: if the files are not existing it will read the information from the fdf file.

6.28 Output of information for Denchar

The program denchar in Util/Denchar can generate charge-density and wavefunction information
in real space.

Write.Denchar false (logical)

Instructs to write information needed by the utility program DENCHAR (by J. Junquera
and P. Ordejón) to generate valence charge densities and/or wavefunctions in real space (see
Util/Denchar). The information is written in files SystemLabel.PLD and SystemLabel.DIM.
To run DENCHAR you will need, apart from the .PLD and .DIM files, the Density-Matrix (DM)
file and/or a wavefunction (.WFSX) file, and the .ion files containing the information about the
basis orbitals.

6.29 NetCDF (CDF4) output file

NOTE: this requires SIESTA compiled with CDF4 support.

To unify and construct a simple output file for an entire SIESTA calculation a generic NetCDF file
will be created if SIESTA is compiled with ncdf support, see Sec. 2.4 and the ncdf section.
Generally all output to NetCDF flags, SaveElectrostaticPotential, etc. apply to this file as well.
One may control the output file with compressibility and parallel I/O, if needed.

CDF.Save false (logical)

Create the SystemLabel.nc file which is a NetCDF file.
This file will be created with a large set of groups which make separating the quantities easily.
Also it will inherently denote the units for the stored quantities.
NOTE: this option is not available for MD/relaxations, only for force constant runs.

CDF.Compress 0 (integer)
Integer between 0 and 9. The former represents no compressing and the latter is the highest
compressing.
The higher the number the more computation time is spent on compressing the data. A good
compromise between speed and compression is 3.

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 NOTE: if one requests parallel I/O (CDF.MPI) this will automatically be set to 0. One
cannot perform parallel IO and compress the data simultaneously.
NOTE: instead of using SIESTA for compression you may compress after execution by:
nccopy -d 3 -s noncompressed.nc compressed.nc

CDF.MPI false (logical)

Write SystemLabel.nc in parallel using MPI for increased performance. This has almost no
memory overhead but may for very large number of processors saturate the file-system.
NOTE: this is an experimental flag.

CDF.Grid.Precision single|double (string)

At which precision should the real-space grid quantities be stored, such as the density, electro-
static potential etc.

7 STRUCTURAL RELAXATION, PHONONS, AND MOLECU-

LAR DYNAMICS

This functionality is not SIESTA-specific, but is implemented to provide a more complete simulation
package. The program has an outer geometry loop: it computes the electronic structure (and thus the
forces and stresses) for a given geometry, updates the atomic positions (and maybe the cell vectors)
accordingly and moves on to the next cycle. If there are molecular dynamics options missing you
are highly recommend to look into MD.TypeOfRun Lua or MD.TypeOfRun Master.
Several options for MD and structural optimizations are implemented, selected by

MD.TypeOfRun CG (string)
CG Coordinate
optimization by conjugate gradients). Optionally (see variable MD.VariableCell below),
the optimization can include the cell vectors.
Broyden Coordinate optimization by a modified Broyden scheme). Optionally, (see variable
MD.VariableCell below), the optimization can include the cell vectors.
FIRE Coordinate optimization by Fast Inertial Relaxation Engine (FIRE) (E. Bitzek et al, PRL
97, 170201, (2006)). Optionally, (see variable MD.VariableCell below), the optimization
can include the cell vectors.
Verlet Standard Verlet algorithm MD
Nose MD with temperature controlled by means of a Nosé thermostat
ParrinelloRahman MD with pressure controlled by the Parrinello-Rahman method
NoseParrinelloRahman MD with temperature controlled by means of a Nosé thermostat and
pressure controlled by the Parrinello-Rahman method
Anneal MD with annealing to a desired temperature and/or pressure (see variable
MD.AnnealOption below)
FC Compute force constants matrix for phonon calculations.

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 Master|Forces Receive coordinates from, and return forces to, an external driver program, us-
ing MPI, Unix pipes, or Inet sockets for communication. The routines in module fsiesta
allow the user’s program to perform this communication transparently, as if SIESTA
were a conventional force-field subroutine. See Util/SiestaSubroutine/README for details.
WARNING: if this option is specified without a driver program sending data, siesta may hang
without any notice.
See directory Util/Scripting for other driving options.
Lua Fully control the MD cycle and convergence path using an external Lua script.
With an external Lua script one may control nearly everything from a script. One can query
any internal data-structures in SIESTA and, similarly, return any data thus overwriting the
internals. A list of ideas which may be implemented in such a Lua script are:
• New geometry relaxation algorithms
• NEB calculations
• New MD routines
• Convergence tests of MeshCutoff and kgrid.MonkhorstPack, or other parameters
(currently basis set optimizations cannot be performed in the Lua script).
Sec. 9 for additional details (and a description of flos which implements some of the above
mentioned items).
Using this option requires the compilation of SIESTA with the flook library.If SIESTA is
not compiled as prescribed in Sec. 2.4 this option will make SIESTA die.
NOTE: if Compat.Pre-v4-Dynamics is true this will default to Verlet.
Note that some options specified in later variables (like quenching) modify the behavior of these
MD options.
Appart from being able to act as a force subroutine for a driver program that uses
module fsiesta, SIESTA is also prepared to communicate with the i-PI code (see
http://epfl-cosmo.github.io/gle4md/index.html?page=ipi). To do this, SIESTA must
be started after i-PI (it acts as a client of i-PI, communicating with it through Inet or Unix
sockets), and the following lines must be present in the .fdf data file:
MD.TypeOfRun Master # equivalent to ’Forces’
Master.code i-pi # ( fsiesta | i-pi )
Master.interface socket # ( pipes | socket | mpi )
Master.address localhost # or driver’s IP, e.g. 150.242.7.140
Master.port 10001 # 10000+siesta_process_order
Master.socketType inet # ( inet | unix )

7.1 Compatibility with pre-v4 versions

Starting in the summer of 2015, some changes were made to the behavior of the program regarding
default dynamics options and choice of coordinates to work with during post-processing of the
electronic structure. The changes are:

• The default dynamics option is “CG” instead of “Verlet”.

• The coordinates, if moved by the dynamics routines, are reset to their values at the previous
step for the analysis of the electronic structure (band structure calculations, DOS, LDOS, etc).

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 • Some output files reflect the values of the “un-moved” coordinates.
• The default convergence criteria is now both density and Hamiltonian convergence, see
SCF.DM.Converge and SCF.H.Converge.

To recover the previous behavior, the user can turn on the compatibility switch Compat.Pre-v4-
Dynamics, which is off by default.
Note that complete compatibility cannot be perfectly guaranteed.

7.2 Structural relaxation

In this mode of operation, the program moves the atoms (and optionally the cell vectors) trying to
minimize the forces (and stresses) on them.
These are the options common to all relaxation methods. If the Zmatrix input option is in effect
(see Sec. 6.4.2) the Zmatrix-specific options take precedence. The ’MD’ prefix is misleading but kept
for historical reasons.

MD.VariableCell false (logical)

If true, the lattice is relaxed together with the atomic coordinates. It allows to target hydro-
static pressures or arbitrary stress tensors. See MD.MaxStressTol, MD.TargetPressure,
MD.TargetStress, MD.ConstantVolume, and MD.PreconditionVariableCell.
NOTE: only compatible with MD.TypeOfRun CG, Broyden or fire.

MD.ConstantVolume false (logical)

If true, the cell volume is kept constant in a variable-cell relaxation: only the cell shape and
the atomic coordinates are allowed to change. Note that it does not make much sense to
specify a target stress or pressure in this case, except for anisotropic (traceless) stresses. See
MD.VariableCell, MD.TargetStress.
NOTE: only compatible with MD.TypeOfRun CG, Broyden or fire.

MD.RelaxCellOnly false (logical)

If true, only the cell parameters are relaxed (by the Broyden or FIRE method, not CG). The
atomic coordinates are re-scaled to the new cell, keeping the fractional coordinates constant.
For Zmatrix calculations, the fractional position of the first atom in each molecule is kept
fixed, and no attempt is made to rescale the bond distances or angles.
NOTE: only compatible with MD.TypeOfRun Broyden or fire.

MD.MaxForceTol 0.04 eV/Ang (force)

Force tolerance in coordinate optimization. Run stops if the maximum atomic force is smaller
than MD.MaxForceTol (see MD.MaxStressTol for variable cell).

MD.MaxStressTol 1 GPa (pressure)

Stress tolerance in variable-cell CG optimization. Run stops if the maximum atomic force
is smaller than MD.MaxForceTol and the maximum stress component is smaller than
MD.MaxStressTol.
Special consideration is needed if used with Sankey-type basis sets, since the combination of
orbital kinks at the cutoff radii and the finite-grid integration originate discontinuities in the

111
 stress components, whose magnitude depends on the cutoff radii (or energy shift) and the mesh
cutoff. The tolerance has to be larger than the discontinuities to avoid endless optimizations if
the target stress happens to be in a discontinuity.

MD.Steps 0 (integer)
depends on: MD.NumCGsteps
Maximum number of steps in a minimization routine (the minimization will stop if tolerance is
reached before; see MD.MaxForceTol below).
NOTE: The old flag MD.NumCGsteps will remain for historical reasons.

MD.MaxDispl 0.2 Bohr (length)

depends on: MD.MaxCGDispl
Maximum atomic displacements in an optimization move.
In the Broyden optimization method, it is also possible to limit indirectly the initial atomic
displacements using MD.Broyden.Initial.Inverse.Jacobian. For the FIRE method, the
same result can be obtained by choosing a small time step.
Note that there are Zmatrix-specific options that override this option.
NOTE: The old flag MD.MaxCGDispl will remain for historical reasons.

MD.PreconditionVariableCell 5 Ang (length)

A length to multiply to the strain components in a variable-cell optimization. The strain
components enter the minimization on the same footing as the coordinates. For good efficiency,
this length should make the scale of energy variation with strain similar to the one due to atomic
displacements. It is also used for the application of the MD.MaxCGDispl value to the strain
components.

ZM.ForceTolLength 0.00155574 Ry/Bohr (force)

Parameter that controls the convergence with respect to forces on Z-matrix lengths

ZM.ForceTolAngle 0.00356549 Ry/rad (torque)

Parameter that controls the convergence with respect to forces on Z-matrix angles

ZM.MaxDisplLength 0.2 Bohr (length)

Parameter that controls the maximum change in a Z-matrix length during an optimisation step.

ZM.MaxDisplAngle 0.003 rad (angle)

Parameter that controls the maximum change in a Z-matrix angle during an optimisation step.

7.2.1 Conjugate-gradients optimization

This was historically the default geometry-optimization method, and all the above options were
introduced specifically for it, hence their names. The following pertains only to this method:

MD.UseSaveCG false (logical)

Instructs to read the conjugate-gradient hystory information stored in file SystemLabel.CG by
a previous run.
NOTE: to get actual continuation of iterrupted CG runs, use together with MD.UseSaveXV

112
 true with the .XV file generated in the same run as the CG file. If the required file does not
exist, a warning is printed but the program does not stop. Overrides UseSaveData.
NOTE: no such feature exists yet for a Broyden-based relaxation.

7.2.2 Broyden optimization

It uses the modified Broyden algorithm to build up the Jacobian matrix. (See D.D. Johnson, PRB
38, 12807 (1988)). (Note: This is not BFGS.)

MD.Broyden.History.Steps 5 (integer)
Number of relaxation steps during which the modified Broyden algorithm builds up the Jacobian
matrix.

MD.Broyden.Cycle.On.Maxit true (logical)

Upon reaching the maximum number of history data sets which are kept for Jacobian estimation,
throw away the oldest and shift the rest to make room for a new data set. The alternative is
to re-start the Broyden minimization algorithm from a first step of a diagonal inverse Jacobian
(which might be useful when the minimization is stuck).

MD.Broyden.Initial.Inverse.Jacobian 1 (real)
Initial inverse Jacobian for the optimization procedure. (The units are those implied by the
internal Siesta usage. The default value seems to work well for most systems.

7.2.3 FIRE relaxation

Implementation of the Fast Inertial Relaxation Engine (FIRE) method (E. Bitzek et al, PRL 97,
170201, (2006) in a manner compatible with the CG and Broyden modes of relaxation. (An older
implementation activated by the MD.FireQuench variable is still available).

MD.FIRE.TimeStep 〈MD.LengthTimeStep〉 (time)

The (fictitious) time-step for FIRE relaxation. This is the main user-variable when the option
FIRE for MD.TypeOfRun is active.
NOTE: the default value is encouraged to be changed as the link to MD.LengthTimeStep
is misleading.
There are other low-level options tunable by the user (see the routines fire_optim and
cell_fire_optim for more details.

7.3 Target stress options

Useful for structural optimizations and constant-pressure molecular dynamics.

MD.TargetPressure 0 GPa (pressure)

Target pressure for Parrinello-Rahman method, variable cell optimizations, and annealing op-
tions.
NOTE: this is only compatible with MD.TypeOfRun ParrinelloRahman, NoseParrinel-
loRahman, CG, Broyden or FIRE (variable cell), or Anneal (if MD.AnnealOption Pres-

113
 sure or TemperatureandPressure).

%block MD.TargetStress −1 − 1 − 1000 (block)

External or target stress tensor for variable cell optimizations. Stress components are given
in a line, in the order xx, yy, zz, xy, xz, yz. In units of MD.TargetPressure, but with
the opposite sign. For example, a uniaxial compressive stress of 2 GPa along the 100 direction
would be given by
MD.TargetPressure 2. GPa
%block MD.TargetStress
-1.0 0.0 0.0 0.0 0.0 0.0
%endblock MD.TargetStress

Only used if MD.TypeOfRun is CG, Broyden or FIRE and MD.VariableCell is true.

MD.RemoveIntramolecularPressure false (logical)

If true, the contribution to the stress coming from the internal degrees of freedom of the
molecules will be subtracted from the stress tensor used in variable-cell optimization or variable-
cell molecular-dynamics. This is done in an approximate manner, using the virial form of the
stress, and assumming that the “mean force” over the coordinates of the molecule represents
the “inter-molecular” stress. The correction term was already computed in earlier versions of
SIESTA and used to report the “molecule pressure”. The correction is now computed molecule-
by-molecule if the Zmatrix format is used.
If the intra-molecular stress is removed, the corrected static and total stresses are printed in
addition to the uncorrected items. The corrected Voigt form is also printed.

7.4 Molecular dynamics

In this mode of operation, the program moves the atoms (and optionally the cell vectors) in response
to the forces (and stresses), using the classical equations of motion.
Note that the Zmatrix input option (see Sec. 6.4.2) is not compatible with molecular dynamics. The
initial geometry can be specified using the Zmatrix format, but the Zmatrix generalized coordinates
will not be updated.

MD.InitialTimeStep 1 (integer)
Initial time step of the MD simulation. In the current version of SIESTA it must be 1.
Used only if MD.TypeOfRun is not CG or Broyden.

MD.FinalTimeStep 〈MD.Steps〉 (integer)

Final time step of the MD simulation.

MD.LengthTimeStep 1 fs (time)
Length of the time step of the MD simulation.

MD.InitialTemperature 0 K (temperature/energy)
Initial temperature for the MD run. The atoms are assigned random velocities drawn from the
Maxwell-Bolzmann distribution with the corresponding temperature. The constraint of zero
center of mass velocity is imposed.

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 NOTE: only used if MD.TypeOfRun Verlet, Nose, ParrinelloRahman, NoseParrinel-
loRahman or Anneal.

