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Index

.DM
Output
.TSDE
Output
.TSHS
Output
AllocReportLevel
Memory accounting options
animation
Output of structural information
antiferromagnetic initial DM
Initialization of the density-matrix
AtomCoorFormatOut
Traditional structure input in
AtomicCoordinatesAndAtomicSpecies
Traditional structure input in
AtomicCoordinatesFormat
Traditional structure input in
AtomicCoordinatesOrigin
Traditional structure input in
AtomicMass
General system descriptors
band structure
Band-structure analysis
BandLines
Band-structure analysis
BandLinesScale
Band-structure analysis
BandPoints
Band-structure analysis
basis
Saving and reading basis-set
basis set superposition error (BSSE)
The PAO.Basis block
Bessel functions
The PAO.Basis block
default soft confinement
Soft-confinement options
default soft confinement potential
Soft-confinement options
default soft confinement radius
Soft-confinement options
effective pressure
Basis optimization
filtering
Filtering | Filtering
fix split-valence table
Generation of multiple-zeta orbitals
Gen-basis standalone program
Saving and reading basis-set | Saving and reading basis-set | Saving and reading basis-set
ghost atoms
The PAO.Basis block
minimal
Size of the basis
new split-valence code
Generation of multiple-zeta orbitals | Generation of multiple-zeta orbitals
PAO
Type of basis sets | Size of the basis | Size of the basis | The PAO.Basis block | The PAO.Basis block
per-shell split norm
The PAO.Basis block
point at infinity
Low-level options regarding the
polarization
Size of the basis | The PAO.Basis block
reparametrization of pseudopotential
Low-level options regarding the | Low-level options regarding the
soft confinement potential
The PAO.Basis block
split valence
Generation of multiple-zeta orbitals
split valence for H
Generation of multiple-zeta orbitals
User basis
Saving and reading basis-set
User basis (NetCDF format)
Saving and reading basis-set
BasisPressure
Basis optimization
Berry phase
Macroscopic polarization
Bessel functions
The PAO.Basis block
%block
THE FLEXIBLE DATA FORMAT
Blocksize
Parallel options | APPENDIX: Parallel SIESTA
BLYP
Exchange-correlation functionals
Born effective charges
Macroscopic polarization
BornCharge
Macroscopic polarization | Phonon calculations
Broyden mixing
Mixing options | APPENDIX: Selection of precision
Broyden optimization
Broyden optimization
bug reports
REPORTING BUGS
bulk polarization
Macroscopic polarization
CA
Exchange-correlation functionals
cell relaxation
Structural relaxation
CERIUS2
Output of structural information
ChangeKgridInMD
$k$-point sampling
Charge of the system
Systems with net charge
Chebyshev Polynomials
Order(N) calculations
Chemical Potential
Order(N) calculations | Order(N) calculations | Order(N) calculations | Order(N) calculations | Order(N) calculations
ChemicalSpeciesLabel
General system descriptors | Structural information
CML
APPENDIX: XML Output
Conjugate-gradient history information
Conjugate-gradients optimization
constant-volume cell relaxation
Structural relaxation
constraints in relaxations
Use of general constraints
COOP.Write
Crystal-Orbital overlap and hamilton
COOP/COHP curves
Crystal-Orbital overlap and hamilton
Folding in Gamma-point calculations
The auxiliary supercell
cutoff radius
The PAO.Basis block
denchar
Output of information for
density of states
Output of eigenvalues and | Total density of states
Diag.AllInOne
Diagonalization options
Diag.DivideAndConquer
Diagonalization options
Diag.Memory
Parallel options
Diag.NoExpert
Diagonalization options
Diag.ParallelOverK
Parallel options
Diag.PreRotate
Diagonalization options
Diag.Use2D
Diagonalization options
Dielectric function, optical absorption
