Utilities::

Volume
Section: Utilities::
Type: block

Describes a volume in space defined through the addition and substraction of spheres. The first field is always "+" (include points inside the volume) or "-" (exclude points inside the volume)
Options:


Utilities::oct-casida_spectrum

CasidaSpectrumBroadening
Section: Utilities::oct-casida_spectrum
Type: float
Default: 0.005 Ha

Width of the Lorentzian used to broaden the excitations.


CasidaSpectrumEnergyStep
Section: Utilities::oct-casida_spectrum
Type: float
Default: 0.001 Ha

Sampling rate for the spectrum.


CasidaSpectrumMaxEnergy
Section: Utilities::oct-casida_spectrum
Type: float
Default: 1.0 Ha

The broadening is done for energies smaller than CasidaSpectrumMaxEnergy.


CasidaSpectrumMinEnergy
Section: Utilities::oct-casida_spectrum
Type: float
Default: 0.0

The broadening is done for energies greater than CasidaSpectrumMinEnergy.


CasidaSpectrumRotationMatrix
Section: Utilities::oct-casida_spectrum
Type: block
Default: identity

Supply a rotation matrix to apply to the transition dipoles in generating the spectrum. The rotated atomic structure will also be output. Size of matrix must be Dimensions.


Utilities::oct-center-geom

AxisType
Section: Utilities::oct-center-geom
Type: integer
Default: inertia

After the structure is centered, it is also aligned to a set of orthogonal axes. This variable decides which set of axes to use. Only implemented for 3D, in which case the default is inertia; otherwise none is default and the only legal value.
Options:


MainAxis
Section: Utilities::oct-center-geom
Type: block

A vector of reals defining the axis to which the molecule should be aligned. If not present, the default value will be the x-axis. For example in 3D:
%MainAxis
1 | 0 | 0
%


Utilities::oct-conductivity_spectrum

ConductivityFromForces
Section: Utilities::oct-conductivity_spectrum
Type: logical
Default: no

(Experimental) If enabled, Octopus will attempt to calculate the conductivity from the forces instead of the current.


ConductivitySpectrumTimeStepFactor
Section: Utilities::oct-conductivity_spectrum
Type: integer
Default: 1

In the calculation of the conductivity, it is not necessary to read the velocity at every time step. This variable controls the integer factor between the simulation time step and the time step used to calculate the conductivity.


Utilities::oct-convert

ConvertEnd
Section: Utilities::oct-convert
Type: integer
Default: 1

The last number of the filename or folder.


ConvertEnergyMax
Section: Utilities::oct-convert
Type: float
Default: w_max

Maximum energy to output from Fourier transform.


ConvertEnergyMin
Section: Utilities::oct-convert
Type: float
Default: 0.0

Minimum energy to output from Fourier transform.


ConvertEnergyStep
Section: Utilities::oct-convert
Type: float
Default: \(2 \pi / T\), where \(T\) is the total propagation time

Energy step to output from Fourier transform. Sampling rate for the Fourier transform. If you supply a number equal or smaller than zero, then the sampling rate will be \(2 \pi / T\), where \(T\) is the total propagation time.


ConvertFTMethod
Section: Utilities::oct-convert
Type: integer
Default: FAST_FOURIER

Describes the method used to perform the Fourier Transform
Options:


ConvertFilename
Section: Utilities::oct-convert
Type: string
Default: "density"

Input filename. The original filename which is going to be converted in the format specified in OutputFormat. It is going to convert various files, it should only contain the beginning of the name. For instance, in the case of the restart files, it should be one space ' '.


ConvertFolder
Section: Utilities::oct-convert
Type: string

The folder name where the input files are. The default is td. if ConvertIterateFolder = true, otherwise restart.


ConvertHow
Section: Utilities::oct-convert
Type: integer
Default: convert_format

Select how the mesh function will be converted.
Options:


ConvertIterateFolder
Section: Utilities::oct-convert
Type: logical
Default: true

This variable decides if a folder is going to be iterated or the filename is going to be iterated.