MD.TargetTemperature 0 K (temperature/energy)
Target temperature for Nose thermostat and annealing options.
NOTE: only used if MD.TypeOfRun Nose, NoseParrinelloRahman or Anneal if
MD.AnnealOption is Temperature or TemperatureandPressure.

MD.NoseMass 100 Ry fs2 (moment of inertia)

Generalized mass of Nose variable. This determines the time scale of the Nose variable dynamics,
and the coupling of the thermal bath to the physical system.
Only used for Nose MD runs.

MD.ParrinelloRahmanMass 100 Ry fs2 (moment of inertia)

Generalized mass of Parrinello-Rahman variable. This determines the time scale of the
Parrinello-Rahman variable dynamics, and its coupling to the physical system.
Only used for Parrinello-Rahman MD runs.

MD.AnnealOption TemperatureAndPressure (string)

Type of annealing MD to perform. The target temperature or pressure are achieved by velocity
and unit cell rescaling, in a given time determined by the variable MD.TauRelax below.
Temperature Reach a target temperature by velocity rescaling
Pressure Reach a target pressure by scaling of the unit cell size and shape
TemperatureandPressure Reach a target temperature and pressure by velocity rescaling and
by scaling of the unit cell size and shape
Only applicable for MD.TypeOfRun Anneal.

MD.TauRelax 100 fs (time)

Relaxation time to reach target temperature and/or pressure in annealing MD. Note that this
is a “relaxation time”, and as such it gives a rough estimate of the time needed to achieve the
given targets. As a normal simulation also exhibits oscillations, the actual time needed to reach
the averaged targets will be significantly longer.
Only applicable for MD.TypeOfRun Anneal.

MD.BulkModulus 100 Ry/Bohr3 (pressure)

Estimate (may be rough) of the bulk modulus of the system. This is needed to set the rate of
change of cell shape to reach target pressure in annealing MD.
Only applicable for MD.TypeOfRun Anneal, when MD.AnnealOption is Pressure or
TemperatureAndPressure

7.5 Output options for dynamics

Every time the atoms move, either during coordinate relaxation or molecular dynamics, their po-
sitions predicted for next step and current velocities are stored in file SystemLabel.XV. The
shape of the unit cell and its associated ’velocity’ (in Parrinello-Rahman dynamics) are also stored

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in this file.

WriteCoorInitial true (logical)

It determines whether the initial atomic coordinates of the simulation are dumped into the main
output file. These coordinates correspond to the ones actually used in the first step (see the
section on precedence issues in structural input) and are output in Cartesian coordinates in
Bohr units.
It is not affected by the setting of LongOutput.

WriteCoorStep false (logical)

If true, it writes the atomic coordinates to standard output at every MD time step or relax-
ation step. The coordinates are always written in the SystemLabel.XV file, but overriden at
every step. They can be also accumulated in the .MD or SystemLabel.MDX files depending on
WriteMDHistory.

WriteForces false (logical)

If true, it writes the atomic forces to the output file at every MD time step or relaxation step.
Note that the forces of the last step can be found in the file SystemLabel.FA. If constraints are
used, the file SystemLabel.FAC is also written.

WriteMDHistory false (logical)

If true, SIESTA accumulates the molecular dynamics trajectory in the following files:
• SystemLabel.MD : atomic coordinates and velocities (and lattice vectors and their time
derivatives, if the dynamics implies variable cell). The information is stored unformatted
for postprocessing with utility programs to analyze the MD trajectory.
• SystemLabel.MDE : shorter description of the run, with energy, temperature, etc., per time
step.
These files are accumulative even for different runs.
The trajectory of a molecular dynamics run (or a conjugate gradient minimization) can be
accumulated in different files: SystemLabel.MD, SystemLabel.MDE, and SystemLabel.ANI.
The first file keeps the whole trajectory information, meaning positions and velocities at every
time step, including lattice vectors if the cell varies. NOTE that the positions (and maybe the
cell vectors) stored at each time step are the predicted values for the next step. Care should
be taken if joint position-velocity correlations need to be computed from this file. The second
gives global information (energy, temperature, etc), and the third has the coordinates in a form
suited for XMol animation. See the WriteMDHistory and WriteMDXmol data descriptors
above for information. SIESTA always appends new information on these files, making them
accumulative even for different runs.
The iomd subroutine can generate both an unformatted file .MD (default) or ASCII formatted
files .MDX and .MDC containing the atomic and lattice trajectories, respectively. Edit the file to
change the settings if desired.

Write.OrbitalIndex true (logical)

If true it causes the writing of an extra file named SystemLabel.ORB_INDX containing all
orbitals used in the calculation.
Its formatting is clearly specified at the end of the file.

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7.6 Restarting geometry optimizations and MD runs

Every time the atoms move, either during coordinate relaxation or molecular dynamics, their posi-
tions predicted for next step and current velocities are stored in file SystemLabel.XV, where
SystemLabel is the value of that fdf descriptor (or ’siesta’ by default). The shape of the unit cell and
its associated ’velocity’ (in Parrinello-Rahman dynamics) are also stored in this file. For MD runs of
type Verlet, Parrinello-Rahman, Nose, Nose-Parrinello-Rahman, or Anneal, a file named SystemLa-
bel.VERLET_RESTART, SystemLabel.PR_RESTART, SystemLabel.NOSE_RESTART, System-
Label.NPR_RESTART, or SystemLabel.ANNEAL_RESTART, respectively, is created to hold the
values of auxiliary variables needed for a completely seamless continuation.
If the restart file is not available, a simulation can still make use of the XV information, and “restart”
by basically repeating the last-computed step (the positions are shifted backwards by using a single
Euler-like step with the current velocities as derivatives). While this feature does not result in
seamless continuations, it allows cross-restarts (those in which a simulation of one kind (e.g., Anneal)
is followed by another (e.g., Nose)), and permits to re-use dynamical information from old runs.
This restart fix is not satisfactory from a fundamental point of view, so the MD subsystem in Siesta
will have to be redesigned eventually. In the meantime, users are reminded that the scripting hooks
being steadily introduced (see Util/Scripting) might be used to create custom-made MD scripts.

7.7 Use of general constraints

Note: The Zmatrix format (see Sec. 6.4.2) provides an alternative constraint formulation which can
be useful for system involving molecules.

%block Geometry.Constraints 〈None〉 (block)

Constrains certain atomic coordinates or cell parameters in a consistent method.
There are a high number of configurable parameters that may be used to control the relaxation
of the coordinates.
NOTE: SIESTA prints out a small section of how the constraints are recognized.
atom|position Fix certain atomic coordinates.
This option takes a variable number of integers which each correspond to the atomic index
(or input sequence) in AtomicCoordinatesAndAtomicSpecies.
atom is now the preferred input option while position still works for backwards compatibility.
One may also specify ranges of atoms according to:
atom A [B [C [. . . ]]] A sequence of atomic indices which are constrained.
atom from A to B [step s] Here atoms A up to and including B are constrained. If step
<s> is given, the range A:B will be taken in steps of s.
atom from 3 to 10 step 2
will constrain atoms 3, 5, 7 and 9.
atom from A plus/minus B [step s] Here atoms A up to and including A + B − 1 are
constrained. If step <s> is given, the range A:A + B − 1 will be taken in steps of s.
atom [A, B -- C [step s], D] Equivalent to from . . . to specification, however in a shorter
variant. Note that the list may contain arbitrary number of ranges and/or individual

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 indices.
atom [2, 3 -- 10 step 2, 6]
will constrain atoms 2, 3, 5, 7, 9 and 6.
atom [2, 3 -- 6, 8]
will constrain atoms 2, 3, 4, 5, 6 and 8.
atom all Constrain all atoms.
NOTE: these specifications are apt for directional constraints.
Z Equivalent to atom with all indices of the atoms that have atomic number equal to the
specified number.
NOTE: this specification is apt for directional constraints.
species-i Equivalent to atom with all indices of the atoms that have species according to the
ChemicalSpeciesLabel and AtomicCoordinatesAndAtomicSpecies.
NOTE: this specification is apt for directional constraints.
center One may retain the coordinate center of a range of atoms (say molecules or other groups
of atoms).
Atomic indices may be specified according to atom.
NOTE: this specification is apt for directional constraints.
rigid|molecule Move a selection of atoms together as though they where one atom.
The forces are summed and averaged to get a net-force on the entire molecule.
Atomic indices may be specified according to atom.
NOTE: this specification is apt for directional constraints.
rigid-max|molecule-max Move a selection of atoms together as though they where one atom.
The maximum force acting on one of the atoms in the selection will be expanded to act on
all atoms specified.
Atomic indices may be specified according to atom.
cell-angle Control whether the cell angles (α, β, γ) may be altered.
This takes either one or more of alpha/beta/gamma as argument.
alpha is the angle between the 2nd and 3rd cell vector.
beta is the angle between the 1st and 3rd cell vector.
gamma is the angle between the 1st and 2nd cell vector.
NOTE: currently only one angle can be constrained at a time and it forces only the spanning
vectors to be relaxed.
cell-vector Control whether the cell vectors (A, B, C) may be altered.
This takes either one or more of A/B/C as argument.
Constraining the cell-vectors are only allowed if they only have a component along their
respective Cartesian direction. I.e. B must only have a y-component.
stress Control which of the 6 stress components are constrained.
This takes a number of integers 1 ≤ i ≤ 6 where 1 corresponds to the AA stress-component,
2 is BB, 3 is CC, 4 is BC /CB, 5 is AC /CA and 6 is AB/BA.

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routine This calls the constr routine specified in the file: constr.f. Without having changed
the corresponding source file, this does nothing. See details and comments in the source-file.
clear Remove constraints on selected atoms from all previously specified constraints.
This may be handy when specifying constraints via Z or species-i.
Atomic indices may be specified according to atom.
clear-prev Remove constraints on selected atoms from the previous specified constraint.
This may be handy when specifying constraints via Z or species-i.
Atomic indices may be specified according to atom.
NOTE: two consecutive clear-prev may be used in conjunction as though the atoms where
specified on the same line.
It is instructive to give an example of the input options presented.
Consider a benzene molecule (C6 H6 ) and we wish to relax all Hydrogen atoms. This may be
accomplished in this fashion
%block Geometry.Constraints
Z 6
%endblock

Or as in this example
%block AtomicCoordinatesAndAtomicSpecies
... ... ... 1 # C 1
... ... ... 2 # H 2
... ... ... 1 # C 3
... ... ... 2 # H 4
... ... ... 1 # C 5
... ... ... 2 # H 6
... ... ... 1 # C 7
... ... ... 2 # H 8
... ... ... 1 # C 9
... ... ... 2 # H 10
... ... ... 1 # C 11
... ... ... 2 # H 12
%endblock
%block Geometry.Constraints
atom from 1 to 12 step 2
%endblock
%block Geometry.Constraints
atom [1 -- 12 step 2]
%endblock
%block Geometry.Constraints
atom all
clear-prev [2 -- 12 step 2]
%endblock

where the 3 last blocks all create the same result.

Finally, the directional constraint is an important and often useful feature. When relaxing
complex structures it may be advantageous to first relax along a given direction (where you
expect the stress to be largest) and subsequently let it fully relax. Another example would be to
relax the binding distance between a molecule and a surface, before relaxing the entire system

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 by forcing the molecule and adsorption site to relax together. To use directional constraint
one may provide an additional 3 reals after the atom/rigid. For instance in the previous
example (benzene) one may first relax all Hydrogen atoms along the y and z Cartesian vector
by constraining the x Cartesian vector
%block Geometry.Constraints
Z 6 # constrain Carbon
Z 1 1. 0. 0. # constrain Hydrogen along x Cartesian vector
%endblock

Note that you must append a “.” to denote it a real. The vector specified need not be normalized.
Also, if you want it to be constrained along the x-y vector you may do
%block Geometry.Constraints
Z 6
Z 1 1. 1. 0.
%endblock

7.8 Phonon calculations

If MD.TypeOfRun is FC, SIESTA sets up a special outer geometry loop that displaces individual
atoms along the coordinate directions to build the force-constant matrix.
The output (see below) can be analyzed to extract phonon frequencies and vectors with the VIBRA
package in the Util/Vibra directory. For computing the Born effective charges together with the
force constants, see BornCharge.

MD.FCDispl 0.04 Bohr (length)

Displacement to use for the computation of the force constant matrix for phonon calculations.

MD.FCFirst 1 (integer)
Index of first atom to displace for the computation of the force constant matrix for phonon
calculations.

MD.FCLast 〈MD.FCFirst〉 (integer)

Index of last atom to displace for the computation of the force constant matrix for phonon
calculations.

The force-constants matrix is written in file SystemLabel.FC. The format is the following: for the
displacement of each atom in each direction, the forces on each of the other atoms is writen (divided
by the value of the displacement), in units of eV/Å2 . Each line has the forces in the x, y and z
direction for one of the atoms.
If constraints are used, the file SystemLabel.FCC is also written.

8 LDA+U

Important note: Current implementation is based on the simplified rotationally invariant LDA+U
formulation of Dudarev and collaborators [see, Dudarev et al., Phys. Rev. B 57, 1505 (1998)].
Although the input allows to define independent values of the U and J parameters for each atomic

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shell, in the actual calculation the two parameters are combined to produce an effective Coulomb
repulsion Ueff = U − J. Ueff is the parameter actually used in the calculations for the time being.
For large or intermediate values of Ueff the convergence is sometimes difficult. A step-by-step increase
of the value of Ueff can be advisable in such cases.
Currently, the LDA+U implementation does not support non-colinear, nor spin-orbit coupling.

LDAU.ProjectorGenerationMethod 2 (integer)
Generation method of the LDA+U projectors. The LDA+U projectors are the localized func-
tions used to calculate the local populations used in a Hubbard-like term that modifies the LDA
Hamiltonian and energy. It is important to recall that LDA+U projectors should be quite local-
ized functions. Otherwise the calculated populations loose their atomic character and physical
meaning. Even more importantly, the interaction range can increase so much that jeopardizes
the efficiency of the calculation.
Two methods are currently implemented:
1 Projectors are slightly-excited numerical atomic orbitals similar to those used as an auto-
matic basis set by SIESTA. The radii of these orbitals are controlled using the parameter
LDAU.EnergyShift and/or the data included in the block LDAU.Proj (quite similar to
the data block PAO.Basis used to specify the basis set, see below).
2 Projectors are exact solutions of the pseudoatomic problem (and, in principle, are not strictly
localized) which are cut using a Fermi function 1/{1 + exp[(r − rc )ω]}. The values of rc and
ω are controlled using the parameter LDAU.CutoffNorm and/or the data included in the
block LDAU.Proj.

LDAU.EnergyShift 0.05 Ry (energy)

Energy increase used to define the localization radius of the LDA+U projectors (similar to the
parameter PAO.EnergyShift).
NOTE: only used when LDAU.ProjectorGenerationMethod is 1.

LDAU.CutoffNorm 0.9 (real)

Parameter used to define the value of rc used in the Fermi distribution to cut the LDA+U
projectors generated according to generation method 2 (see above). LDAU.CutoffNorm is
the norm of the original pseudoatomic orbital contained inside a sphere of radius equal to rc .
NOTE: only used when LDAU.ProjectorGenerationMethod is 2.