Optical properties
diffuse orbitals
Type of basis sets
DirectPhi
Efficiency options
DM.AllowExtrapolation
Initialization of the density-matrix
DM.AllowReuse
Initialization of the density-matrix
DM.Broyden.Cycle.On.Maxit
Mixing options
DM.Broyden.Variable.Weight
Mixing options
DM.EnergyTolerance
Convergence criteria
DM.FormattedFiles
Initialization of the density-matrix
DM.FormattedOutput
Initialization of the density-matrix | Initialization of the density-matrix
DM.Harris.Tolerance
Convergence criteria
DM.InitSpin
Initialization of the density-matrix
DM.InitSpinAF
Initialization of the density-matrix
DM.KickMixingWeight
Mixing options
DM.MixingWeight
Mixing options
DM.MixSCF1
Mixing options | Systems with net charge
DM.NumberBroyden
Mixing options
DM.NumberKick
Mixing options
DM.NumberPulay
Mixing options
DM.Pulay.Avoid.First.After.Kick
Mixing options
DM.PulayOnFile
Mixing options
DM.Require.Energy.Convergence
Convergence criteria
DM.Require.Harris.Convergence
Convergence criteria
DM.Tolerance
Convergence criteria
DM.UseSaveDM
Initialization of the density-matrix
DZ
Size of the basis
DZP
Size of the basis
egg-box effect
The real-space grid and | The real-space grid and | The real-space grid and
EggboxRemove
The real-space grid and
EggboxScale
The real-space grid and
EIG2DOS
Output of eigenvalues and | Total density of states
ElectronicTemperature
Occupation of electronic states | Occupation of electronic states
ExternalElectricField
Systems with net charge
FDF
THE FLEXIBLE DATA FORMAT
fdf.log
EXECUTION OF THE PROGRAM | EXECUTION OF THE PROGRAM | THE FLEXIBLE DATA FORMAT
ferromagnetic initial DM
Initialization of the density-matrix
files (ON.functional)
Order(N) calculations
FilterCutoff
Filtering
FilterTol
Filtering
finite-range pseudo-atomic orbitals
Type of basis sets
FixAuxiliaryCell
The auxiliary supercell
fixed spin state
Spin polarization | Spin polarization
FixSpin
Spin polarization
Force Constants Matrix
STRUCTURAL RELAXATION, PHONONS, AND | Phonon calculations | Phonon calculations | Phonon calculations
using PHONON
STRUCTURAL RELAXATION, PHONONS, AND | Interface to the PHONON
FoX XML library
APPENDIX: XML Output
fractional program
General system descriptors
Gaussians
Type of basis sets
GEN-BASIS
Overview of atomic-orbital bases
GEN-BASIS
Saving and reading basis-set | Saving and reading basis-set
GeometryConstraints
Use of general constraints
GGA
Exchange-correlation functionals | Exchange-correlation functionals | Exchange-correlation functionals | Exchange-correlation functionals | Exchange-correlation functionals
ghost atoms
General system descriptors | The PAO.Basis block
GNUBANDS
Format of the .bands
grid
The real-space grid and | The real-space grid and
GridCellSampling
The real-space grid and
Ground-state atomic configuration
Size of the basis
Harris_functional
The self-consistent-field loop
input file
THE FLEXIBLE DATA FORMAT
interatomic distances
Interatomic distances
isotopes
General system descriptors
JMOL
Output of structural information
kgrid_cutoff
$k$-point sampling
kgrid_Monkhorst_Pack
$k$-point sampling
Kim
Order(N) calculations
Kleinman-Bylander projectors
Kleinman-Bylander projectors
LatticeConstant
Traditional structure input in
LatticeParameters
Traditional structure input in
LatticeVectors
Traditional structure input in
LDA
Exchange-correlation functionals
Linear mixing kick
Mixing options
LocalDensityOfStates
Local density of states
Localized Wave Functions
Order(N) calculations | Order(N) calculations
LongOutput
Standard output
Lower order N memory
Order(N) calculations
LSD
Exchange-correlation functionals | Spin polarization | Spin polarization | Spin polarization
Makefile
The arch.make file
MaxBondDistance
Interatomic distances