ConvertOutputFilename
Section: Utilities::oct-convert
Type: string
Default: "density"

Output filename. The name of the file in which the converted mesh function will be written in the format specified in OutputFormat.


ConvertOutputFolder
Section: Utilities::oct-convert
Type: string

The folder name where the output files will be write. The default is convert.


ConvertReadSize
Section: Utilities::oct-convert
Type: integer
Default: mesh%np

How many points are read at once. For the parallel run this has not been yet tested, so it should be one. For the serial run, a number of 100-1000 will speed-up the execution time by this factor.


ConvertScalarOperation
Section: Utilities::oct-convert
Type: block

This variable is used to generate a new mesh function as a linear combination different mesh function having the same mesh. Each row defines an operation for for a single mesh function. The format of the block is the following:
'variable name' | 'folder' | 'file' | 'operation'


ConvertStart
Section: Utilities::oct-convert
Type: integer

The starting number of the filename or folder. Default is 0 if ConvertIterateFolder = true, otherwise 1.


ConvertStep
Section: Utilities::oct-convert
Type: integer
Default: 1

The padding between the filenames or folder.


ConvertSubtract
Section: Utilities::oct-convert
Type: logical
Default: false

Decides if a reference file is going to be subtracted.


ConvertSubtractFilename
Section: Utilities::oct-convert
Type: string
Default: density

Input filename. The file which is going to subtracted to rest of the files.


ConvertSubtractFolder
Section: Utilities::oct-convert
Type: string
Default: .

The folder name which is going to be subtracted.


Utilities::oct-local_multipoles

LDBaderThreshold
Section: Utilities::oct-local_multipoles
Type: float
Default: 0.01

This variable sets the threshold for the basins calculations. Recommended values: 0.01 -> intramolecular volumes; 0.2 -> intermolecular volumes


LDEnd
Section: Utilities::oct-local_multipoles
Type: integer
Default: 0

The last number of the filename or folder.


LDExtraWrite
Section: Utilities::oct-local_multipoles
Type: logical
Default: false

Writes additional information to files, when computing local multipoles. For example, it writes coordinates of each local domain.


LDFilename
Section: Utilities::oct-local_multipoles
Type: string
Default: 'density'

Input filename. The original filename for the density which is going to be fragmented into domains.


LDFolder
Section: Utilities::oct-local_multipoles
Type: string

The folder name where the density used as input file is.


LDIonicDipole
Section: Utilities::oct-local_multipoles
Type: logical
Default: yes

Describes if the ionic dipole has to be take into account when computing the multipoles.


LDIterateFolder
Section: Utilities::oct-local_multipoles
Type: logical
Default: false

This variable decides if a folder is going to be iterated.


LDMultipoleLmax
Section: Utilities::oct-local_multipoles
Type: integer
Default: 1

Maximum electric multipole of the density output to the file local.multipoles/<>domain%<>.multipoles during a time-dependent simulation. Must be non-negative.


LDOutput
Section: Utilities::oct-local_multipoles
Type: flag
Default: multipoles

Defines what should be output during the local domains simulation. Many of the options can increase the computational cost of the simulation, so only use the ones that you need. In most cases the default value is enough, as it is adapted to the details.
Options:


LDOutputFormat
Section: Utilities::oct-local_multipoles
Type: flag
Default: none

Describes the format of the output files (see LDOutput). It can take the same values as OutputFormat flag.


LDOverWrite
Section: Utilities::oct-local_multipoles
Type: logical
Default: true

Controls whether to over-write existing files.


LDRadiiFile
Section: Utilities::oct-local_multipoles
Type: string
Default: 'default'

Full path for the radii file. If set, def_rsize will be reset to the new values. This file should have the same format as share/PP/default.


LDRestart
Section: Utilities::oct-local_multipoles
Type: logical
Default: false

Restart information will be read from LDRestartFolder.


LDRestartFolder
Section: Utilities::oct-local_multipoles
Type: string
Default: "ld.general"

The folder name where the density used as input file is.


LDStart
Section: Utilities::oct-local_multipoles
Type: integer
Default: 0

The starting number of the filename or folder.