%block LDAU.Proj 〈None〉 (block)

Data block used to specify the LDA+U projectors.
• If LDAU.ProjectorGenerationMethod is 1, the syntax is as follows:
%block LDAU.Proj # Define LDA+U projectors
Fe 2 # Label, l_shells
n=3 2 E 50.0 2.5 # n (opt if not using semicore levels),l,Softconf(opt)
5.00 0.35 # U(eV), J(eV) for this shell
2.30 # rc (Bohr)
0.95 # scaleFactor (opt)
0 # l
1.00 0.05 # U(eV), J(eV) for this shell
0.00 # rc(Bohr) (if 0, automatic r_c from LDAU.EnergyShift)

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 %endblock LDAU.Proj
• If LDAU.ProjectorGenerationMethod is 2, the syntax is as follows:
%block LDAU.Proj # Define LDAU projectors
Fe 2 # Label, l_shells
n=3 2 E 50.0 2.5 # n (opt if not using semicore levels),l,Softconf(opt)
5.00 0.35 # U(eV), J(eV) for this shell
2.30 0.15 # rc (Bohr), \omega(Bohr) (Fermi cutoff function)
0.95 # scaleFactor (opt)
0 # l
1.00 0.05 # U(eV), J(eV) for this shell
0.00 0.00 # rc(Bohr), \omega(Bohr) (if 0 r_c from LDAU.CutoffNorm
%endblock LDAU.Proj # and \omega from default value)
Certain of the quantites have default values:
U 0.0 eV
J 0.0 eV
ω 0.05 Bohr
Scale factor 1.0
rc depends on LDAU.EnergyShift or LDAU.CutoffNorm depending on the generation
method.

LDAU.FirstIteration false (logical)

If true, local populations are calculated and Hubbard-like term is switch on in the first iteration.
Useful if restarting a calculation reading a converged or an almost converged density matrix
from file.

LDAU.ThresholdTol 0.01 (real)

Local populations only calculated and/or updated if the change in the density matrix elements
(dDmax) is lower than LDAU.ThresholdTol.

LDAU.PopTol 0.001 (real)

Convergence criterium for the LDA+U local populations. In the current implementation the
Hubbard-like term of the Hamiltonian is only updated (except for the last iteration) if the
variations of the local populations are larger than this value.

LDAU.PotentialShift false (logical)

If set to true, the value given to the U parameter in the input file is interpreted as a local
potential shift. Recording the change of the local populations as a function of this potential
shift, we can calculate the appropriate value of U for the system under study following the
methology proposed by Cococcioni and Gironcoli in Phys. Rev. B 71, 035105 (2005).

9 External control of SIESTA

Since SIESTA 4.1 an additional method of controlling the convergence and MD of SIESTA is
enabled through external scripting capability. The external control comes in two variants:

• Implicit control of MD through updating/changing parameters and optimizing forces. For

instance one may use a Verlet MD method but additionally update the forces through some

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 external force-field to amend limitations by the Verlet method for your particular case. In
the implicit control the molecular dynamics is controlled by SIESTA.

• Explicit control of MD. In this mode the molecular dynamics must be controlled in the external
Lua script and the convergence of the geometry should also be controlled via this script.

The implicit control is in use if MD.TypeOfRun is something other than lua, while if the option
is lua the explicit control is in use.
For examples on the usage of the Lua scripting engine and the power you may find the library
flos7 , see https://github.com/siesta-project/flos. At the time of writing the flos library
already implements new geometry/cell relaxation schemes and new force-constants algorithms. You
are highly encouraged to use the new relaxation schemes as they may provide faster convergence of
the relaxation.

Lua.Script 〈none〉 (file)

Specify a Lua script file which may be used to control the internal variables in SIESTA. Such
a script file must contain at least one function named siesta_comm with no arguments.
An example file could be this (note this is Lua code):
-- This function (siesta_comm) is REQUIRED
function siesta_comm()

-- Define which variables we want to retrieve from SIESTA

get_tbl = {"geom.xa", "E.total"}

-- Signal to SIESTA which variables we want to explore

siesta.receive(get_tbl)

-- Now we have the required variables,

-- convert to a simpler variable name (not nested tables)
-- (note the returned quantities are in SIESTA units (Bohr, Ry)
xa = siesta.geom.xa
Etot = siesta.E.total

-- If we know our energy is wrong by 0.001 Ry we may now

-- change the total energy
Etot = Etot - 0.001

-- Return to SIESTA the total energy such that

-- it internally has the "correct" energy.

siesta.E.total = Etot
ret_tbl = {"E.total"}

siesta.send(ret_tbl)

end

Within this function there are certain states which defines different execution points in SIESTA:
7
This library is implemented by Nick R. Papior to further enhance the inter-operability with SIESTA and external
contributions.

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 Initialization This is right after SIESTA has read the options from the FDF file. Here you
may query some of the FDF options (and even change them) for your particular problem.
NOTE: siesta.state == siesta.INITIALIZE.
Initialize-MD Right before the SCF step starts. This point is somewhat superfluous, but is
necessary to communicate the actual meshcutoff used8 .
NOTE: siesta.state == siesta.INIT_MD.
SCF Right after SIESTA has calculated the output density matrix, and just after SIESTA has
performed mixing.
NOTE: siesta.state == siesta.SCF_LOOP.
Forces This stage is right after SIESTA has calculated the forces.
NOTE: siesta.state == siesta.FORCES.
Move This state will only be reached if MD.TypeOfRun is lua.
If one does not return updated atomic coordinates SIESTA will reuse the same geometry as
just analyzed.
NOTE: siesta.state == siesta.MOVE.
Analysis Just before SIESTA completes and exits.
NOTE: siesta.state == siesta.ANALYSIS.
Beginning with implementations of Lua scripts may be cumbersome. It is recommended to
start by using flos, see https://github.com/siesta-project/flos which contains several
examples on how to start implementing your own scripts. Currently flos implements a larger
variety of relaxation schemes, for instance:
local flos = require "flos"
LBFGS = flos.LBFGS()
function siesta_comm()
LBFGS:SIESTA(siesta)
end
which is the most minimal example of using the L-BFGS algorithm for geometry relaxation.
Note that flos reads the parameters MD.MaxCGDispl and MD.MaxForceTol through
SIESTA automatically.
NOTE: The number of available variables continues to grow and to find which quantities are
accessible in Lua you may add this small code in your Lua script:
siesta.print_allowed()
which prints out a list of all accessible variables (note they are not sorted).
If there are any variables you require which are not in the list, please contact the developers.
Remark that since anything may be changed via Lua one may easily make SIESTA crash due to
inconsistencies in the internal logic. This is because SIESTA does not check what has changed,
it accepts everything as is and continues. Hence, one should be careful what is changed.

Lua.Debug false (logical)

Debug the Lua script mode by printing out (on stdout) information everytime SIESTA com-
municates with Lua.
8
Remember that the MeshCutoff defined is the minimum cutoff used.

124
 Lua.Debug.MPI false (logical)
Debug all nodes (if in a parallel run).

Lua.Interactive false (logical)

Start an interactive Lua session at all the states in the program and ask for user-input. This is
primarily intended for debugging purposes. The interactive session is executed just before the
siesta_comm function call (if the script is used).
For serial runs siesta.send may be used. For parallel runs do not use siesta.send as the
code is only executed on the first MPI node.
There are various commands that are caught if they are the only content on a line:
/debug Turn on/off debugging information.
/show Show the currently collected lines of code.
/clear Clears the currently collected lines of code.
; Run the currently collected lines of code and continue collecting lines.
/run Same as ;.
/cont Run the currently collected lines of code and continue SIESTA.
/stop Run the currently collected lines of code and stop all future interactive Lua sessions.
Currently this only works if Lua.Script is having a valid Lua file (note the file may be empty).

9.1 Examples of Lua programs

Please look in the Tests/lua_* folders where examples of basic Lua scripts are found. Below is a
description of the * examples.

h2o Changes the mixing weight continuously in the SCF loop. This will effectively speed up con-
vergence time if one can attain the best mixing weight per SCF-step.

si111 Change the mixing method based on certain convergence criteria. I.e. after a certain conver-
gence one can switch to a more aggressive mixing method.

A combination of the above two examples may greatly improve convergence, however, creating a
generic method to adaptively change the mixing parameters may be very difficult to implement. If
you do create such a Lua script, please share it on the mailing list.

9.2 External MD/relaxation methods

Using the Lua interface allows a very easy interface for creating external MD and/or relaxation
methods.
A public library (flos, https://github.com/siesta-project/flos) already implements a wider
range of relaxation methods than intrinsically enabled in SIESTA. Secondly, by using external
scripting mechanisms one can customize the routines to a much greater extend while simultaneously
create custom constraints.

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You are highly encouraged to try out the flos library (please note that flook is required, see
installation instructions above).

10 TRANSIESTA

SIESTA includes the possibility of performing calculations of electronic transport properties using
the TranSIESTA method. This Section describes how to use these capabilities, and a reference
guide to the relevant fdf options. We describe here only the additional options available for Tran-
SIESTA calculations, while the rest of the Siesta functionalities and variables are described in the
previous sections of this User’s Guide.
An accompanying Python toolbox is available which will assist with TranSIESTA calculations.
Please use (and cite) sisl [11] .

10.1 Source code structure

In this implementation, the TranSIESTA routines have been grouped in a set of modules whose
file names begin with m_ts or ts.

10.2 Compilation

Prior to SIESTA 4.1 TranSIESTA was a separate executable. Now TranSIESTA is fully incor-
porated into SIESTA. Hence simply compile SIESTA and the full functionality is present. Sec. 2
for details on compiling SIESTA.

10.3 Brief description

The TranSIESTA method is a procedure to solve the electronic structure of an open system formed
by a finite structure sandwiched between semi-infinite metallic leads. A finite bias can be applied
between both leads, to drive a finite current. The method is described in detail in Brandbyge
et al. [4] ; Papior et al. [10] . In practical terms, calculations using TranSIESTA involve the solution
of the electronic density from the DFT Hamiltonian using Greens functions techniques, instead of the
usual diagonalization procedure. Therefore, TranSIESTA calculations involve a SIESTA run, in
which a set of routines are invoked to solve the Greens functions and the charge density for the open
system. These routines are packed in a set of modules, and we will refer to it as the ’TranSIESTA
module’ in what follows.
TranSIESTA was originally developed by Mads Brandbyge, José-Luis Mozos, Pablo Ordejón,
Jeremy Taylor and Kurt Stokbro [4] . It consisted, mainly, in setting up an interface between SIESTA
and the (tight-binding) transport codes developed by M. Brandbyge and K. Stokbro. Initially ev-
erything was written in Fortran-77. As SIESTA started to be translated to Fortran-90, so were the
TranSIESTA parts of the code. This was accomplished by José-Luis Mozos, who also worked on
the parallelization of TranSIESTA. Subsequently Frederico D. Novaes extended TranSIESTA to
allow k-point sampling for transverse directions. Additional extensions was added by Nick R. Papior
during 2012.

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The current TranSIESTA module has been completely rewritten by Nick R. Papior and encom-
pass highly advanced inversion algorithms as well as allowing N electrode setups among many new
features. Furthermore, the utility TBtrans has also been fully re-coded (by Nick R. Papior) to be
a generic tight-binding code capable of analyzing physics from the Greens function perspective in
N ≥ 1 setups [10] .

• Transport calculations involve electrode (EL) calculations, and subsequently the Scattering
Region (SR) calculation. The electrode calculations are usual SIESTA calculations, but where
a file SystemLabel.TSHS is generated. These files contain the information necessary for cal-
culation of the self-energies. If any electrodes have identical structures (see below) the same
SystemLabel.TSHS file can be used to describe those. In general, however, electrodes can be
different and therefore two different SystemLabel.TSHS files must be generated. The location
of these electrode files must be specified in the fdf input file of the SR calculation.
• For the SR, TranSIESTA starts with the usual SIESTA procedure, converging a Density
Matrix (DM) with the usual Kohn-Sham scheme for periodic systems. It uses this solution
as an initial input for the Greens function self consistent cycle. As it is known, SIESTA
stores the DM in a file with extension SystemLabel.DM. In the case of TranSIESTA, this is
done in a file named SystemLabel.TSDE. In a rerun of the same system (meaning the same
SystemLabel), if the code finds a SystemLabel.TSDE file in the directory, it will take this
DM as the initial input and this is then considered a continuation run. In this case it does
not perform an initial SIESTA run. It must be clear that when starting a calculation from
scratch, in the end one will find both files, SystemLabel.DM and SystemLabel.TSDE. The first
one stores the SIESTA density matrix (periodic boundary conditions in all directions and no
voltage), and the latter the TranSIESTA solution.
• When performing several bias calculations, it is heavily advised to run different bias’ in dif-
ferent directories. To drastically improve convergence (and throughput) one should copy the
SystemLabel.TSDE from the closest, previously, calculated bias to the current bias.
• The SystemLabel.TSDE may be read equivalently as the SystemLabel.DM. Thus, it may be
used by fx. denchar to analyze the non-equilibrium charge density.
• As in the case of SIESTA calculations, what TranSIESTA does is to obtain a converged DM,
but for open boundary conditions and possibly a finite bias applied between the electrodes.
The corresponding Hamiltonian matrix (once self consistency is achieved) of the SR is also
stored in a SystemLabel.TSHS file. Subsequently, transport properties are obtained in a post-
processing procedure using the TBtrans code (located in the Util/TS/TBtrans directory).
It is to be noted that the SystemLabel.TSHS files contain all the needed structural information
(atomic positions, matrix elements, . . . ), and so this kind of parameters will not be changed
by input (fdf) flags once a SystemLabel.TSHS file is read.
• When the non-equilibrium calculation uses different electrodes one may use so-called buffer
atoms behind the electrodes to act as additional screening regions when calculating the initial
guess (using SIESTA) for TranSIESTA. Essentially they may be used to achieve a better
“bulk-like” environment at the electrodes.
• An important parameter is the lower bound of the energy contours. It is a good practice, to
start with a SIESTA calculation for the SR and look at the eigenvalues of the system. The
lower bound of the contours must be well below the lowest eigenvalue.

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 • TranSIESTA assumes periodic boundary conditions in directions orthogonal to the electrodes
semi-infinite directions. If N > 2 TranSIESTA does not assume anything and one is required
to specify the periodicity (via k-points) separately.

• The default algorithm for matrix inversion is the BTD method, before starting a TranSIESTA
calculation please run with the analyzation step TS.Analyze.

• Importantly(!) the k-point sampling need typically be much higher in a TBtrans calculation
to achieve a converged transmission function.

10.4 Electrodes

To calculate the electronic structure of a system under external bias, TranSIESTA attaches the
system to semi-infinite electrodes which extend to their respective semi-infinite directions. Examples
of electrodes would include surfaces, nanowires, nanotubes or even atomic chains. The electrode must
be large enough (in the semi-infinite direction) so that orbitals within the unit cell only interact
with a single nearest neighbor cell in the semi-infinite direction (the size of the unit cell can thus be
derived from the range of support for the orbital basis functions). TranSIESTA will stop if this
is not enforced. The electrodes are generated by a separate TranSIESTA run on a bulk system.
This implies that the proper bulk properties are obtained by a sufficiently high k-point sampling.
If in doubt, use 100 k-points along the semi-infinite direction. The results are saved in a file with
extension SystemLabel.TSHS which contains a description of the electrode unit cell, the position
of the atoms within the unit cell, as well as the Hamiltonian and overlap matrices that describe
the electronic structure of the lead. One can generate a variety of electrodes and the typical use
of TranSIESTA would involve reusing the same electrode for several setups. At runtime, the
TranSIESTA coordinates are checked against the electrode coordinates and the program stops
if there is a mismatch to a certain precision (10−4 Bohr). Note that the atomic coordinates are
compared relatively. Hence the input atomic coordinates of the electrode and the device need not
be the same (see e.g. the tests in the Tests directory.
To run an electrode calculation one should do:

siesta --electrode RUN.fdf

or define these options in the electrode fdf files: TS.HS.Save and TS.DE.Save to true (the above
–electrode is a shorthand for setting the two options).