MaxSCFIterations
The self-consistent-field loop
MD.AnnealOption
Molecular dynamics
MD.Broyden.Cycle.On.Maxit
Broyden optimization
MD.Broyden.History.Steps
Broyden optimization
MD.Broyden.Initial.Inverse.Jacobian
Broyden optimization
MD.BulkModulus
Molecular dynamics
MD.ConstantVolume
Structural relaxation
MD.FCDispl
Phonon calculations
MD.FCfirst
Phonon calculations
MD.FClast
Phonon calculations
MD.FinalTimeStep
Molecular dynamics
MD.FIRE.TimeStep
FIRE relaxation
MD.FireQuench
Quenched MD
MD.InitialTemperature
Molecular dynamics
MD.InitialTimeStep
Molecular dynamics
MD.LengthTimeStep
Molecular dynamics
MD.MaxCGDispl
Structural relaxation
MD.MaxForceTol
Structural relaxation
MD.MaxStressTol
Structural relaxation
MD.NoseMass
Molecular dynamics
MD.NumCGsteps
Structural relaxation
MD.ParrinelloRahmanMass
Molecular dynamics
MD.PreconditionVariableCell
Structural relaxation
MD.Quench
Quenched MD
MD.RelaxCellOnly
Structural relaxation
MD.RemoveIntramolecularPressure
Target stress options
MD.TargetPressure
Target stress options
MD.TargetTemperature
Molecular dynamics
MD.TauRelax
Molecular dynamics
MD.TypeOfRun
STRUCTURAL RELAXATION, PHONONS, AND
MD.UseSaveCG
Conjugate-gradients optimization
MD.UseSaveXV
Input of structural information | Input of structural information | Input of structural information
MD.UseSaveZM
Input of structural information
MD.UseStructFile
Output of structural information | Output of structural information
MD.VariableCell
Structural relaxation
mesh
The real-space grid and | The real-space grid and
MeshCutoff
The real-space grid and
MeshSubDivisions
The real-space grid and
MINIMAL
Size of the basis
minimal basis
Type of basis sets
mixps program
General system descriptors
MM.Cutoff
Auxiliary Force field
MM.Grimme.D
Auxiliary Force field
MM.Grimme.S6
Auxiliary Force field
MM.Potentials
Auxiliary Force field
MM.UnitsDistance
Auxiliary Force field
MM.UnitsEnergy
Auxiliary Force field
Mulliken population analysis
Standard output | Mulliken charges and overlap
MullikenInSCF
Mulliken charges and overlap | Mulliken charges and overlap
multiple-$\zeta$
Type of basis sets
multiple-$\zeta$
Generation of multiple-zeta orbitals
NaiveAuxiliaryCell
The auxiliary supercell
NeglNonOverlapInt
Matrix elements of the
NetCDF format
Saving and reading basis-set | Saving and reading basis-set | APPENDIX: NetCDF
NetCDF library
APPENDIX: NetCDF
NetCharge
Systems with net charge
New.A.Parameter
Low-level options regarding the
New.B.Parameter
Low-level options regarding the
NEXT_ITER.UCELL.ZMATRIX
Output of structural information
nodes
Type of basis sets
NonCollinearSpin
Spin polarization
nonodes
Type of basis sets
NumberOfAtoms
General system descriptors | Structural information
NumberOfEigenStates
Diagonalization options
NumberOfSpecies
General system descriptors | Structural information
OccupationFunction
Occupation of electronic states | Occupation of electronic states | Occupation of electronic states
OccupationMPOrder
Occupation of electronic states
ON.ChemicalPotential
Order(N) calculations
ON.ChemicalPotentialOrder
Order(N) calculations
ON.ChemicalPotentialRc
Order(N) calculations
ON.ChemicalPotentialTemperature
Order(N) calculations
ON.ChemicalPotentialUse
Order(N) calculations
ON.eta
Order(N) calculations | Order(N) calculations
ON.eta_alpha
Order(N) calculations
ON.eta_beta
Order(N) calculations
ON.etol
Order(N) calculations
ON.functional
Order(N) calculations
ON.LowerMemory
Order(N) calculations
ON.MaxNumIter
Order(N) calculations
ON.RcLWF
Order(N) calculations
ON.UseSaveLWF
Order(N) calculations
Optical.Broaden
Optical properties
Optical.EnergyMaximum
Optical properties
Optical.EnergyMinimum
Optical properties
Optical.Mesh
Optical properties
Optical.NumberOfBands
