P
Name ParallelizationNumberSlaves
Section Execution::Parallelization
Type integer
Default 0
Slaves are nodes used for task parallelization. The number of
such nodes is given by this variable multiplied by the number
of domains used in domain parallelization.
Name ParallelizationOfDerivatives
Section Execution::Parallelization
Type integer
Default non_blocking
This option selects how the communication of mesh boundaries is performed.
Options:
- blocking:
Blocking communication.
- non_blocking:
Communication is based on non-blocking point-to-point communication.
Name ParallelizationPoissonAllNodes
Section Execution::Parallelization
Type logical
Default true
When running in parallel, this variable selects whether the
Poisson solver should divide the work among all nodes or only
among the parallelization-in-domains groups.
Name ParallelXC
Section Execution::Parallelization
Type logical
Default true
When enabled, additional parallelization
will be used for the calculation of the XC functional.
Name ParDomains
Section Execution::Parallelization
Type integer
Default auto
This variable controls the number of processors used for the
parallelization in domains.
The special value auto, the default, lets Octopus
decide how many processors will be assigned for this
strategy. To disable parallelization in domains, you can use
ParDomains = no (or set the number of processors to
1).
The total number of processors required is the multiplication
of the processors assigned to each parallelization strategy.
Options:
- auto:
The number of processors is assigned automatically.
- no:
This parallelization strategy is not used.
Name ParKPoints
Section Execution::Parallelization
Type integer
Default auto
This variable controls the number of processors used for the
parallelization in K-Points and/or spin.
The special value auto lets Octopus decide how many processors will be
assigned for this strategy. To disable parallelization in
KPoints, you can use ParKPoints = no (or set the
number of processors to 1).
The total number of processors required is the multiplication
of the processors assigned to each parallelization strategy.
Options:
- auto:
The number of processors is assigned automatically.
- no:
This parallelization strategy is not used.
Name ParOther
Section Execution::Parallelization
Type integer
Default auto
This variable controls the number of processors used for the
‘other’ parallelization mode, that is CalculatioMode
dependent. For CalculationMode = casida, it means
parallelization in electron-hole pairs.
The special value auto, the default, lets Octopus decide how many processors will be assigned for this strategy. To disable parallelization in Other, you can use ParOther = no (or set the number of processors to 1).
The total number of processors required is the multiplication
of the processors assigned to each parallelization strategy.
Options:
- auto:
The number of processors is assigned automatically.
- no:
This parallelization strategy is not used.
Name ParStates
Section Execution::Parallelization
Type integer
This variable controls the number of processors used for the
parallelization in states. The special value auto lets
Octopus decide how many processors will be assigned for this
strategy. To disable parallelization in states, you can use
ParStates = no (or set the number of processors to 1).
The default value depends on the CalculationMode. For CalculationMode = td the default is auto, while for for other modes the default is no.
The total number of processors required is the multiplication
of the processors assigned to each parallelization strategy.
Options:
- auto:
The number of processors is assigned automatically.
- no:
This parallelization strategy is not used.
Name ParticleCharge
Section ClassicalParticles
Type float
Charge of classical particle
Name ParticleInitialPosition
Section ClassicalParticles
Type block
Initial position of classical particle, in Km.
Name ParticleInitialVelocity
Section ClassicalParticles
Type block
Initial velocity of classical particle in Km/s.
Name ParticleMass
Section Hamiltonian
Type float
Default 1.0
It is possible to make calculations for a particle with a mass
different from one (atomic unit of mass, or mass of the electron).
This is useful to describe non-electronic systems, or for
esoteric purposes.
Name PartitionPrint
Section Execution::Parallelization
Type logical
Default true
(experimental) If disabled, Octopus will not compute
nor print the partition information, such as local points,
no. of neighbours, ghost points and boundary points.
Name PauliHamiltonianTerms
Section Hamiltonian
Type flag
Default non_uniform_vector_potential + zeeman_term
Terms to be included in the Pauli Hamiltonnian.
Options:
- non_uniform_vector_potential:
Adds non-uniform vector potential to the canonical momentum.
- zeeman_term:
Adds the non-uniform Zeeman potential.
Name PCMCalcMethod
Section Hamiltonian::PCM
Type integer
Default pcm_direct
Defines the method to be used to obtain the PCM potential.
Options:
- pcm_direct:
Direct sum of the potential generated by the polarization charges regularized
with a Gaussian smearing [A. Delgado, et al., J Chem Phys 143, 144111 (2015)].
- pcm_poisson:
Solving the Poisson equation for the polarization charge density.