10.4.1 Matching coordinates

Here are some rules required to successfully construct the appropriate coordinates of the scattering
region. Contrary to versions prior to 4.1, the order of atoms is largely irrelevant. One may define
all electrodes, then subsequently the device, or vice versa. Similarly, buffer atoms are not restricted
to be the first/last atoms.
However, atoms in any given electrode must be consecutive in the device file. I.e. if an electrode
input option is given by:

%block TS.Elec.<>
HS ../elec-<>/siesta.TSHS

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 bloch 1 3 1
used-atoms 4
electrode-position 10
...
%endblock

then the atoms from 10 to 10 + 4 ∗ 3 − 1 must coincide with the atoms of the calculation performed
in the ../elec-<>/ subdirectory. The above options will be discussed in the coming section.
When using the Bloch expansion (highly recommended if your system allows it) it is advised to
follow the tiling method. However both of the below sequences are allowed.

Tile Here the atoms are copied and displaced by the full electrode. Generally this expansion should
be preferred over the repeat expansion due to faster execution.

iaD = 10 ! as per the above input option

do iC = 0 , nC - 1
do iB = 0 , nB - 1
do iA = 0 , nA - 1
do iaE = 1 , na_u
xyz_device(:, iaD) = xyz_elec(:, iaE) + &
cell_elec(:, 1) * iA + &
cell_elec(:, 2) * iB + &
cell_elec(:, 3) * iC
iaD = iaD + 1
end do
end do
end do
end do

Repeat Here the atoms are copied individually. Generally this expansion should not be used.

iaD = 10 ! as per the above input option

do iaE = 1 , na_u
do iC = 0 , nC - 1
do iB = 0 , nB - 1
do iA = 0 , nA - 1
xyz_device(:, iaD) = xyz_elec(:, iaE) + &
cell_elec(:, 1) * iA + &
cell_elec(:, 2) * iB + &
cell_elec(:, 3) * iC
iaD = iaD + 1
end do
end do
end do
end do

As a help if the electrode coordinates does not coincide, TranSIESTA prints out the expected
coordinates as though the first device atom coincides with the first electrode atom. Another means
to create this is using the sisl [11] program and this command line:

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 sgeom -tx 1 -ty 3 -tz 1 ELEC.fdf DEVICE_ELEC.fdf # Tile
sgeom -rz 1 -ry 3 -rx 1 ELEC.fdf DEVICE_ELEC.fdf # Repeat

and then shift the coordinates according to the placement in the device region. Note how repeating
has different argument order of tiling.

10.4.2 Principal layer interactions

It is extremely important that the electrodes only interact with one neighboring supercell due to the
self-energy calculation [12] . TranSIESTA will print out a block as this

<> principal cell is perfect!

if the electrode is correctly setup and it only interacts with its neighboring supercell. In case the
electrode is erroneously setup, something similar to the following will be shown in the output file.

<> principal cell is extending out with 96 elements:

Atom 1 connects with atom 3
Orbital 8 connects with orbital 26
Hamiltonian value: |H(8,6587)|@R=-2 = 0.651E-13 eV
Overlap : S(8,6587)|@R=-2 = 0.00

It is imperative that you have a perfect electrode as otherwise nonphysical results will occur.
By default TranSIESTA will die if there are connections beyond the principal cell. One may control
whether this is allowed or not by using TS.Elecs.Neglect.Principal.

10.5 TranSIESTA Options

The fdf options shown here are only to be used at the input file for the scattering region. When
using TranSIESTA for electrode calculations, only the usual SIESTA options are relevant. Note
that since TranSIESTA is a generic N electrode NEGF code the input options are heavily changed
compared to versions prior to 4.1.

10.5.1 Quick and dirty

Since 4.1, TranSIESTA has been fully re-implemented. And so have every input fdf-flag. To
accommodate an easy transition between previous input files and the new version format a small
utility called ts2ts. It may be compiled in Util/TS/ts2ts. It is recommended that you use this
tool if you are familiar with previous TranSIESTA versions.
One may input options as in the old TranSIESTA version and then run

ts2ts OLD.fdf > NEW.fdf

which translates all keys to the new, equivalent, input format. If you are familiar with the old-style
flags this is highly recommendable while becoming comfortable with the new input format. Please
note that some defaults have changed to more conservative values in the newer release.

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If one does not know the old flags and wish to get a basic example of an input file, a script
Util/TS/tselecs.sh exists that can create the basic input for N electrodes. One may call it
like:

tselecs.sh -2 > TWO_ELECTRODE.fdf

tselecs.sh -3 > THREE_ELECTRODE.fdf
tselecs.sh -4 > FOUR_ELECTRODE.fdf
...

where the first call creates an input fdf for 2 electrode setups, the second for a 3 electrode setup,
and so on. See the help (-h) for the program for additional options.
Before endeavoring on large scale calculations you are advised to run an analyzation of the system
at hand, you may run your system as

siesta -fdf TS.Analyze RUN.fdf > analyze.out

which will analyze the sparsity pattern and print out several different pivoting schemes. Please see
TS.Analyze for additional information.

10.5.2 General options

One have to set SolutionMethod to transiesta to enable TranSIESTA.

TS.SolutionMethod btd|mumps|full (string)

Control the algorithm used for calculating the Green function. Generally the BTD method is
the fastest and this option need not be changed.
BTD Use the block-tri-diagonal algorithm for matrix inversion.
This is generally the recommended method.
MUMPS Use sparse matrix inversion algorithm (MUMPS). This requires TranSIESTA to be
compiled with MUMPS.
full Use full matrix inversion algorithm (LAPACK). Generally only usable for debugging pur-
poses.

TS.Voltage 0 eV (energy)
Define the reference applied bias. For N = 2 electrode calculations this refers to the actual
potential drop between the electrodes, while for N 6= 2 this is a reference bias. In the latter
case it must be equivalent to the maximum difference between the chemical potential of any
two electrodes.

TS.Atoms.Buffer 〈None〉 (block/list)

Specify atoms that will be removed in the TranSIESTA SCF. They are not considered in the
calculation and may be used to improve the initial guess for the Hamiltonian. Their main usage
is to extend electrodes in their semi-infinite directions.
NOTE: all lines are additive for the buffer atoms and the input method is similar to that of
Geometry.Constraints for the atom line(s).

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 %block TS.Atoms.Buffer
atom [ 1 -- 5 ]
%endblock
# Or equivalently as a list
TS.Atoms.Buffer [1 -- 5]
will remove atoms [1–5] from the calculation.

TS.ElectronicTemperature 〈ElectronicTemperature〉 (energy)

Define the temperature used for the Fermi distributions for the chemical potentials. See
TS.ChemPot.<>.ElectronicTemperature.

TS.SCF.Initialize diagon|transiesta (string)

Control which initial guess should be used for TranSIESTA. The general way is the diagon
solution method (which is preferred), however, one can start a TranSIESTA run immedi-
ately. If you start directly with TranSIESTA please refer to these flags: TS.Elecs.DM.Init,
DM.Init.Bulk and TS.Fermi.Initial.
NOTE: Setting this to transiesta is highly experimental and convergence may be extremely
poor.
P NE i
TS.Fermi.Initial i EF /NE (energy)
Manually set the initial Fermi level to a predefined value.
NOTE: this may also be used to change the Fermi level for calculations where you restart
calculations. Using this feature is highly experimental.

TS.Weight.Method orb-orb|[[un]correlated+][sum|tr]-atom-[atom|orb]|mean (string)

Control how the NEGF weighting scheme is conducted. Generally one should only use the
orb-orb while the others are present for more advanced usage. They refer to how the weighting
coefficients of the different non-equilibrium contours are performed. In the following the weight
are denoted in a two-electrode setup while they are generalized for multiple electrodes.
Define the normalised geometric mean as ∝|| via
|| h·L i
w ∝ h·L i ≡ . (19)
h·L i + h·R i

orb-orb Weight each orbital-density matrix element individually.

tr-atom-atom Weight according to the trace of the atomic density matrix sub-blocks
||
sX X
Tr
wij ∝ (∆ρL
µµ )
2 (∆ρL
µµ )
2 (20)
∈{i} ∈{j}

tr-atom-orb Weight according to the trace of the atomic density matrix sub-block times the
weight of the orbital weight
||
q
Tr Tr w
wij,µν ∝ wij ij,µν (21)

sum-atom-atom Weight according to the total sum of the atomic density matrix sub-blocks
||
sX X
Σ
wij,µν ∝ (∆ρL
µν )
2 (∆ρL
µν )
2 (22)
∈{i} ∈{j}

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 sum-atom-orb Weight according to the total sum of the atomic density matrix sub-block times
the weight of the orbital weight
||
q
Σ Σw
wij,µν ∝ wij ij,µν (23)

mean A standard average.

P
Each of the methods (except mean) comes in a correlated and uncorrelated variant where
is either outside or inside the square, respectively.

TS.Weight.k.Method correlated|uncorrelated (string)

Control weighting per k-point or the full sum. I.e. if uncorrelated is used it will weight nk
times if there are nk k-points in the Brillouin zone.

TS.Forces true (logical)

Control whether the forces are calculated. If not TranSIESTA will use slightly less memory
and the performance slightly increased, however the final forces shown are incorrect.

TS.ChargeCorrection none|buffer|fermi (string)

Any excess/deficiency of charge can be re-adjusted after each TranSIESTA cycle to reduce
charge fluctuations in the cell.
none No charge corrections are introduced.
buffer Excess/missing electrons are placed in the buffer regions (buffer atoms are required to
exist)
fermi Correct the filling by calculating a new Fermi-level (reference energy).
We approximate the contribution to be constant around the Fermi level and find
Q0 − Q
dEF = , (24)
Q|EF

where Q0 is the charge from a converged TranSIESTA calculation and Q|EF is the equilib-
rium charge at the current Fermi level, Q is the supposed charge to reside in the calculation.
Fermi correction utilizes Eq. (24) for the first correction and all subsequent corrections are
based on a cubic spline interpolation to much faster converge to the “correct” Fermi level.
This method will create a file called TS_FERMI.

TS.ChargeCorrection.Factor 0.75 (real)

Should be between 0 and 1 to lower the charge adjustment. 0 means no charge correction. 1
means total charge correction. This will reduce the fluctuations in the SCF and setting this to
1 may result in difficulties in converging.

TS.ChargeCorrection.Fermi.Tolerance 0.01 (real)

The tolerance at which the charge correction will converge. Any excess/missing charge (|Q0 −
Q| > Tol) will result in a correction for the Fermi level.

TS.ChargeCorrection.Fermi.Max 1.5 eV (energy)

The maximally allowed value that the Fermi level will change from a charge correction using
the Fermi correction method. In case the Fermi level lies in between two bands a DOS of 0 at

133
 the Fermi level will make the Fermi change equal to ∞. This is not physical and the user can
thus truncate the correction.
If you know the band-gab, setting this to 1/4 (or smaller) of the band gab seems like a better
value than the rather arbitrarily default one.

TS.HS.Save true (logical)

Must be true for saving the Hamiltonian (SystemLabel.TSHS). Can only be set if Solution-
Method is not transiesta.
The default is false for SolutionMethod different from transiesta and if –electrode has
not been passed as a command line argument.

TS.DE.Save true (logical)

Must be true for saving the density and energy density matrix for continuation runs
(SystemLabel.TSDE). Can only be set if SolutionMethod is not transiesta.
The default is false for SolutionMethod different from transiesta and if –electrode has
not been passed as a command line argument.

TS.S.Save false (logical)

This is a flag mainly used for the Inelastica code to produce overlap matrices for Pulay correc-
tions. This should only be used by advanced users.

TS.SIESTA.Only false (logical)

Stop TranSIESTA right after the initial diagonalization run in SIESTA. Upon exit it will
also create the SystemLabel.TSDE file which may be used for initialization runs later.
This may be used to start several calculations from the same initial density matrix, and it
may also be used to rescale the Fermi level of electrodes. The rescaling is primarily used for
semi-conductors where the Fermi levels of the device and electrodes may be misaligned.

TS.Analyze false (logical)

When using the BTD solution method (TS.SolutionMethod) this will analyze the Hamilto-
nian and printout an analysis of the sparsity pattern for optimal choice of the BTD partitioning
algorithm.
This yields information regarding the TS.BTD.Pivot flag.
NOTE: we advice users to always run an analyzation step prior to actual calculation and
select the best BTD format. This analyzing step is very fast and may be performed on small
work-station computers, even on systems of  10, 000 orbitals.
To run the analyzing step you may do:
siesta -fdf TS.Analyze RUN.fdf > analyze.out

note that there is little gain on using MPI and it should complete within a few minutes, no
matter the number of orbitals.
Choosing the best one may be difficult. Generally one should choose the pivoting scheme that
uses the least amount of memory. However, one should also choose the method with the largest
block-size being as small as possible. As an example:
TS.BTD.Pivot atom+GPS
...
BTD partitions (7):

134
 [ 2984, 2776, 192, 192, 1639, 4050, 105 ]
BTD matrix block size [max] / [average]: 4050 / 1705.429
BTD matrix elements in % of full matrix: 47.88707 %

TS.BTD.Pivot atom+GGPS
...
BTD partitions (6):
[ 2880, 2916, 174, 174, 2884, 2910 ]
BTD matrix block size [max] / [average]: 2916 / 1989.667
BTD matrix elements in % of full matrix: 48.62867 %

Although the GPS method uses the least amount of memory, the GGPS will likely perform
better as the largest block in GPS is 4050 vs. 2916 for the GGPS method.

TS.Analyze.Graphviz false (logical)

depends on: TS.Analyze
If performing the analysis, also create the connectivity graph and store it as GRAPHVIZ_atom.gv
or GRAPHVIZ_orbital.gv to be post-processed in Graphviz9 .

10.5.3 Algorithm specific options

These options adhere to the specific solution methods available for TranSIESTA. For instance the
TS.BTD.* options adhere only when using TS.SolutionMethod BTD, similarly for options with
MUMPS.

TS.BTD.Pivot 〈first electrode〉 (string)

Decide on the partitioning for the BTD matrix. One may denote either atom+ or orb+ as a
prefix which does the analysis on the atomic sparsity pattern or the full orbital sparsity pattern,
respectively. If neither are used it will default to atom+.
Please see TS.Analyze.
<elec-name>|CG-<elec-name> The partitioning will be a connectivity graph starting from
the electrode denoted by the name. This name must be found in the TS.Elecs block. One
can append more than one electrode to simultaneously start from more than 1 electrode. This
may be necessary for multi-terminal calculations.
rev-CM Use the reverse Cuthill-McKee for pivoting the matrix elements to reduce bandwidth.
One may omit rev- to use the standard Cuthill-McKee algorithm (not recommended).
This pivoting scheme depends on the initial starting electrodes, append +<elec-name> to
start the Cuthill-McKee algorithm from the specified electrode.
GPS Use the Gibbs-Poole-Stockmeyer algorithm for reducing the bandwidth.
GGPS Use the generalized Gibbs-Poole-Stockmeyer algorithm for reducing the bandwidth.
NOTE: this algorithm does not work on dis-connected graphs.
PCG Use the perphiral connectivity graph algorithm for reducing the bandwidth.
This pivoting scheme may depend on the initial starting electrode(s), append +<elec-
name> to initialize the PCG algorithm from the specified electrode.
9
www.graphviz.org

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 Examples are
TS.BTD.Pivot atom+GGPS
TS.BTD.Pivot GGPS
TS.BTD.Pivot orb+GGPS
TS.BTD.Pivot orb+PCG+Left

where the first two are equivalent. The 3rd and 4th are more heavy on analysis and will typically
not improve the bandwidth reduction.