LDStep
Section: Utilities::oct-local_multipoles
Type: integer
Default: 1

The padding between the filenames or folder.


LDUpdate
Section: Utilities::oct-local_multipoles
Type: logical
Default: false

Controls if the calculation of the local domains is desired at each iteration.


LDUseAtomicRadii
Section: Utilities::oct-local_multipoles
Type: logical
Default: false

If set, atomic radii will be used to assign lone pairs to ion.


LocalDomains
Section: Utilities::oct-local_multipoles
Type: block

The LocalDomains are by definition part of the global grid. The domains are defined by selecting a type shape. The domain box will be constructed using the given parameters. A local domain could be construct by addition of several box centered on the ions. The grid points inside this box will belong to the local domain.

The format of this block is the following:
'Label' | Shape | %< | Shape dependencies >%
The first field is the label of the domain. Label = string with the name of the new local domain. The second is the shape type of the box used to define the domain. Shape = SPHERE, CYLINDER, PARALLELEPIPED, MINIMUM, BADER. Some types may need some parameters given in the remaining fields of the row. (the valid options are detailed below).

%LocalDomains
case(SPHERE): | rsize | %
case(CYLINDER): | rsize | xsize | %
case(PARALLELEPIPED): | % | %
case(MINIMUM): | rsize | 'center_list'
case(BADER): | 'center_list'
%

rsize: Radius in input length units
xsize: the length of the cylinder in the x-direction
origin coordinates: in input length units separated by |, where the box is centered.
lsize: half of the length of the parallelepiped in each direction.
center_list: string containing the list of atoms in xyz file for each domain in the form "2,16-23"


Utilities::oct-photoelectron_spectrum

PhotoelectronSpectrumOutput
Section: Utilities::oct-photoelectron_spectrum
Type: flag
Default: none

Specifies what to output extracting the photoelectron cross-section informations. When we use polar coordinates the zenith axis is set by vec (default is the first laser field polarization vector), theta is the inclination angle measured from vec (from 0 to \pi), and phi is the azimuthal angle on a plane perpendicular to vec (from 0 to 2\pi). Example: energy_tot + velocity_map
Options:


PhotoelectronSpectrumResolveStates
Section: Utilities::oct-photoelectron_spectrum
Type: block

If yes calculate the photoelectron spectrum resolved in each K.S. state. Optionally a range of states can be given as two slot block where the first slot is the lower state index and the second is the highest one. For example to calculate the spectra from state i to state j:

%PhotoelectronSpectrumResolveStates
i | j
%


Utilities::oct-propagation_spectrum

PropagationSpectrumDampFactor
Section: Utilities::oct-propagation_spectrum
Type: float
Default: -1.0

If PropagationSpectrumDampMode = exponential, gaussian, the damping parameter of the exponential is fixed through this variable. Default value ensure that the damping function adquires a 0.0001 value at the end of the propagation time.


PropagationSpectrumDampMode
Section: Utilities::oct-propagation_spectrum
Type: integer

Decides which damping/filtering is to be applied in order to calculate spectra by calculating a Fourier transform. The default is polynomial damping, except when SpectrumMethod = compressed_sensing. In that case the default is none.
Options:


PropagationSpectrumEndTime
Section: Utilities::oct-propagation_spectrum
Type: float
Default: -1.0 au

Processing is done for the given function in a time-window that ends at the value of this variable. If set to a negative value, the maximum value from the corresponding multipole file will used.


PropagationSpectrumEnergyStep
Section: Utilities::oct-propagation_spectrum
Type: float
Default: 0.01 eV

Sampling rate for the spectrum. If you supply a number equal or smaller than zero, then the sampling rate will be \(2 \pi / T\), where \(T\) is the total propagation time.


PropagationSpectrumMaxEnergy
Section: Utilities::oct-propagation_spectrum
Type: float
Default: 20 eV

The Fourier transform is calculated for energies smaller than this value.


PropagationSpectrumSigmaDiagonalization
Section: Utilities::oct-propagation_spectrum
Type: logical
Default: .false.