Optical properties
Optical.OffsetMesh
Optical properties
Optical.PolarizationType
Optical properties
Optical.Scissor
Optical properties
Optical.Vector
Optical properties
Ordejon-Mauri
Order(N) calculations
OUT.UCELL.ZMATRIX
Output of structural information
output
$\delta \rho(\vec r)$
Output of charge densities
atomic coordinates
in a dynamics step
Standard output | Output options for dynamics
initial
Output options for dynamics
band $\vec k$ points
Standard output
band $\vec k$ points
Band-structure analysis
band structure
Band-structure analysis
basis
Saving and reading basis-set
charge density
Output of charge densities | Output of charge densities
charge density and/or wfs for DENCHAR code
Output of information for
customization
Standard output
dedicated files
Output to dedicated files
density matrix
Output of density matrix | Output of density matrix | Output of density matrix | Output of density matrix | Output of density matrix
density matrix history
Output of density matrix | Output of density matrix
eigenvalues
Standard output | Output of eigenvalues and | Total density of states
electrostatic potential
Output of charge densities | Output of charge densities
forces
Standard output | Output options for dynamics
grid $\vec k$ points
Standard output
grid $\vec k$ points
Output of k-point information
grid $\vec k$ points
Output of k-point information
Hamiltonian
Output of density matrix
Hamiltonian & overlap
Matrix elements of the
Hamiltonian history
Output of density matrix
HSX file
Matrix elements of the
Information for COOP/COHP curves
Crystal-Orbital overlap and hamilton
ionic charge
Output of charge densities
local density of states
Local density of states
long
Standard output
main output file
Standard output
molecular dynamics
Force Constants Matrix
Phonon calculations
history
Output options for dynamics | Output options for dynamics
PHONON forces file
Interface to the PHONON
Mulliken analysis
Standard output | Mulliken charges and overlap
overlap matrix
Output of density matrix | Output of density matrix
projected density of states
Partial (projected) density of
total charge
Output of charge densities
total potential
Output of charge densities
wave functions
Standard output | Output of wavefunctions
PAO.Basis
The PAO.Basis block
PAO.BasisSize
Size of the basis
PAO.BasisSizes
Size of the basis
PAO.BasisType
Type of basis sets
PAO.FixSplitTable
Generation of multiple-zeta orbitals
PAO.NewSplitCode
Generation of multiple-zeta orbitals
PAO.SoftDefault
Soft-confinement options
PAO.SoftInnerRadius
Soft-confinement options
PAO.SoftPotential
Soft-confinement options
PAO.SplitNorm
Generation of multiple-zeta orbitals
PAO.SplitNormH
Generation of multiple-zeta orbitals
PAO.SplitTailNorm
Generation of multiple-zeta orbitals
Parallel SIESTA
APPENDIX: Parallel SIESTA
ParallelOverK
APPENDIX: Parallel SIESTA
PBE
Exchange-correlation functionals
PBEsol
Exchange-correlation functionals
perturbative polarization
Size of the basis | The PAO.Basis block
PHONON PROGRAM
STRUCTURAL RELAXATION, PHONONS, AND | Interface to the PHONON
PhononLabels
Interface to the PHONON
polarization orbitals
Type of basis sets
PolarizationGrids
Macroscopic polarization
Precision selection
APPENDIX: Selection of precision
ProcessorY
Parallel options | APPENDIX: Parallel SIESTA
ProjectedDensityOfStates
Partial (projected) density of
PS.KBprojectors
Kleinman-Bylander projectors
PS.lmax
Kleinman-Bylander projectors
pseudopotential
example generation
EXECUTION OF THE PROGRAM
files
Pseudopotentials
generation
Pseudopotentials
Pulay mixing
Mixing options
PW92
Exchange-correlation functionals
PZ
Exchange-correlation functionals
RcSpatial
Parallel decompositions for O(N)
reading saved data