TS.BTD.Optimize speed|memory (string)

When selecting the smallest blocks for the BTD matrix there are certain criteria that may
change the size of each block. For very memory consuming jobs one may choose the memory.
NOTE: often both methods provide exactly the same BTD matrix due to constraints on the
matrix.

TS.BTD.Guess1.Min 〈empirically determined〉 (int)

depends on: TS.BTD.Guess1.Max
Constructing the blocks for the BTD starts by guessing the first block size. One could guess on
all different block sizes, but to speed up the process one can define a smaller range of guesses
by defining TS.BTD.Guess1.Min and TS.BTD.Guess1.Max.
The initial guessed block size will be between the two values.
By default this is 1/4 of the minimum bandwidth for a selected first set of orbitals.
NOTE: setting this to 1 may sometimes improve the final BTD matrix blocks.

TS.BTD.Guess1.Max 〈empirically determined〉 (int)

depends on: TS.BTD.Guess1.Min
See TS.BTD.Guess1.Min.
NOTE: for improved initialization performance setting Min/Max flags to the first block size for
a given pivoting scheme will drastically reduce the search space and make initialization much
faster.

TS.BTD.Spectral propagation|column (string)

How to compute the spectral function (GΓG† ).
For N < 4 this defaults to propagation which should be the fastest.
For N ≥ 4 this defaults to column.
Check which has the best performance for your system if you endeavor on huge amounts of
calculations for the same system.

TS.MUMPS.Ordering 〈read MUMPS manual〉 (string)

One may select from a number of different matrix orderings which are all described in the
MUMPS manual.
The following list of orderings are available (without detailing their differences): auto, AMD,
AMF, SCOTCH, PORD, METIS, QAMD.

TS.MUMPS.Memory 20 (integer)
Specify a factor for the memory consumption in MUMPS. See the INFOG(9) entry in the
MUMPS manual. Generally if TranSIESTA dies and INFOG(9)=-9 one should increase

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 this number.

TS.MUMPS.BlockingFactor 112 (integer)

Specify the number of internal block sizes. Larger numbers increases performance at the cost
of memory.
NOTE: this option may heavily influence performance.

10.5.4 Poisson solution for fixed boundary conditions

TranSIESTA requires fixed boundary conditions and forcing this is an intricate and important
detail.

TS.Poisson ramp-central|elec-box|〈file〉|ramp-cell (string)

Define how the correction of the Poisson equation is superimposed. The default is to apply
the linear correction across the central region (if there are two semi-infinite aligned electrodes).
Otherwise this defaults to the box solution which will introduce spurious effects at the electrode
boundaries. In this case you are encouraged to supply a file.
If the input is a file, it should be a NetCDF file containing the grid information which acts as
the boundary conditions for the SCF cycle. The grid information should conform to the grid
size of the unit-cell in the simulation. NOTE: the file option is only applicable if compiled with
CDF4 compliance.
ramp-central Apply the bias-ramp between the leads. For a bulk electrode (see
TS.Elec.<>.Bulk) the ramp will start at the electrode-device interface, otherwise it will
start at the beginning of the electrode.
<file> Specify an external file used as the boundary conditions for the applied bias. This is
encouraged to use for N > 2 electrode calculations but may also be used when an a priori
potential profile is know.
The file should contain something similar to this output (ncdump -h):
netcdf <file> {
dimensions:
one = 1 ;
a = 43 ;
b = 451 ;
c = 350 ;
variables:
double Vmin(one) ;
Vmin:unit = "Ry" ;
double Vmax(one) ;
Vmax:unit = "Ry" ;
double V(c, b, a) ;
V:unit = "Ry" ;
}
Note that the units should be in Ry. Vmax/Vmin should contain the maximum/minimum
fixed boundary conditions in the Poisson solution. This is used internally by TranSIESTA
to scale the potential to arbitrary V . This enables the Poisson solution to only be solved
once independent on subsequent calculations For some chemical potential configurations the
Poisson solution cannot be linearly extrapolated, in which case a separate file is required for

137
 each applied bias.
elec-box The default potential profile for N > 2, or when the electrodes does are not aligned
(in terms of their transport direction).
NOTE: usage of this Poisson solution is highly discouraged. Please see TS.Poisson <file>.
ramp-cell Apply the ramp for the full cell. This option should only be used for testing against
older versions of TranSIESTA.

TS.Hartree.Fix plane|elec-plane|elec-box (string)

As the fixed boundary conditions requires a fixed reference potential. For two electrode calcu-
lations this defaults to taking the plane at one of the electrodes basal-planes (plane).
For anything but two electrodes this defaults to elec-plane because the plane should be at a
fixed position in the cell.
NOTE: generally this need not be changed.

TS.Hartree.Fix.Elec electrode name (string)

depends on: TS.Hartree.Fix
Specifically select an electrode’s boundary plane to be used as the constant potential boundary.
The electrode unit-cell plane is integrated and subtracted from all potential grid-points to ensure
a constant potential at the interface between the electrode in the pristine calculation and in the
device calculation.
TranSIESTA defaults to select the electrode plane which has the largest area.
NOTE: this may be important in N > 2 electrode calculations where some electrodes may
have a huge semi-infinite surface plane but a limited amount of atoms. It is heavily advised
to select the electrode with the largest number of atoms in a plane-cut perpendicular to the
semi-infinite direction.

TS.Hartree.Fix.Frac 1. (real)
Fraction of the correction that is applied.
NOTE: this is an experimental feature!

TS.Hartree.Offset 0 eV (energy)
An offset in the Hartree potential to match the electrode potential.
This value may be useful in certain cases where the Hartree potentials are very different between
the electrode and device region calculations.

TS.Elec.<>.Hartree.Extend 0. Ang (length)

depends on: TS.Poisson ramp-central, TS.Poisson ramp-cell
The potential profile will by default be terminated at the interface between the electrode and
the device. However, as one requires a screening region between the electrode and the actual
scattering region one may argue that the electrode potential will extend further into the device.
This flag increases the electrode potentials extend into the device region.
It may help convergence but should not be so large it extends into the scattering region.
NOTE: This only affects 2 electrode calculations when TS.Poisson ramp-central or
TS.Poisson ramp-cell.

138
10.5.5 Electrode description options

As TranSIESTA supports N electrodes one needs to specify all electrodes in a generic input format.

%block TS.Elecs 〈None〉 (block)

Each line denote an electrode which is queried in TS.Elec.<> for its setup.

%block TS.Elec.<> 〈None〉 (block)

Each line represents a setting for electrode <>. There are a few lines that must be present,
HS, semi-inf-dir, electrode-pos, chem-pot. The remaining options are optional.
NOTE: Options prefixed with tbt are neglected in TranSIESTA calculations. In TBtrans
calculations these flags has precedence over the other options.
HS The Hamiltonian information from the initial electrode calculation. This file retains the
geometrical information as well as the Hamiltonian, overlap matrix and the Fermi-level of the
electrode. This is a file-path and the electrode SystemLabel.TSHS need not be located in the
simulation folder.
semi-inf-direction|semi-inf-dir|semi-inf The semi-infinite direction of the electrode with re-
spect to the electrode unit-cell.
NOTE: this direction is not with respect to the scattering region unit cell. It is with respect
to the electrode unit cell. TranSIESTA will figure out the alignment of the electrode unit
cell and the scattering region unit-cell.
chemical-potential|chem-pot|mu The chemical potential that is associated with this elec-
trode. This is a string that should be present in the TS.ChemPots block.
electrode-position|elec-pos The index of the electrode in the scattering region. This may
be given by either elec-pos <idx>, which refers to the first atomic index of the electrode
residing at index <idx>. Else the electrode position may be given via elec-pos end <idx>
where the last index of the electrode will be located at <idx>.
used-atoms Number of atoms from the electrode calculation that is used in the scattering
region as electrode. This may be useful when the periodicity of the electrodes forces extensive
electrodes in the semi-infinite direction.
NOTE: do not set this if you use all atoms in the electrode.
Bulk Logical controlling whether the Hamiltonian of the electrode region in the scattering region
is enforced bulk or whether the Hamiltonian is taken from the scattering region elements. If
DM-update depends on: TS.Elec.<>.Bulk
String of values none, cross-terms or all which controls which part of the electrode density
matrix elements that are updated. If all, both the density matrix elements in the electrode
and the coupling elements between the electrode and scattering region are updated. If cross-
terms (default) only the coupling elements between the electrode and the scattering region
are updated.
If TS.Elec.<>.Bulk false this is forced to all.
Gf String with filename of the surface Green function data. This may be used to place a common
surface Green function file in a top directory which may then be used in all calculations using
the same electrode and the same contour. If many calculations are performed this will heavily

139
 increase performance at the cost of disk-space.
Gf-Reuse Logical deciding whether the surface Green function file should be re-used or deleted.
If this is false the surface Green function file is deleted and re-created upon start.
Eta depends on: TS.Elecs.Eta
Control the imaginary part of the surface Green function for this electrode.
Accuracy depends on: TS.Elecs.Accuracy
Control the convergence accuracy required for the self-energy calculation when using the
Lopez-Sanchez, Lopez-Sanchez iterative scheme.
NOTE: advanced use only.
DE Density and energy density matrix file for the electrode. This may be used to initialize the
density matrix elements in the electrode region by the bulk values. This may be used to
increase the bulk-like behavior of the electrodes.
NOTE: this should only be performed on one TranSIESTA calculation as then the scat-
tering region SystemLabel.TSDE contains the electrode density matrix.
Bloch 3 integers should be present on this line which each denote the number of times bigger
the scattering region electrode is compared to the electrode, in each lattice direction. Remark
that these expansion coefficients are with regard to the electrode unit-cell. This is denoted
“Bloch” because it is an expansion based on Bloch waves.
Bloch-A/a1|B/a2|C/a3 Specific Bloch expansions in each of the electrode unit-cell direction.
See Bloch for details.
pre-expand String denoting how the expansion of the surface Green function file will be per-
formed. This only affects the Green function file if Bloch is larger than 1. By default the
Green function file will contain the fully expanded surface Green function, but not Hamilto-
nian and overlap matrices (Green). One may reduce the file size by setting this to Green
which only expands the surface Green function. Finally none may be passed to reduce the
file size to the bare minimum. For performance reasons all is preferred.
out-of-core If true (default) the GF files are created which contain the surface Green function.
If false the surface Green function will be calculated when needed. Setting this to false will
heavily degrade performance and it is highly discouraged!
check-kgrid For N electrode calculations the k mesh will sometimes not be equivalent for the
electrodes and the device region calculations. However, TranSIESTA requires that the
device and electrode k samplings are commensurate. This flag controls whether this check is
enforced.
NOTE: only use if fully aware of the implications!

There are several flags which are globally controlling the variables for the electrodes (with
TS.Elec.<> taking precedence).

TS.Elecs.Bulk true (logical)

This globally controls how the Hamiltonian is treated in all electrodes. See TS.Elec.<>.Bulk.

TS.Elecs.Eta 10−4 eV (energy)

Globally control the imaginary part used for the surface Green function calculation. See

140
 TS.Elec.<>.Eta.

TS.Elecs.Accuracy 10−13 eV (energy)

Globally control the accuracy required for convergence of the self-energy. See
TS.Elec.<>.Accuracy.

TS.Elecs.Neglect.Principal false (logical)

If this is false TranSIESTA dies if there are connections beyond the principal cell.
NOTE: set this to true with care, non-physical results may arise. Use at your own risk!

TS.Elecs.Gf.Reuse true (logical)

Globally control whether the surface Green function files should be re-used (true) or re-created
(false). See TS.Elec.<>.Gf-Reuse.

TS.Elecs.Out-of-core true (logical)

Whether the electrodes will calculate the self energy at each SCF step. Using this will not
require the surface Green function files but at the cost of heavily degraded performance. You
are not encouraged to set this to false. See TS.Elec.<>.Out-of-core.

TS.Elecs.DM.Update cross-terms|all|none (string)

This globally controls which parts of the electrode density matrix gets updated. See
TS.Elec.<>.DM-Update.

TS.Elecs.DM.Init diagon|bulk (string)

The density matrix elements in the electrodes may be forcefully set to the bulk values by reading
in the DM of the corresponding electrode. This may be set to bulk to forcefully set the bulk
values.
NOTE: this will automatically be set to diagon for non-equilibrium calculations. If bulk
density matrix elements are wanted in the electrodes it is vital to have this option set to bulk
when performing the equilibrium calculation.

TS.Elecs.Coord.EPS 0.001 Ang (length)

When using Bloch expansion of the self-energies one may experience difficulties in obtaining
perfectly aligned electrode coordinates.
This parameter controls how strict the criteria for equivalent atomic coordinates is. If Tran-
SIESTA crashes due to mismatch between the electrode atomic coordinates and the scattering
region calculation, one may increase this criteria. This should only be done if one is sure that
the atomic coordinates are almost similar and that the difference in electronic structures of the
two may be negligible.

10.5.6 Chemical potentials

For N electrodes there will also be Nµ chemical potentials. They are defined via blocks similar to
TS.Elecs.

%block TS.ChemPots 〈None〉 (block)

Each line denotes a new chemical potential which is defined in the TS.ChemPot.<> block.

141
 %block TS.ChemPot.<> 〈None〉 (block)
Each line defines a setting for the chemical potential named <>.
chemical-shift|mu Define the chemical shift (an energy) for this chemical potential. One may
specify the shift in terms of the applied bias using V/<integer> instead of explicitly typing
the energy.
contour.eq A subblock which defines the integration curves for the equilibrium contour for
this equilibrium chemical potential. One may supply as many different contours to create
whatever shape of the contour
Its format is
contour.eq
begin
<contour-name-1>
<contour-name-2>
...
end
NOTE: If you do not specify contour.eq in the block one will automatically use the con-
tinued fraction method and you are encouraged to use 50 or more poles [8] .
ElectronicTemperature|Temp|kT Specify the electronic temperature (as an energy or in
Kelvin). This defaults to TS.ElectronicTemperature.
One may specify this in units of TS.ElectronicTemperature by using the unit kT.
contour.eq.pole Define the number of poles used via an energy specification. TranSIESTA
will automatically convert the energy to the closest number of poles (rounding up).
NOTE: this has precedence over TS.ChemPot.<>.contour.eq.pole.N if it is specified
and a positive energy. Set this to a negative energy to directly control the number of poles.
contour.eq.pole.N Define the number of poles via an integer.
NOTE: this will only take effect if TS.ChemPot.<>.contour.eq.pole is a negative energy.
It is important to realize that the parameterization of the voltage into the chemical potentials
enables one to have a single input file which is never required to be changed, even when changing
the applied bias.