Name PCMCalculation
Section Hamiltonian::PCM
Type logical
Default no
If true, the calculation is performed accounting for solvation effects
by using the Integral Equation Formalism Polarizable Continuum Model IEF-PCM
formulated in real-space and real-time (J. Chem. Phys. 143, 144111 (2015),
Chem. Rev. 105, 2999 (2005), J. Chem. Phys. 139, 024105 (2013)).
At the moment, this option is available only for TheoryLevel = DFT.
PCM is tested for CalculationMode = gs, while still experimental for other values (in particular, CalculationMode = td).
Name PCMCavity
Section Hamiltonian::PCM
Type string
Name of the file containing the geometry of the cavity hosting the solute molecule.
The data must be in atomic units and the file must contain the following information sequentially:
T < Number of tesserae
s_x(1:T) < coordinates x of the tesserae
s_y(1:T) < coordinates y of the tesserae
s_z(1:T) < coordinates z of the tesserae
A(1:T) < areas of the tesserae
R_sph(1:T) < Radii of the spheres to which the tesserae belong
normal(1:T,1:3) < Outgoing unitary vectors at the tesserae surfaces
Name PCMChargeSmearNN
Section Hamiltonian::PCM
Type integer
Default 2 * max_area * PCMSmearingFactor
Defines the number of nearest neighbor mesh-points to be taken around each
cavity tessera in order to smear the charge when PCMCalcMethod = pcm_poisson.
Setting PCMChargeSmearNN = 1 means first nearest neighbors, PCMChargeSmearNN = 2
second nearest neighbors, and so on.
The default value is such that the neighbor mesh contains points in a radius
equal to the width used for the gaussian smearing.
Name PCMDebyeRelaxTime
Section Hamiltonian::PCM
Type float
Default 0.0
Relaxation time of the solvent within Debye model ($\tau$). Recall Debye dieletric function:
$\varepsilon(\omega)=\varepsilon_d+\frac{\varepsilon_0-\varepsilon_d}{1-i\omega\tau}$
Name PCMDrudeLDamping
Section Hamiltonian::PCM
Type float
Default 0.0
Damping factor of the solvent charges oscillations within Drude-Lorentz model ($\gamma$).
Recall Drude-Lorentz dielectric function: $\varepsilon(\omega)=1+\frac{A}{\omega_0^2-\omega^2+i\gamma\omega}$
Name PCMDrudeLOmega
Section Hamiltonian::PCM
Type float
Default
Resonance frequency of the solvent within Drude-Lorentz model ($\omega_0$).
Recall Drude-Lorentz dielectric function: $\varepsilon(\omega)=1+\frac{A}{\omega_0^2-\omega^2+i\gamma\omega}$
Default values of $\omega_0$ guarantee to recover static dielectric constant.
Name PCMDynamicEpsilon
Section Hamiltonian::PCM
Type float
Default PCMStaticEpsilon
High-frequency dielectric constant of the solvent ($\varepsilon_d$).
$\varepsilon_d=\varepsilon_0$ indicate equilibrium with solvent.
Name PCMEoMInitialCharges
Section Hamiltonian::PCM
Type integer
Default 0
If =0 the propagation of the solvent polarization charges starts from internally generated initial charges
in equilibrium with the initial potential.
For Debye EOM-PCM, if >0 the propagation of the solvent polarization charges starts from initial charges from input file.
if =1, initial pol. charges due to solute electrons are read from input file.
else if =2, initial pol. charges due to external potential are read from input file.
else if =3, initial pol. charges due to solute electrons and external potential are read from input file.
Files should be located in pcm directory and are called ASC_e.dat and ASC_ext.dat, respectively.
The latter files are generated after any PCM run and contain the last values of the polarization charges.
Name PCMEpsilonModel
Section Hamiltonian::PCM
Type integer
Default pcm_debye
Define the dielectric function model.
Options:
- pcm_debye:
Debye model: $\varepsilon(\omega)=\varepsilon_d+\frac{\varepsilon_0-\varepsilon_d}{1-i\omega\tau}$
- pcm_drude:
Drude-Lorentz model: $\varepsilon(\omega)=1+\frac{A}{\omega_0^2-\omega^2+i\gamma\omega}$
Name PCMGamessBenchmark
Section Hamiltonian::PCM
Type logical
Default .false.
If PCMGamessBenchmark is set to "yes", the pcm_matrix is also written in a Gamess format.
for benchamarking purposes.
Name PCMKick
Section Hamiltonian::PCM
Type logical
Default no
This variable controls the effect the kick has on the polarization of the solvent.
If .true. ONLY the FAST degrees-of-freedom of the solvent follow the kick. The potential due to polarization charges behaves
as another kick, i.e., it is a delta-perturbation.
If .false. ALL degrees-of-freedom of the solvent follow the kick. The potential due to polarization charges evolves
following an equation of motion. When Debye dielectric model is used, just a part of the potential behaves as another kick.