The catch-all option UseSaveData
all
The catch-all option UseSaveData
CG
Conjugate-gradients optimization
charge density
Initialization of the SCF
deformation charge density
Initialization of the SCF
density matrix
Initialization of the density-matrix | Initialization of the density-matrix | Initialization of the density-matrix | Initialization of the density-matrix
localized wave functions (order-)
Order(N) calculations
XV
Input of structural information
ZM
Input of structural information
readwf
Output of wavefunctions
readwfsx
Output of wavefunctions
relaxation of cell parameters only
Structural relaxation
removal of intramolecular pressure
Target stress options
Reparametrize.Pseudos
Low-level options regarding the
Restart of O(N) calculations
Order(N) calculations
Restricted.Radial.Grid
Low-level options regarding the
revPBE
Exchange-correlation functionals
rippling
The real-space grid and | The real-space grid and | The real-space grid and
Rmax.Radial.Grid
Low-level options regarding the
RPBE
Exchange-correlation functionals
SaveDeltaRho
Output of charge densities
SaveElectrostaticPotential
Output of charge densities
SaveHS
Matrix elements of the
SaveInitialChargeDensity
Output of charge densities
SaveIonicCharge
Output of charge densities
SaveNeutralAtomPotential
Output of charge densities
SaveRho
Output of charge densities
SaveTotalCharge
Output of charge densities
SaveTotalPotential
Output of charge densities
scale factor
The PAO.Basis block
SCF
The self-consistent-field loop
mixing
Mixing options | Mixing options | Mixing options | Mixing options | Mixing options
Broyden
Mixing options | Mixing options | Mixing options
energy convergence
Convergence criteria
harris energy convergence
Convergence criteria
linear
Mixing options | Mixing options | Mixing options
Pulay
Mixing options
Broyden
Mixing options
SCF convergence criteria
Convergence criteria
SCF.Read.Charge.NetCDF
Initialization of the SCF
SCF.Read.Deformation.Charge.NetCDF
Initialization of the SCF
SCFMustConverge
The self-consistent-field loop
Scripting
STRUCTURAL RELAXATION, PHONONS, AND
SIES2ARC
Output of structural information | Output of structural information
SIESTA
INTRODUCTION | General system descriptors
SimulateDoping
Systems with net charge
single-$\zeta$
Size of the basis
SingleExcitation
Spin polarization
Slab dipole correction
Systems with net charge
SlabDipoleCorrection
Systems with net charge
Slabs with net charge
Systems with net charge
SolutionMethod
Calculation of the electronic | General options
species
General system descriptors
species.ion
EXECUTION OF THE PROGRAM
spin
Spin polarization | Spin polarization | Spin polarization | Initialization of the density-matrix
initialization
Initialization of the density-matrix
non-collinear
Spin polarization
SpinPolarized
Spin polarization
split valence
Type of basis sets
splitgauss
Type of basis sets
STANDARD
Size of the basis
structure input precedence issues
Precedence issues in structural
SuperCell
Traditional structure input in
synthetic atoms
General system descriptors
SyntheticAtoms
General system descriptors
SystemLabel
EXECUTION OF THE PROGRAM | General system descriptors
Systemlabel..ANI
EXECUTION OF THE PROGRAM
Systemlabel.DM
EXECUTION OF THE PROGRAM
Systemlabel..EIG
EXECUTION OF THE PROGRAM
Systemlabel..FA
EXECUTION OF THE PROGRAM
Systemlabel.STRUCT_IN
Input of structural information
Systemlabel.STRUCT_NEXT_ITER
Output of structural information
Systemlabel.STRUCT_OUT
EXECUTION OF THE PROGRAM | Output of structural information
Systemlabel.xml
EXECUTION OF THE PROGRAM
Systemlabel.XV
EXECUTION OF THE PROGRAM
SystemName
General system descriptors
SZ
Size of the basis
SZP
Size of the basis
tbtrans
Utilities for analysis: tbtrans.