These options complicate the input sequence for regular 2 electrode which is unfortunate.
Using tselecs.sh -only-mu yields this output:

%block TS.ChemPots
Left
Right
%endblock
%block TS.ChemPot.Left
mu V/2
contour.eq
begin
C-Left
T-Left
end
%endblock

142
 %block TS.ChemPot.Right
mu -V/2
contour.eq
begin
C-Right
T-Right
end
%endblock

Note that the default is a 2 electrode setup with chemical potentials associated directly with the
electrode names “Left”/“Right”. Each chemical potential has two parts of the equilibrium contour
named according to their name.

10.5.7 Complex contour integration options

Specifying the contour for N electrode systems is a bit extensive due to the possibility of more than 2
chemical potentials. Please use the Util/TS/tselecs.sh as a means to create default input blocks.
The contours are split in two segments. One, being the equilibrium contour of each of the different
chemical potentials. The second for the non-equilibrium contour. The equilibrium contours are
shifted according to their chemical potentials with respect to a reference energy. Note that for
TranSIESTA the reference energy is named the Fermi-level, which is rather unfortunate (for non-
equilibrium but not equilibrium). Fortunately the non-equilibrium contours are defined from different
chemical potentials Fermi functions, and as such this contour is defined in the window of the minimum
and maximum chemical potentials. Because the reference energy is the periodic Fermi level it is
advised to retain the average chemical potentials equal to 0. Otherwise applying different bias will
shift transmission curves calculated via TBtrans relative to the average chemical potential.
In this section the equilibrium contours are defined, and in the next section the non-equilibrium
contours are defined.

TS.Contours.Eq.Pole 2.5 eV (energy)

The imaginary part of the line integral crossing the chemical potential. Note that the actual
number of poles may differ between different calculations where the electronic temperatures are
different.
NOTE: if the energy specified is negative, TS.Contours.Eq.Pole.N takes effect.

TS.Contours.Eq.Pole.N 8 (integer)
Manually select the number poles for the equilibrium contour.
NOTE: this flag will only take effect if TS.Contours.Eq.Pole is a negative energy.

%block TS.Contour.<> 〈None〉 (block)

Specify a contour named <> with options within the block.
The names <> are taken from the TS.ChemPot.<>.contour.eq block in the chemical po-
tentials.
The format of this block is made up of at least 4 lines, in the following order of appearance.
part Specify which part of the equilibrium contour this is:
circle The initial circular part of the contour

143
 square The initial square part of the contour
line The straight line of the contour
tail The final part of the contour must be a tail which denotes the Fermi function tail.
from a to b Define the integration range on the energy axis. Thus a and b are energies.
The parameters may also be given values prev/next which is the equivalent of specifying
the same energy as the previous contour it is connected to.
NOTE: that b may be supplied as inf for tail parts.
points/delta Define the number of integration points/energy separation. If specifying the num-
ber of points an integer should be supplied.
If specifying the separation between consecutive points an energy should be supplied.
method Specify the numerical method used to conduct the integration. Here a number of
different numerical integration schemes are accessible
mid|mid-rule Use the mid-rule for integration.
simpson|simpson-mix Use the composite Simpson 3/8 rule (three point Newton-Cotes).
boole|boole-mix Use the composite Booles rule (five point Newton-Cotes).
G-legendre Gauss-Legendre quadrature.
NOTE: has opt left
NOTE: has opt right
tanh-sinh Tanh-Sinh quadrature.
NOTE: has opt precision <>
NOTE: has opt left
NOTE: has opt right
G-Fermi Gauss-Fermi quadrature (only on tails).
opt Specify additional options for the method. Only a selected subset of the methods have
additional options.

These options complicate the input sequence for regular 2 electrode which is unfortunate. However,
it allows highly customizable contours.
Using tselecs.sh -only-c yields this output:

TS.Contours.Eq.Pole 2.5 eV
%block TS.Contour.C-Left
part circle
from -40. eV + V/2 to -10 kT + V/2
points 25
method g-legendre
%endblock
%block TS.Contour.T-Left
part tail
from prev to inf
points 10
method g-fermi

144
 %endblock
%block TS.Contour.C-Right
part circle
from -40. eV -V/2 to -10 kT -V/2
points 25
method g-legendre
%endblock
%block TS.Contour.T-Right
part tail
from prev to inf
points 10
method g-fermi
%endblock

These contour options refer to input options for the chemical potentials as shown in Sec. 10.5.6
(p. 141). Importantly one should note the shift of the contours corresponding to the chemical
potential (the shift corresponds to difference from the reference energy used in TranSIESTA).

10.5.8 Bias contour integration options

The bias contour is similarly defined as the equilibrium contours. Please use the
Util/TS/tselecs.sh as a means to create default input blocks.

TS.Contours.nEq.Eta 0 eV (energy)
The imaginary part (η) of the device states. Generally this is not necessary to define as the
imaginary part naturally arises from the self-energies (where η > 0).

TS.Contours.nEq.Fermi.Cutoff 5 kB T (energy)
The bias contour is limited by the Fermi function tails. Numerically it does not make sense to
integrate to infinity. This energy defines where the bias integration window is turned into zero.
Thus above −|V |/2 − E or below |V |/2 + E the DOS is defined as exactly zero.

%block TS.Contours.nEq 〈None〉 (block)

Each line defines a new contour on the non-equilibrium bias window. The contours defined must
be defined in TS.Contour.nEq.<>.
These contours must all be part line or part tail.

%block TS.Contour.nEq.<> 〈None〉 (block)

This block is exactly equivalently defined as the TS.Contour.<>. See page 143.

The default options related to the non-equilibrium bias contour are defined as this:
%block TS.Contours.nEq
neq-1
%endblock TS.Contours.nEq
%block TS.Contour.nEq.neq-1
part line
from -|V|/2 - 5 kT to |V|/2 + 5 kT
delta 0.01 eV
method mid-rule
%endblock TS.Contour.nEq.neq-1

145
If one chooses a different reference energy than 0, then the limits should change accordingly. Note
that here kT refers to TS.ElectronicTemperature.

10.6 Output

TranSIESTA generates several output files.

SystemLabel.DM : The SIESTA density matrix. SIESTA initially performs a calculation at zero
bias assuming periodic boundary conditions in all directions, and no voltage, which is used as
a starting point for the TranSIESTA calculation.

SystemLabel.TSDE : The TranSIESTA density matrix and energy density matrix. During a
TranSIESTA run, the SystemLabel.DM values are used for the density matrix in the buffer
(if used) and electrode regions. The coupling terms may or may not be updated in a Tran-
SIESTA run, see TS.Elec.<>.DM-Update.

SystemLabel.TSHS : The Hamiltonian corresponding to SystemLabel.TSDE. This file also contains

geometry information etc. needed by TranSIESTA and TBtrans.

SystemLabel.TS.KP : The k-points used in the TranSIESTA calculation. See SIESTA

SystemLabel.KP file for formatting information.

SystemLabel.TSCCEQ* : The equilibrium complex contour integration paths.

SystemLabel.TSCCNEQ* : The non-equilibrium complex contour integration paths.

SystemLabel.TSGF* : Self-energy files containing the used self-energies from the leads. These are
very large files used in the SCF loop. Once completed one can safely delete these files. For
heavily increased throughput these files may be re-used for the same electrode settings in
various calculations.

10.7 Utilities for analysis: TBtrans

Please see the separate TBtrans manual (tbtrans.pdf).

11 ANALYSIS TOOLS

There are a number of analysis tools and programs in the Util directory. Some of them have
been directly or indirectly mentioned in this manual. Their documentation is the appropriate sub-
directory of Util. See Util/README.
In addition to the shipped utilities SIESTA is also officially supported by sisl [11] which is a Python
library enabling many of most commonly encountered things.

146
12 SCRIPTING

In the Util/Scripting directory we provide an experimental python scripting framework built

on top of the “Atomic Simulation Environment” (see https://wiki.fysik.dtu.dk/ase2) by the
Campos group at DTU, Denmark.
(NOTE: “ASE version 2”, not the new version 3, is needed)
There are objects implementing the “Siesta as server/subroutine” feature, and also hooks for file-
oriented-communication usage. This interface is different from the SIESTA-specific functionality
already contained in the ASE framework.
Users can create their own scripts to customize the “outer geometry loop” in SIESTA, or to perform
various repetitive calculations in compact form.
Note that the interfaces in this framework are still evolving and are subject to change.
Suggestions for improvements can be sent to Alberto Garcia ([email protected])

13 PROBLEM HANDLING

13.1 Error and warning messages

chkdim: ERROR: In routine dimension parameter = value. It must be ... And other
similar messages.
Description: Some array dimensions which change infrequently, and do not lead to much
memory use, are fixed to oversized values. This message means that one of this parameters
is too small and neads to be increased. However, if this occurs and your system is not very
large, or unusual in some sense, you should suspect first of a mistake in the data file (incorrect
atomic positions or cell dimensions, too large cutoff radii, etc).
Fix: Check again the data file. Look for previous warnings or suspicious values in the output.
If you find nothing unusual, edit the specified routine and change the corresponding parameter.

14 REPORTING BUGS

Your assistance is essential to help improve the program. If you find any problem, or would like to
offer a suggestion for improvement, please follow the instructions in the file Docs/REPORTING_BUGS.
Since SIESTA has moved to Launchpad you are encouraged to follow the instructions presented at:
https://answers.launchpad.net/siesta/+faq/2779.

15 ACKNOWLEDGMENTS

We want to acknowledge the use of a small number of routines, written by other authors, in de-
veloping the siesta code. In most cases, these routines were acquired by now-forgotten routes, and
the reported authorships are based on their headings. If you detect any incorrect or incomplete
attribution, or suspect that other routines may be due to different authors, please let us know.

147
 • The main nonpublic contribution, that we thank thoroughly, are modified versions of a number
of routines, originally written by A. R. Williams around 1985, for the solution of the radial
Schrödinger and Poisson equations in the APW code of Soler and Williams (PRB 42, 9728
(1990)). Within SIESTA, they are kept in files arw.f and periodic_table.f, and they are used
for the generation of the basis orbitals and the screened pseudopotentials.

• The exchange-correlation routines contained in file xc.f were written by J.M.Soler in 1996 and
1997, in collaboration with C. Balbás and J. L. Martins. Routine pzxc (in the same file),
which implements the Perdew-Zunger LDA parametrization of xc, is based on routine velect,
written by S. Froyen.

• The serial version of the multivariate fast fourier transform used to solve Poisson’s equation
was written by Clive Temperton.

• Subroutine iomd.f for writing MD history in files was originally written by J. Kohanoff.

We want to thank very specially O. F. Sankey, D. J. Niklewski and D. A. Drabold for making
the FIREBALL code available to P. Ordejón. Although we no longer use the routines in that code,
it was essential in the initial development of the SIESTA project, which still uses many of the
algorithms developed by them.
We thank V. Heine for his support and encouraging us in this project.
The SIESTA project is supported by the Spanish DGES through several contracts. We also ac-
knowledge past support by the Fundación Ramón Areces.

148
16 APPENDIX: Physical unit names recognized by FDF

Magnitude Unit name MKS value

mass kg 1.E0
mass g 1.E-3
mass amu 1.66054E-27
length m 1.E0
length cm 1.E-2
length nm 1.E-9
length Ang 1.E-10
length Bohr 0.529177E-10
time s 1.E0
time fs 1.E-15
time ps 1.E-12
time ns 1.E-9
time mins 60.E0
time hours 3.6E3
time days 8.64E4
energy J 1.E0
energy erg 1.E-7
energy eV 1.60219E-19
energy meV 1.60219E-22
energy Ry 2.17991E-18
energy mRy 2.17991E-21
energy Hartree 4.35982E-18
energy Ha 4.35982E-18
energy K 1.38066E-23
energy kcal/mol 6.94780E-21
energy mHartree 4.35982E-21
energy mHa 4.35982E-21
energy kJ/mol 1.6606E-21
energy Hz 6.6262E-34
energy THz 6.6262E-22
energy cm-1 1.986E-23
energy cm**-1 1.986E-23
energy cmˆ -1 1.986E-23
force N 1.E0
force eV/Ang 1.60219E-9
force Ry/Bohr 4.11943E-8

149
Magnitude Unit name MKS value
pressure Pa 1.E0
pressure MPa 1.E6
pressure GPa 1.E9
pressure atm 1.01325E5
pressure bar 1.E5
pressure Kbar 1.E8
pressure Mbar 1.E11
pressure Ry/Bohr**3 1.47108E13
pressure eV/Ang**3 1.60219E11
charge C 1.E0
charge e 1.602177E-19
dipole C*m 1.E0
dipole D 3.33564E-30
dipole debye 3.33564E-30
dipole e*Bohr 8.47835E-30
dipole e*Ang 1.602177E-29
MomInert Kg*m**2 1.E0
MomInert Ry*fs**2 2.17991E-48
Efield V/m 1.E0
Efield V/nm 1.E9
Efield V/Ang 1.E10
Efield V/Bohr 1.8897268E10
Efield Ry/Bohr/e 2.5711273E11
Efield Har/Bohr/e 5.1422546E11
Efield Ha/Bohr/e 5.1422546E11
angle deg 1.d0
angle rad 5.72957795E1
torque eV/deg 1.E0
torque eV/rad 1.745533E-2
torque Ry/deg 13.6058E0
torque Ry/rad 0.237466E0
torque meV/deg 1.E-3
torque meV/rad 1.745533E-5
torque mRy/deg 13.6058E-3
torque mRy/rad 0.237466E-3

150
17 APPENDIX: XML Output

From version 2.0, SIESTA includes an option to write its output to an XML file. The XML
it produces is in accordance with the CMLComp subset of version 2.2 of the Chemical Markup
Language. Further information and resources can be found at http://cmlcomp.org/ and tools for
working with the XML file can be found in the Util/CMLComp directory.
The main motivation for standarised XML (CML) output is as a step towards standarising formats
for uses like the following.

• To have SIESTA communicating with other software, either for postprocessing or as part of a
larger workflow scheme. In such a scenario, the XML output of one SIESTA simulation may
be easily parsed in order to direct further simulations. Detailed discussion of this is out of the
scope of this manual.

• To generate webpages showing SIESTA output in a more accessible, graphically rich, fashion.
This section will explain how to do this.

17.1 Controlling XML output

XML.Write true (logical)
Determine if the main XML file should be created for this run.

17.2 Converting XML to XHTML

The translation of the SIESTA XML output to a HTML-based webpage is done using XSLT tech-
nology. The stylesheets conform to XSLT-1.0 plus EXSLT extensions; an xslt processor capable of
dealing with this is necessary. However, in order to make the system easy to use, a script called
ccViz is provided in Util/CMLComp that works on most Unix or Mac OS X systems. It is run like so:
./ccViz SystemLabel.xml
A new file will be produced. Point your web-browser at SystemLabel.xhtml to view the output.
The generated webpages include support for viewing three-dimensional interactive images of the
system. If you want to do this, you will either need jMol (http://jmol.sourceforge.net) installed
or access to the internet. As this is a Java applet, you will also need a working Java Runtime
Environment and browser plugin - installation instructions for these are outside the scope of this
manual, though. However, the webpages are still useful and may be viewed without this plugin.
An online version of this tool is avalable from http://cmlcomp.org/ccViz/, as are updated versions
of the ccViz script.

