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:

• vol_sphere:
  
  %Volume
     "+"/"-" | vol_sphere | center_x | center_y | center_z | radius
  %
• vol_slab:
  
  %Volume
     "+"/"-" | vol_slab | thickness
  %
  
  

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.

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:

• none: Do not rotate. Will still give output regarding center of mass and moment of inertia.
• inertia: The axis of inertia.
• pseudo_inertia: Pseudo-axis of inertia, calculated considering all species to have equal mass.
• large_axis: The larger axis of the molecule.

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
%

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.

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:

• fast_fourier: Uses Fast Fourier Transform as implemented in the external library.
• standard_fourier: Uses polinomial approach to the computation of discrete Fourier Transform. It uses the same variable described in how to obtain spectrum from a time-propagation calculation.

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:

• format: The format of the mesh function will be convert from the binary file.obf. The format of the output function is set by OutputHow variable.
• fourier_transform: A fourier transform of the mesh function will be computed. It requieres that ConvertStart and ConvertEnd have to be set.
• operation: Convert utility will generate a new mesh function constructed by linear combination of scalar function of different mesh functions,

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.

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:

• energy: If set, octopus outputs the different components of the energy of the local domains to the folder ld.general/energy.
• multipoles: Outputs the (electric) multipole moments of the density to the file ld.general/multipoles. This is required to, e.g., calculate optical absorption spectra of finite systems. The maximum value of \(l\) can be set with the variable LDMultipoleLmax.
• density: If set, octopus outputs the densities corresponding to the local domains to the folder ld.general/densities. The output format is set by the LDOutputFormat input variable.
• local_v: If set, octopus outputs the different components of the potential to the folder ld.general/potential. The output format is set by the LDOutputFormat input variable.

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"

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:

• energy_tot: Output the energy-resolved photoelectron spectrum: E.
• energy_angle: Output the energy and angle resolved spectrum: (theta, E) The result is integrated over phi.
• velocity_map_cut: Velocity map on a plane orthogonal to pvec: (px, py). The allowed cutting planes (pvec) can only be parallel to the x,y,z=0 planes. Space is oriented so that the z-axis is along vec. Supports the -I option.
• energy_xy: Angle and energy-resolved spectrum on the inclination plane: (Ex, Ey). The result is integrated over ph;
• energy_th_ph: Ionization probability integrated on spherical cuts: (theta, phi).
• velocity_map: Full momentum-resolved ionization probability: (px, py, pz). The output format can be controlled with OutputHow and can be vtk or ncdf.
• arpes: Full ARPES for semi-periodic systems (vtk).
• arpes_cut: ARPES cut on a plane following a zero-weight path in reciprocal space.

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
%

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:

• none: No filtering at all.
• exponential: Exponential filtering, corresponding to a Lorentzian-shaped spectrum.
• polynomial: Third-order polynomial damping.
• gaussian: Gaussian damping.

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.

PropagationSpectrumMinEnergy
Section: Utilities::oct-propagation_spectrum
Type: float
Default: 0

The Fourier transform is calculated for energies larger 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:

• laplace: Real exponential transform: \(\int dt e^{-wt} f(t)\). Produces the real part of the polarizability at imaginary frequencies, e.g. for Van der Waals \(C_6\) coefficients. This is the only allowed choice for complex scaling.
• sine: Sine transform: \(\int dt \sin(wt) f(t)\). Produces the imaginary part of the polarizability.
• cosine: Cosine transform: \(\int dt \cos(wt) f(t)\). Produces the real part of the polarizability.

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

Type of spectrum to calculate.
Options:

• AbsorptionSpectrum: Photoabsorption spectrum.
• EnergyLossSpectrum: Dynamic structure factor (also known as energy-loss function or spectrum).
• DipolePower: Power spectrum of the dipole moment.
• RotatoryStrength: Rotatory strength spectrum.

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

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

• fourier: The standard Fourier transform. Further specified by PropagationSpectrumTransform.
• compressed_sensing: (Experimental) Uses the compressed sensing technique.

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

TestBatchOps
Section: Utilities::oct-test
Type: flag
Default: ops_axpy + ops_scal + ops_nrm2

Decides which part of the Hamiltonian is applied.
Options:

• ops_axpy: Tests batch_axpy operation
• ops_scal: Tests batch_scal operation
• ops_nrm2: Tests batch_nrm2 operation
• ops_dotp_matrix: Tests X(mesh_batch_dotp_matrix)
• ops_dotp_self: Tests X(mesh_batch_dotp_self)
• ops_dotp_vector: Tests X(mesh_batch_dotp_vector)

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

Decides which part of the Hamiltonian is applied.
Options:

• term_all: Apply the full Hamiltonian.
• term_kinetic: Apply only the kinetic operator
• term_local_potential: Apply only the local potential.
• term_non_local_potential: Apply only the non_local potential.