If PropagationSpectrumSigmaDiagonalization = yes, the polarizability tensor is diagonalizied. This variable is only used if the cross_section_tensor is computed.


PropagationSpectrumStartTime
Section: Utilities::oct-propagation_spectrum
Type: float
Default: 0.0

Processing is done for the given function in a time-window that starts at the value of this variable.


PropagationSpectrumSymmetrizeSigma
Section: Utilities::oct-propagation_spectrum
Type: logical
Default: .false.

The polarizablity tensor has to be real and symmetric. Due to numerical accuracy, that is not extricly conserved when computing it from different time-propations. If PropagationSpectrumSymmetrizeSigma = yes, the polarizability tensor is symmetrized before its diagonalizied. This variable is only used if the cross_section_tensor is computed.


PropagationSpectrumTransform
Section: Utilities::oct-propagation_spectrum
Type: integer
Default: sine

Decides which transform to perform, if SpectrumMethod = fourier.
Options:


PropagationSpectrumType
Section: Utilities::oct-propagation_spectrum
Type: integer
Default: AbsorptionSpectrum

Type of spectrum to calculate.
Options:


SpectrumMethod
Section: Utilities::oct-propagation_spectrum
Type: integer
Default: fourier

Decides which method is used to obtain the spectrum.
Options:


SpectrumSignalNoise
Section: Utilities::oct-propagation_spectrum
Type: float
Default: 0.0

For compressed sensing, the signal to process, the time-dependent dipole in this case, is assumed to have some noise that is given by this dimensionless quantity.


TransientAbsorptionReference
Section: Utilities::oct-propagation_spectrum
Type: string
Default: "."

In case of delayed kick, the calculation of the transient absorption requires to substract a reference calculation, containing the gauge-field without the kick This reference must be computed using GaugeFieldPropagate=yes and to have TDOutput = gauge_field. This variables defined the directory in which the reference gauge_field field is, relative to the current folder


Utilities::oct-test

TestHamiltonianApply
Section: Utilities::oct-test
Type: integer
Default: term_all

Decides which part of the Hamiltonian is applied.
Options:


TestMaxBlockSize
Section: Utilities::oct-test
Type: integer
Default: 128

Some tests can work with multiple blocksizes, in this case of range of blocksizes will be tested. This variable sets the lower bound of that range.

Currently this variable is only used by the derivatives test.


TestMinBlockSize
Section: Utilities::oct-test
Type: integer
Default: 1

Some tests can work with multiple blocksizes, in this case of range of blocksizes will be tested. This variable sets the lower bound of that range.

Currently this variable is only used by the derivatives test.


TestMode
Section: Utilities::oct-test
Type: integer
Default: hartree

Decides what kind of test should be performed.
Options:


TestRepetitions
Section: Utilities::oct-test
Type: integer
Default: 1

This variable controls the behavior of oct-test for performance benchmarking purposes. It sets the number of times the computational kernel of a test will be executed, in order to provide more accurate timings.

Currently this variable is used by the hartree_test, derivatives, and projector tests.


TestType
Section: Utilities::oct-test
Type: integer
Default: all

Decides on what type of values the test should be performed.
Options:


Utilities::oct-vibrational_spectrum

VibrationalSpectrumTime
Section: Utilities::oct-vibrational_spectrum
Type: integer

This variable controls the maximum time for the calculation of the velocity autocorrelation function. The default is the total propagation time.


VibrationalSpectrumTimeStepFactor
Section: Utilities::oct-vibrational_spectrum
Type: integer
Default: 10

In the calculation of the vibrational spectrum, it is not necessary to read the velocity at every time step. This variable controls the integer factor between the simulation time step and the time step used to calculate the vibrational spectrum.


Utilities::oct-xyz-anim

AnimationMultiFiles
Section: Utilities::oct-xyz-anim
Type: logical
Default: false

If true, each iteration written will be in a separate file.


AnimationSampling
Section: Utilities::oct-xyz-anim
Type: integer
Default: 100

Sampling rate of the animation. The animation will be constructed using the iteration numbers that are multiples of AnimationSampling.