151
18 APPENDIX: Selection of precision for storage

Some of the real arrays used in Siesta are by default single-precision, to save memory. This applies
to the array that holds the values of the basis orbitals on the real-space grid, to the historical data
sets in Broyden mixing, and to the arrays used in the O(N) routines. Note that the grid functions
(charge densities, potentials, etc) are now (since mid January 2010) in double precision by default.
The following pre-processing symbols at compile time control the precision selection

• Add -DGRID_SP to the DEFS variable in arch.make to use single-precision for all the grid
magnitudes, including the orbitals array and charge densities and potentials. This will cause
some numerical differences and will have a negligible effect on memory consumption, since the
orbitals array is the main user of memory on the grid, and it is single-precision by default.
This setting will recover the default behavior of versions prior to 4.0.

• Add -DGRID_DP to the DEFS variable in arch.make to use double-precision for all the grid
magnitudes, including the orbitals array. This will significantly increase the memory used for
large problems, with negligible differences in accuracy.

• Add -DBROYDEN_DP to the DEFS variable in arch.make to use double-precision arrays for the
Broyden historical data sets. (Remember that the Broyden mixing for SCF convergence ac-
celeration is an experimental feature.)

• Add -DON_DP to the DEFS variable in arch.make to use double-precision for all the arrays in
the O(N) routines.

152
19 APPENDIX: Data structures and reference counting

To implement some of the new features (e.g. charge mixing and DM extrapolation), SIESTA uses
new flexible data structures. These are defined and handled through a combination and extension
of ideas already in the Fortran community:

• Simple templating using the “include file” mechanism, as for example in the FLIBS project led
by Arjen Markus (http://flibs.sourceforge.net).

• The classic reference-counting mechanism to avoid memory leaks, as implemented in the

PyF95++ project (http://blockit.sourceforge.net).

Reference counting makes it much simpler to store data in container objects. For example, a circular
stack is used in the charge-mixing module. A number of future enhancements depend on this
paradigm.

153
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155
Index
animation, 44 compile
antiferromagnetic initial DM, 62 libraries, 13
MPI, 12
Backward compatibility, 58, 110 OpenMP, 12
band structure, 88 pre-processor
basis, 36 -DCDF, 15
basis set superposition error (BSSE), 35 -DMPI, 12
Bessel functions, 35 -DMPI_TIMING, 107
default soft confinement, 30 -DNCDF, 15
default soft confinement potential, 31 -DNCDF_4, 15, 108
default soft confinement radius, 31 -DNCDF_PARALLEL, 15
filteret basis set, 34 -DSIESTA__DIAG_2STAGE, 74
filtering, 35 -DSIESTA__ELPA, 16
fix split-valence table, 30 -DSIESTA__FLOOK, 16
Gen-basis standalone program, 36 -DSIESTA__METIS, 15
Gen-basis standalone program, 36 -DSIESTA__MRRR, 73, 75
ghost atoms, 35 -DSIESTA__MUMPS, 16
minimal, 28 -DSIESTA__PEXSI, 16
new split-valence code, 29, 30 Conjugate-gradient history information, 112
PAO, 28, 29, 32 constant-volume cell relaxation, 111
per-shell split norm, 34 constraints in relaxations, 117
point at infinity, 37 COOP/COHP curves, 93
polarization, 28, 34 Folding in Gamma-point calculations, 71
reparametrization of pseudopotential, 37 Folding in Gamma-point calculations, 71
soft confinement potential, 34 cutoff radius, 33
split valence, 29
split valence for H, 29 Data Structures, 153
User basis, 36 denchar, 108
User basis (NetCDF format), 36 density of states, 75, 90
Berry phase, 95 Dielectric function,optical absorption, 94
Bessel functions, 35 diffuse orbitals, 28
%block, 20 Doping, 99, 102
Born effective charges, 96 double-ζ, 28
Broyden mixing, 152
Broyden optimization, 113 egg-box effect, 67, 69, 70
bug reports, 147 Eig2DOS, 75, 90
bulk polarization, 95 ELPA, 16
exchange-correlation
cell relaxation, 111 AM05, 48
Cerius2, 44 BH, 49
Charge confinement, 27, 34 BLYP, 48
Charge of the system, 99, 102 C09, 49
Chebyshev Polynomials, 79 CA, 48
Chemical Potential, 79, 80 DRSLL, 49
CML, 151 GGA, 48

156
 KBM, 49 box, 100
LDA, 48 infinite plane, 100
LMKLL, 49 spheres, 101
LSD, 48 Gaussians, 28
PBE, 48 Gen-basis, 24
PBEGcGxHEG, 48 Gen-basis, 36
PBEGcGxLO, 48 ghost atoms, 23, 35
PBEJsJrHEG, 48 gnubands, 88
PBEJsJrLO, 48 grid, 67
PBEsol, 48 Grid precision, 152
PW91, 48 Ground-state atomic configuration, 29
PW92, 48
PZ, 48 Hirshfeld population analysis, 92, 93
revPBE, 48
input file, 19
RPBE, 48
interatomic distances, 46
vdW, 49
isotopes, 23
vdW-DF, 49
vdW-DF1, 49 JMol, 44
vdW-DF2, 49 JSON timing report, 107
VV, 49
WC, 48 Kleinman-Bylander projectors, 31
External library
BLAS, 14 Localized Wave Functions, 79, 80
ELPA, 16 Lower order N memory, 80
fdict, 15 LSD, 50
flook, 16, 110
Makefile, 11
LAPACK, 14
mesh, 67
Metis, 15
Metis, 15
MPI, 12
minimal basis, 28
MUMPS, 16
mixps program, 23
ncdf, 15
Molden, 44
NetCDF, 15
Mulliken population analysis, 21, 92
OpenMP, 12
multiple-ζ, 28, 29
PEXSI, 16
MUMPS, 16
ScaLAPACK, 15
NetCDF format, 15, 36
fatbands, 88
3, 15
FDF, 19
4, 15
fdf.log, 19, 20
ferromagnetic initial DM, 62 output
finite-range pseudo-atomic orbitals, 28 δρ(~r), 102
fixed spin state, 50 atomic coordinates
flook, 16, 110 in a dynamics step, 21, 116
Force Constants Matrix, 109, 120 initial, 116
fractional program, 23 Bader charge, 103
Gate, 100 band ~k points, 21, 88
bounded plane, 100 band structure, 88

157
 basis, 36 CG, 112
charge density, 102, 104 charge density, 63
charge density and/or wfs for DENCHAR deformation charge density, 63
code, 108 density matrix, 61, 62
customization, 21 localized wave functions (order-N ), 80
dedicated files, 22 XV, 45
density matrix, 63–65 ZM, 45
density matrix history, 65 readwf, 90
eigenvalues, 21, 75, 90 readwfsx, 90
electrostatic potential, 102 Reference counting, 153
forces, 21, 116 relaxation of cell parameters only, 111
grid ~k points, 21, 47 removal of intramolecular pressure, 114
Hamiltonian, 64 Restart of O(N) calculations, 80
Hamiltonian & overlap, 70 rippling, 67, 69, 70
Hamiltonian history, 65
Hirshfeld analysis, 92, 93 scale factor, 34
HSX file, 70 SCF, 52
Information for COOP/COHP curves, 93 compat-pre4-dm-h, 58
ionic charge, 103 Doping, 99, 102
local density of states, 91 mixing, 53, 58
long, 21 Broyden, 54
main output file, 21 Charge, 53, 58, 60
molecular dynamics Density, 53
Force Constants Matrix, 120 Density matrix convergence, 65
history, 116 end of cycle, 58
Mulliken analysis, 21, 92 energy convergence, 66
overlap matrix, 64, 65 energy density matrix convergence, 66
overlap matrix history, 65 Hamiltonian, 53
projected density of states, 90 Hamiltonian convergence, 65
total charge, 103 harris energy convergence, 66
total potential, 103 Linear, 54
Voronoi analysis, 92, 93 Pulay, 54
wave functions, 21, 89 Potential, 100
output of wave functions for bands, 88, 89 Recomputing H, 58
SCF convergence criteria, 65
perturbative polarization, 28 Scripting, 110
perturbative polarization, 34 Sies2arc, 45
PEXSI, 16 Sies2arc, 44
PEXSI solver, 80 SIESTA, 8
polarization orbitals, 28 single-ζ, 28
Precision selection, 152 Slab dipole correction, 100
pseudopotential Slabs with net charge, 99
example generation, 17 species, 22
files, 24 spin, 50
generation, 23 initialization, 62
split valence, 28
reading saved data, 108
structure input precedence issues, 46
all, 108

158
synthetic atoms, 23

TBtrans, 146
Tests, 16, 17, 128
TranSIESTA, 9
transiesta
electrode
principal layer, 130

Variational character of E_KS, 52

VCA, 23
VIBRA, 120
Voronoi population analysis, 92, 93

XML, 151
XMol, 44

159
List of SIESTA files
arch.make, 11–16, 74, 152 SystemLabel.BADER, 103
SystemLabel.bands, 87, 88
BaderCharge.grid.nc, 104 SystemLabel.bands.WFSX, 88
BASIS_ENTHALPY, 37, 66 SystemLabel.BC, 97
BASIS_HARRIS_ENTHALPY, 66 SystemLabel.BONDS, 46
SystemLabel.BONDS_FINAL, 46
Chlocal.grid.nc, 103
SystemLabel.CG, 112
constr.f, 119
SystemLabel.DIM, 108
DeltaRho.grid.nc, 102 SystemLabel.DM, 50, 61, 64, 108, 127, 146
DeltaRho.IN.grid.nc, 63 SystemLabel.DMF, 62
DM-NNNN.nc, 65 SystemLabel.DOS, 90, 91
DM.nc, 64 SystemLabel.DRHO, 102
DM_MIXED.blocked, 64 SystemLabel.EIG, 75, 86
DM_OUT.blocked, 64 SystemLabel.eigW, 98
DMHS-NNNN.nc, 65 SystemLabel.EPSIMG, 94
DMHS.nc, 65 SystemLabel.FA, 116
SystemLabel.FAC, 116
ElectrostaticPotential.grid.nc, 102 SystemLabel.FC, 120
SystemLabel.FCC, 120
GRAPHVIZ_atom.gv, 135
SystemLabel.fullBZ.WFSX, 75, 93, 94
GRAPHVIZ_orbital.gv, 135
SystemLabel.grid.nc, 63
H_DMGEN, 64 SystemLabel.HS, 70
H_MIXED, 64 SystemLabel.HSX, 70, 93
SystemLabel.IOCH, 103
m_new_dm.F, 71 SystemLabel.KP, 47, 146
SystemLabel.LDOS, 91
NEXT_ITER.UCELL.ZMATRIX, 44 SystemLabel.LDSI, 86
OCCS, 72 SystemLabel.LWF, 80, 108
OUT.UCELL.ZMATRIX, 44 SystemLabel.MD, 44, 116
SystemLabel.MDC, 116
PEXSI_INTDOS, 86 SystemLabel.MDE, 116
SystemLabel.MDX, 44, 116
Rho.grid.nc, 86, 102 SystemLabel.mmn, 97
Rho.IN.grid.nc, 63 SystemLabel.N.TSHS, 65
RhoInit.grid.nc, 104 SystemLabel.nc, 108, 109
RhoXC.grid.nc, 102 SystemLabel.nnkp, 97, 98
SystemLabel.ORB.gv, 29
Src/m_new_dm.F, 60
SystemLabel.ORB_INDX, 116
SystemLabel..arc, 44
SystemLabel.PDOS, 90, 91
SystemLabel..DM, 61
SystemLabel.PDOS.xml, 91
SystemLabel.alloc, 107
SystemLabel.PLD, 108
SystemLabel.amn, 98
SystemLabel.RHO, 102
SystemLabel.ANI, 44
SystemLabel.RHOINIT, 104
SystemLabel.arc, 45
SystemLabel.RHOXC, 102
SystemLabel.ATOM.gv, 29

160
SystemLabel.selected.WFSX, 89
SystemLabel.STRUCT_IN, 43, 45
SystemLabel.STRUCT_NEXT_ITER, 43
SystemLabel.STRUCT_OUT, 43
SystemLabel.times, 107
SystemLabel.TOCH, 103
SystemLabel.TS.KP, 146
SystemLabel.TSCCEQ*, 146
SystemLabel.TSCCNEQ*, 146
SystemLabel.TSDE, 19, 127, 134, 140, 146
SystemLabel.TSGF*, 146
SystemLabel.TSHS, 19, 127, 128, 134, 139, 146
SystemLabel.VH, 102
SystemLabel.VNA, 103
SystemLabel.VT, 103
SystemLabel.WFS, 90, 93
SystemLabel.WFSX, 88–90, 93, 108
SystemLabel.xtl, 44
SystemLabel.XV, 43–45, 108, 113, 115, 116
SystemLabel.xyz, 44
SystemLabel.ZM, 45

time.json, 107
TotalCharge.grid.nc, 103
TotalPotential.grid.nc, 103
TS_FERMI, 133

UNKXXXXX.Y, 98

Vna.grid.nc, 103

WFS.nc, 75, 89

161
List of fdf flags
AllocReportLevel, 107 ELPA-1stage, 73
AllocReportThreshold, 107 ELPA-2stage, 73
AnalyzeChargeDensityOnly, 104 Expert, 73
AtomCoorFormatOut, 39, 44, 45 Expert-2stage, 73
AtomicCoordinatesAndAtomicSpecies, 22, 38, MRRR, 73
40, 62, 117, 118 MRRR-2stage, 73
AtomicCoordinatesFormat, 39, 40, 44, 45 NoExpert, 73
Ang, 39 NoExpert-2stage, 73
Bohr, 39 QR, 73
Fractional, 39 BlockSize, 72, 73
NotScaledCartesianAng, 39 DivideAndConquer, 74, 75
NotScaledCartesianBohr, 39 ELPA, 74, 75
ScaledByLatticeVectors, 39 Memory, 74
ScaledCartesian, 39 MRRR, 74, 75
AtomicCoordinatesOrigin, 39, 44 NoExpert, 74, 75
AtomicMass, 23 OrFac, 74
AtomSetupOnly, 36 ParallelOverK, 50, 72–75
ProcessorY, 72
BandLines, 74, 87, 88 UpperLower, 74
BandLinesScale, 87 Use2D, 72, 73
BandPoints, 74, 87, 88 UseNewDiagk, 72, 75, 89
BasisPressure, 36 DirectPhi, 106
BlockSize, 72, 73, 78, 105 DM
BornCharge, 96, 120 AllowExtrapolation, 63
AllowReuse, 63
CDF
FormattedFiles, 62
Compress, 108
FormattedInput, 62
Grid.Precision, 109
FormattedOutput, 62
MPI, 109
History.Depth, 63
Save, 108
Init.Unfold, 61
ChangeKgridInMD, 46, 47
InitSpin, 62
ChemicalSpeciesLabel, 22–24, 33, 36, 38, 45, 118
AF, 62, 63
Compat
KickMixingWeight, see
Pre-v4-DM-H, 58
SF.Mixer.Kick.Weight55
Pre-v4-Dynamics, 110
MixingWeight, see SF.Mixer.Weight55, 59
Compat.Matel.NRTAB, 70
UseSaveDM, 53, 61
COOP.Write, 70, 75, 89, 93
DM.EnergyTolerance, 66
Debug DM.Init.Bulk, 132
DIIS, 60 DM.InitSpin, 51
Diag DM.MixSCF1, see SF.Mix.First53
AbsTol, 74 DM.Normalization.Tolerance, 65
Algorithm, 72, 73, 75 DM.NumberBroyden, see SF.Mixer.History55
Divide-and-Conquer, 73 DM.NumberKick, see SF.Mixer.Kick55
Divide-and-Conquer-2stage, 73 DM.NumberPulay, see SF.Mixer.History55