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:

• exp_apply: Tests the exponential of the Hamiltonian
• boundaries: Tests the boundaries conditions
• subspace_diag: Tests the subspace diagonalization
• batch_ops: Tests the batch operations
• clock: Tests for clock
• hartree: Tests the Poisson solvers used to calculate the Hartree potential.
• derivatives: Tests and benchmarks the implementation of the finite-difference operators, used to calculate derivatives.
• orthogonalization: Tests the implementation of the orthogonalization routines.
• interpolation: Test the interpolation routines.
• ion_interaction: Tests the ion-ion interaction routines.
• projector: Tests the code that applies the nonlocal part of the pseudopotentials in case of spin-orbit coupling
• dft_u: Tests the DFT+U part of the code for projections on the basis.
• hamiltonian_apply: Tests the application of the Hamiltonian, or a part of it
• density_calc: Calculation of the density.

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:

• real: Test for double-precision real functions.
• all: Tests for double-precision real and complex functions.

UnfoldEnergyStep
Section: Utilities::oct-unfold
Type: float
Default: 0

Specifies the energy resolution for the unfolded band structure. If you specify 0, the resolution will be set to be 1/1000 points between UnfoldMinEnergy and UnfoldMaxEnergy

UnfoldKPointsPath
Section: Utilities::oct-unfold
Type: block

Specifies the k-point path for which the unfolding need to be done. The syntax is identical to KPointsPath.

UnfoldLatticeParameters
Section: Utilities::oct-unfold
Type: block
Default: 1 | 1 | 1

The lattice parameters of the primitive cell, on which unfolding is performed.

UnfoldLatticeVectors
Section: Utilities::oct-unfold
Type: block
Default: simple cubic

Lattice vectors of the primitive cell on which the unfolding is performed.

UnfoldMaxEnergy
Section: Utilities::oct-unfold
Type: float

Specifies the end of the energy range for the unfolded band structure. The default value correspond to the largest eigenvalue.

UnfoldMinEnergy
Section: Utilities::oct-unfold
Type: float

Specifies the start of the energy range for the unfolded band structure. The default value correspond to the samllest eigenvalue.

UnfoldMode
Section: Utilities::oct-unfold
Type: flag
Default: none

Specifies which stage of the unfolding tool to use
Options:

• unfold_setup: Writes the list of k-points corresponding to the path specified by UnfoldKPointPath. This list of k-point (unfold_kpt.dat) must be used for an unocc calculation of the supercell, adding the line "include 'unfold_kpt.dat'" to the inp file and removing the KPointGrid information.
• unfold_run: Perform the actual unfolding, based on the states obtained from the previous unocc run.

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.

SCDMmu
Section: Utilities::oct-wannier90
Type: float

Energy range up to which states are considered for SCDM

SCDMsigma
Section: Utilities::oct-wannier90
Type: float

Broadening of SCDM smearing function

Wannier90Files
Section: Utilities::oct-wannier90
Type: flag
Default: w90_mmn + w90_amn + w90_eig

Specifies which files to generate. Example: w90_mmn + w90_unk
Options:

• w90_mmn: (see Wannier90 documentation)
• w90_unk: (see Wannier90 documentation)
• w90_amn: (see Wannier90 documentation)
• w90_eig: Eigenvalues. See Wannier90 documentation for more details.

Wannier90Mode
Section: Utilities::oct-wannier90
Type: integer
Default: 0

Specifies which stage of the Wannier90 interface to use
Options:

• none: Nothing is done.
• w90_setup: Writes parts of the wannier90 input file w90_prefix.win corresponding to the octopus inp file. Importantly it generates the correct form of Monkhorst-Pack mesh written to the file w90_kpoints that has to be used in a gs calculation of Octopus by as include w90_kpoints instead of the %KpointsGrid block.
• w90_output: Generates the relevant files for a wannier90 run, specified by the variable W90_interface_files. This needs files previously generated by wannier90.x -pp w90
• w90_wannier: Parse the output of wannier90 to generate the Wannier states on the real-space grid. The states will be written in the folder wannier. By default, the states are written as binary files, similar to the Kohn-Sham states.

Wannier90Prefix
Section: Utilities::oct-wannier90
Type: string
Default: w90

Prefix for wannier90 files

Wannier90UseSCDM
Section: Utilities::oct-wannier90
Type: logical
Default: no

By default oct-wannier90 uses the projection method to generate the .amn file. By setting this variable to yes, oct-wannier90 will use SCDM method instead.

Wannier90UseTD
Section: Utilities::oct-wannier90
Type: logical
Default: no

By default oct-wannier90 uses the ground-state states to compute the necessary information. By setting this variable to yes, oct-wannier90 will use the TD states instead.

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.