Tests
EXECUTION OF THE PROGRAM
TotalSpin
Spin polarization
TRANSIESTA
INTRODUCTION
TS.BiasContour.Eta
Bias contour integration options
TS.BiasContour.Method
Bias contour integration options
TS.BiasContour.NumPoints
Bias contour integration options
TS.BufferAtomsLeft
Electrode description options
TS.BufferAtomsRight
Electrode description options
TS.CalcGF
General options
TS.ComplexContour.Emin
Complex contour integration options
TS.ComplexContour.NumCircle
Complex contour integration options
TS.ComplexContour.NumLine
Complex contour integration options
TS.ComplexContour.NumPoles
Complex contour integration options
TS.GFFileLeft
Electrode description options
TS.GFFileRight
Electrode description options
TS.HSFileLeft
Electrode description options | Utilities for analysis: tbtrans.
TS.HSFileRight
Electrode description options
TS.MixH
General options
TS.NumUsedAtomsLeft
Electrode description options
TS.NumUsedAtomsRight
Electrode description options
TS.SaveHS
General options
TS.TBT.Emax
Utilities for analysis: tbtrans.
TS.TBT.Emin
Utilities for analysis: tbtrans.
TS.TBT.NEigen
Utilities for analysis: tbtrans.
TS.TBT.NPoints
Utilities for analysis: tbtrans.
TS.TriDiag
General options
TS.UpdateDMCROnly
General options
Use.New.Diagk
Diagonalization options
UseDomainDecomposition
Parallel decompositions for O(N)
User.Basis
Saving and reading basis-set
User.Basis.NetCDF
Saving and reading basis-set
UseSaveData
The catch-all option UseSaveData
UseSpatialDecomposition
Parallel decompositions for O(N)
UseStructFile
Input of structural information
VCA
General system descriptors
VIBRA
Phonon calculations
WarningMinimumAtomicDistance
Interatomic distances
WaveFuncKPoints
Output of wavefunctions | Output of wavefunctions
WaveFuncKPointsScale
Output of wavefunctions
WC
Exchange-correlation functionals
WFSX file
Output of wavefunctions
WriteBands
Band-structure analysis
WriteCoorCerius
Output of structural information
WriteCoorInitial
Output options for dynamics
WriteCoorStep
Standard output | Output options for dynamics
WriteCoorXmol
Output of structural information
WriteDenchar
Output of information for
WriteDM
Output of density matrix
WriteDM.History.NetCDF
Output of density matrix
WriteDM.NetCDF
Output of density matrix
WriteDMHS.History.NetCDF
Output of density matrix
WriteDMHS.NetCDF
Output of density matrix
WriteEigenvalues
Standard output | Output of eigenvalues and
WriteForces
Standard output | Output options for dynamics
WriteKbands
Standard output | Band-structure analysis
WriteKpoints
Standard output | Output of k-point information
WriteMDhistory
Output options for dynamics
WriteMDXmol
Output of structural information
WriteMullikenPop
Standard output | Mulliken charges and overlap
WriteWaveFunctions
Standard output | Output of wavefunctions
XC.authors
Exchange-correlation functionals
XC.functional
Exchange-correlation functionals
XC.hybrid
Exchange-correlation functionals
XML
APPENDIX: XML Output
XML.AbortOnErrors
Controlling XML output
XML.AbortOnWarnings
Controlling XML output
XML.Write
Controlling XML output
XMOL
Output of structural information | Output of structural information
ZM.ForceTolAngle
Structural relaxation
ZM.ForceTolLength
Structural relaxation
ZM.MaxDisplAngle
Structural relaxation
ZM.MaxDisplLength
Structural relaxation
ZM.UnitsAngle
Z-matrix format and constraints
ZM.UnitsLength
Z-matrix format and constraints
Zmatrix
Z-matrix format and constraints


2011-11-16