162
DM.Require.Harris.Convergence, 66 MaxBondDistance, 46
DM.RequireEnergyConvergence, 66 MaxSCFIterations, 52, 53
DM.Tolerance, 65 MaxWalltime, 107
DM.UseSaveDM, 78, 104 Slack, 107
MD
EggboxRemove, 69, 70 TypeOfRun, 45, 124
EggboxScale, 69, 70 UseSaveXV, 45, 46
ElectronicTemperature, 51, 76, 81, 132 UseSaveZM, 45, 46
ExternalElectricField, 99 MD.AnnealOption, 109, 113, 115
MD.Broyden
FilterCutoff, 34, 35
Cycle.On.Maxit, 113
FilterTol, 35
History.Steps, 113
ForceAuxCell, 71
Initial.Inverse.Jacobian, 113
Geometry MD.Broyden.Initial.Inverse.Jacobian, 112
Charge, 102 MD.BulkModulus, 115
Constraints, 117, 131 MD.ConstantVolume, 111
Hartree, 100, 102 MD.FCDispl, 120
Grid.CellSampling, 67, 68 MD.FCFirst, 120
MD.FCLast, 120
Harris MD.FinalTimeStep, 114
Functional, 53 MD.FIRE.TimeStep, 113
MD.InitialTemperature, 114
KB.New.Reference.Orbitals, 32 MD.InitialTimeStep, 114
kgrid MD.LengthTimeStep, 113, 114
Cutoff, 46, 47 MD.MaxCGDispl, 112, 124
MonkhorstPack, 39, 46 MD.MaxDispl, 112
kgrid.Cutoff, 91 MD.MaxForceTol, 111, 112, 124
kgrid.MonkhorstPack, 91, 110 MD.MaxStressTol, 111
MD.NoseMass, 115
LatticeConstant, 38, 39
MD.NumCGsteps, 112
LatticeParameters, 38
MD.ParrinelloRahmanMass, 115
LatticeVectors, 38, 39, 47
MD.PreconditionVariableCell, 111, 112
LDAU.CutoffNorm, 121, 122
MD.RelaxCellOnly, 111
LDAU.EnergyShift, 121, 122
MD.RemoveIntramolecularPressure, 114
LDAU.FirstIteration, 122
MD.Steps, 112, 114
LDAU.PopTol, 122
MD.TargetPressure, 111, 113, 114
LDAU.PotentialShift, 122
MD.TargetStress, 111, 114
LDAU.Proj, 121
MD.TargetTemperature, 115
LDAU.ProjectorGenerationMethod, 121, 122
MD.TauRelax, 115
LDAU.ThresholdTol, 122
MD.TypeOfRun, 109, 113–115, 120, 123
LocalDensityOfStates, 91
Anneal, 109, 115
LongOutput, 21, 22, 47, 116
Broyden, 109, 111
Lua
CG, 109, 111
Debug, 124
FC, 96, 109
Debug.MPI, 125
FIRE, 109
Interactive, 125
Forces, 110
Script, 123, 125
Lua, 109, 110

163
 Master, 109, 110 WriteCoeffs, 78
Nose, 109 ON
NoseParrinelloRahman, 109 Etol, 78
ParrinelloRahman, 109 ON.ChemicalPotential, 79, 80
Verlet, 109 ON.ChemicalPotential.Order, 80
MD.UseSaveCG, 112 ON.ChemicalPotential.Rc, 80
MD.UseSaveXV, 112 ON.ChemicalPotential.Temperature, 80
MD.VariableCell, 70, 109, 111, 114 ON.ChemicalPotential.Use, 80
MeshCutoff, 35, 51, 67, 110, 124 ON.eta, 77, 79, 80
MeshSubDivisions, 67 ON.eta.alpha, 79
MinSCFIterations, 52 ON.eta.beta, 79
MM, 104 ON.Etol, 79
Cutoff, 105 ON.functional, 79
Grimme.D, 105 ON.LowerMemory, 80
Grimme.S6, 105 ON.MaxNumIter, 79
Potentials, 104 ON.RcLWF, 79
UnitsDistance, 105 ON.UseSaveLWF, 80
UnitsEnergy, 105 Optical.Broaden, 94
MPI Optical.Energy.Maximum, 94
Nprocs.SIESTA, 81 Optical.Energy.Minimum, 94
MullikenInSCF, 92 Optical.Mesh, 94
MullikenInScf, 51 Optical.NumberOfBands, 94
Optical.OffsetMesh, 94
NeglNonOverlapInt, 70 Optical.PolarizationType, 95
NetCharge, 99, 102 Optical.Scissor, 94
New Optical.Vector, 95
A.Parameter, 37 OpticalCalculation, 94
B.Parameter, 37
NumberOfAtoms, 22, 39, 40 PAO
NumberOfEigenStates, 72, 73, 75 Basis, 23, 25, 27–29, 32, 35
NumberOfSpecies, 22 BasisSize, 28, 29, 32
DZ, 28
OccupationFunction, 76
DZP, 28
OccupationMPOrder, 76
minimal, 28
OMM
SZ, 28
BlockSize, 78
SZP, 28
Diagon, 77, 78
BasisSizes, 29
DiagonFirstStep, 78
BasisType, 25, 28, 30, 32, 33
Eigenvalues, 78
filteret, 28
LongOutput, 78
nodes, 28
Precon, 77
nonodes, 28
PreconFirstStep, 77
split, 28
ReadCoeffs, 78
splitgauss, 28
RelTol, 78
ContractionCutoff, 30
TPreconScale, 78
EnergyCutoff, 30
Use2D, 77, 78
EnergyPolCutoff, 30
UseCholesky, 77
EnergyShift, 28, 29, 32, 33, 35, 37
UseSparse, 77

164
 FixSplitTable, 30 safe-dDmax-no-inertia, 84
NewSplitCode, 29, 30 safe-width-ic-bracket, 85
OldStylePolOrbs, 35 safe-width-solver-bracket, 85
SoftDefault, 27, 30, 32 Verbosity, 81, 82
SoftInnerRadius, 31 PolarizationGrids, 95, 96
SoftPotential, 31 ProcessorY, 105, 106
SplitNorm, 28, 29, 32, 33 ProjectedDensityOfStates, 90
SplitNormH, 29, 32 PS
SplitTailNorm, 30 lmax, 31
PAO.Basis, 121 PS.KBprojectors, 31
PAO.EnergyShift, 121
PartialChargesAtEveryGeometry, 93 RcSpatial, 106
PartialChargesAtEverySCFStep, 93 Reparametrize.Pseudos, 37
PDOS.kgrid.Cutoff, 91 Restricted.Radial.Grid, 37
PDOS.kgrid.MonkhorstPack, 91 Rmax.Radial.Grid, 37
PEXSI S.Only, 64
deltaE, 81 SaveBaderCharge, 103
DOS, 86 SaveDeltaRho, 102
Ef.Reference, 86 SaveElectrostaticPotential, 102, 103, 108
Emax, 86 SaveHS, 70
Emin, 86 SaveInitialChargeDensity, 104
NPoints, 86 SaveIonicCharge, 103
Gap, 81 SaveNeutralAtomPotential, 102
Inertia-Counts, 84 SaveRho, 102
Inertia-energy-width-tolerance, 85 SaveRhoXC, 102
Inertia-max-iter, 84 SaveTotalCharge, 103
Inertia-min-num-shifts, 84 SaveTotalPotential, 103
Inertia-mu-tolerance, 84, 85 SCF
lateral-expansion-inertia, 84 MonitorForces, 52
LDOS, 86 MustConverge, 52, 53
Broadening, 87 RecomputeHAfterSCF, 58
Energy, 87 RecomputeHAfterScf, 58
NP-per-pole, 87 Want.Variational.EKS, 52
mu, 83 SCF.DebugRhoGMixing, 60
mu-max, 83, 84 SCF.DM
mu-max-iter, 83 Converge, 65, 66, 111
mu-min, 83, 84 Tolerance, 65, 66
mu-pexsi-safeguard, 83, 84 SCF.EDM
NP-per-pole, 82, 87 Converge, 66
NP-symbfact, 82 Tolerance, 66
num-electron-tolerance, 83 SCF.FreeE
num-electron-tolerance-lower-bound, 83 Converge, 66
num-electron-tolerance-upper-bound, 83 Tolerance, 66
NumPoles, 81 SCF.H
Ordering, 82 Converge, 65, 66, 111
safe-dDmax-ef-inertia, 85 Tolerance, 51, 66
safe-dDmax-ef-solver, 85 SCF.Harris

165
 Converge, 66 Siesta2Wannier90.WriteEig, 98
Tolerance, 66 Siesta2Wannier90.WriteMmn, 97
SCF.Kerker.q0sq, 59 Siesta2Wannier90.WriteUnk, 98
SCF.Mix, 51, 53, 58 SimulateDoping, 99
AfterConvergence, 52, 58, 64 SingleExcitation, 50
First, 53, 58, 100 SlabDipoleCorrection, 99, 100
Spin, 53 SolutionMethod, 47, 71, 75, 77, 131, 134
SCF.MixCharge Spin, 49–51, 61, 62, 77
SCF1, 60 Fix, 50, 77
SCF.Mixer non-colinear, 49
History, 55, 56 non-polarized, 49
Kick, 55 OrbitStrength, 51
Kick.Weight, 55 polarized, 49
Linear.After, 55 spin-orbit, 50
Linear.After.Weight, 56 Spiral, 47
Method, 54–56 Total, 50, 77
Restart, 55, 56 SpinInSCF, 92
Restart.Save, 55, 56 SuperCell, 38, 39, 47
Variant, 54–56 SyntheticAtoms, 23
Weight, 55, 56 SystemLabel, 18, 19, 22, 44, 127
SCF.Mixer.<>, 56 SystemName, 22
history, 56
iterations, 56 TimeReversalSymmetryForKpoints, 47
method, 56 TimerReportThreshold, 107
next, 56 TS
next.conv, 56 Analyze, 128, 131, 134, 135
next.p, 56 Analyze.Graphviz, 135
restart, 56 Atoms.Buffer, 131
restart.p, 57 BTD
restart.save, 56 Guess1.Max, 136
variant, 56 Guess1.Min, 136
weight, 56 Optimize, 136
weight.linear, 55, 56 Pivot, 134, 135
SCF.Mixers, 56 Spectral, 136
SCF.Read.Charge.NetCDF, 63 ChargeCorrection, 133
SCF.Read.Deformation.Charge.NetCDF, 63 Factor, 133
SCF.RhoG.DIIS.Depth, 60 Fermi.Max, 133
SCF.RhoG.Metric.Preconditioner.Cutoff, 60 Fermi.Tolerance, 133
SCF.RhoGMixingCutoff, 59 ChemPot.<>, 141, 142
Siesta2Wannier90.NumberOfBands, 98, 99 chemical-shift, 142
Siesta2Wannier90.NumberOfBandsDown, 99 contour.eq, 142, 143
Siesta2Wannier90.NumberOfBandsUp, 99 contour.eq.pole, 142
Siesta2Wannier90.UnkGrid1, 98 contour.eq.pole.N, 142
Siesta2Wannier90.UnkGrid2, 98 ElectronicTemperature, 132, 142
Siesta2Wannier90.UnkGrid3, 98 kT, 142
Siesta2Wannier90.UnkGridBinary, 98 mu, 142
Siesta2Wannier90.WriteAmn, 97 Temp, 142

166
ChemPots, 139, 141 Hartree.Fix, 138
Contour.<>, 143, 145 Frac, 138
delta, 144 Hartree.Fix.Elec, 138
from, 144 Hartree.Offset, 138
method, 144 HS.Save, 19, 128, 134
opt, 144 MUMPS
part, 143 BlockingFactor, 137
points, 144 Memory, 136
Contour.nEq.<>, 145 Ordering, 136
Contours Poisson, 137
Eq.Pole, 143 <file>, 137, 138
Eq.Pole.N, 143 elec-box, 138
Contours.nEq, 145 ramp-cell, 138
Eta, 145 ramp-central, 137, 138
Fermi.Cutoff, 145 S.Save, 134
DE.Save, 19, 128, 134 SCF.Initialize, 132
Elec.<>, 139, 140 SIESTA.Only, 134
Accuracy, 140, 141 SolutionMethod, 131, 134
Bloch, 129, 140 BTD, 131, 135
Bulk, 137, 139, 140 full, 131
check-kgrid, 140 MUMPS, 131
chemical-potential, 139 Voltage, 131
DE, 140 Weight.k.Method, 133
DM-Update, 139, 141, 146 Weight.Method, 132
electrode-position, 139 mean, 133
Eta, 140, 141 orb-orb, 132
Gf, 139 sum-atom-atom, 132
Gf-Reuse, 140, 141 sum-atom-orb, 133
Hartree.Extend, 138 tr-atom-atom, 132
HS, 139 tr-atom-orb, 132
Out-of-core, 140, 141 TS.Voltage, 19
pre-expand, 140
semi-inf-direction, 139 Use.Blocked.WriteMat, 63, 64
used-atoms, 139 UseDomainDecomposition, 106
Elecs, 135, 139, 141 UseParallelTimer, 107
Accuracy, 140, 141 User
Bulk, 140 Basis, 36
Coord.EPS, 141 Basis.NetCDF, 36
DM.Init, 132, 141 User.Basis, 24
DM.Update, 141 UseSaveData, 45, 108, 113
Eta, 140 UseSpatialDecomposition, 106
Gf.Reuse, 141 UseStructFile, 43, 45, 46
Neglect.Principal, 130, 141 UseTreeTimer, 107
Out-of-core, 141 WarningMinimumAtomicDistance, 46
ElectronicTemperature, 132, 142, 146 WaveFuncKPoints, 74, 89, 90, 93
Fermi.Initial, 132 WaveFuncKPointsScale, 89
Forces, 133 WFS.Band.Max, 89, 93

167
WFS.Band.Min, 89, 93 ZM.MaxDisplLength, 112
WFS.Energy.Max, 89, 93, 94 Zmatrix, 38, 40, 111, 114
WFS.Energy.Min, 89, 93
WFS.Write.For.Bands, 88
Write
Denchar, 108
DM, 64
DM.end.of.cycle, 64
DM.History.NetCDF, 64, 65
DM.NetCDF, 64, 65
DMHS.History.NetCDF, 65, 70
DMHS.NetCDF, 64, 65, 70
Graphviz, 29
H, 64
H.end.of.cycle, 64
TSHS.History, 65
Write.OrbitalIndex, 116
WriteBands, 88
WriteCoorCerius, 44
WriteCoorInitial, 116
WriteCoorStep, 21, 45, 116
WriteCoorXmol, 44
WriteEigenvalues, 21, 75, 90
WriteForces, 21, 116
WriteHirshfeldPop, 92
WriteIonPlotFiles, 36
WriteKbands, 21, 88
WriteKpoints, 21, 47
WriteMDHistory, 44, 116
WriteMDXmol, 44, 116
WriteMullikenPop, 21, 51, 92
WriteOrbMom, 51
WriteVoronoiPop, 92
WriteWaveFunctions, 21, 89

XC
Authors, 48
Functional, 48
Hybrid, 49
XML
Write, 151

ZM
UnitsAngle, 43
UnitsLength, 43
ZM.ForceTolAngle, 112
ZM.ForceTolLength, 112
ZM.MaxDisplAngle, 112

168