Name PCMLocalField
Section Hamiltonian::PCM
Type logical
Default no
This variable is a flag for including local field effects when an external field is applied. The total field interacting with
the molecule (also known as cavity field) is not the bare field in the solvent (the so-called Maxwell field), but it also
include a contribution due to the polarization of the solvent. The latter is calculated here within the PCM framework.
See [G. Gil, et al., J. Chem. Theory Comput., 2019, 15 (4), pp 2306–2319].
Name PCMQtotTol
Section Hamiltonian::PCM
Type float
Default 0.5
If PCMRenormCharges=.true. and $\delta Q = |[\sum_i q_i| - ((\epsilon-1)/\epsilon)|Q_M]|>PCMQtotTol$
the polarization charges will be normalized as
$q_i^\prime=q_i + signfunction(e, n, \delta Q) (q_i/q_{tot})\delta Q$
with $q_{tot} = \sum_i q_i$. For values of $\delta Q > 0.5$
(printed by the code in the file pcm/pcm_info.out) even, if polarization charges are renormalized,
the calculated results might be inaccurate or erroneous.
Name PCMRadiusScaling
Section Hamiltonian::PCM
Type float
Scales the radii of the spheres used to build the solute cavity surface.
The default value depends on the choice of PCMVdWRadii:
1.2 for pcm_vdw_optimized and 1.0 for pcm_vdw_species.
Name PCMRenormCharges
Section Hamiltonian::PCM
Type logical
Default .false.
If .true. renormalization of the polarization charges is performed to enforce fulfillment
of the Gauss law, $\sum_i q_i^{e/n} = -[(\epsilon-1)/\epsilon] Q_M^{e/n}$ where
$q_i^{e/n}$ are the polarization charges induced by the electrons/nuclei of the molecule
and $Q_M^{e/n}$ is the nominal electronic/nuclear charge of the system. This can be needed
to treat molecules in weakly polar solvents.
Name PCMSmearingFactor
Section Hamiltonian::PCM
Type float
Default 1.0
Parameter used to control the width (area of each tessera) of the Gaussians used to distribute
the polarization charges on each tessera (arXiv:1507.05471). If set to zero, the solvent
reaction potential in real-space is defined by using point charges.
Name PCMSolute
Section Hamiltonian::PCM
Type logical
Default yes
This variable is a flag for including polarization effects of the solvent due to the solute.
(Useful for analysis) When external fields are applied, turning off the solvent-molecule interaction (PCMSolute=no) and
activating the solvent polarization due to the applied field (PCMLocalField=yes) allows to include only local field effects.
Name PCMSpheresOnH
Section Hamiltonian::PCM
Type logical
Default no
If true, spheres centered at the Hydrogens atoms are included to build the solute cavity surface.
Name PCMStaticEpsilon
Section Hamiltonian::PCM
Type float
Default 1.0
Static dielectric constant of the solvent ($\varepsilon_0$). 1.0 indicates gas phase.
Name PCMTDLevel
Section Hamiltonian::PCM
Type integer
Default eq
When CalculationMode=td, PCMTDLevel it sets the way the time-depenendent solvent polarization is propagated.
Options:
- eq:
If PCMTDLevel=eq, the solvent is always in equilibrium with the solute or the external field, i.e.,
the solvent polarization follows instantaneously the changes in solute density or in the external field.
PCMTDLevel=neq and PCMTDLevel=eom are both nonequilibrium runs.
- neq:
If PCMTDLevel=neq, solvent polarization charges are splitted in two terms:
one that follows instantaneously the changes in the solute density or in the external field (dynamical polarization charges),
and another that lag behind in the evolution w.r.t. the solute density or the external field (inertial polarization charges).
- eom:
If PCMTDLevel=eom, solvent polarization charges evolves following an equation of motion, generalizing 'neq' propagation.
The equation of motion used here depends on the value of PCMEpsilonModel.
Name PCMTessMinDistance
Section Hamiltonian::PCM
Type float
Default 0.1
Minimum distance between tesserae.
Any two tesserae having smaller distance in the starting tesselation will be merged together.
Name PCMTessSubdivider
Section Hamiltonian::PCM
Type integer
Default 1
Allows to subdivide further each tessera refining the discretization of the cavity tesselation.
Can take only two values, 1 or 4. 1 corresponds to 60 tesserae per sphere, while 4 corresponds to 240 tesserae per sphere.
Name PCMUpdateIter
Section Hamiltonian::PCM
Type integer
Default 1
Defines how often the PCM potential is updated during time propagation.
Name PCMVdWRadii
Section Hamiltonian::PCM
Type integer
Default pcm_vdw_optimized
This variable selects which van der Waals radius will be used to generate the solvent cavity.
Options:
- pcm_vdw_optimized:
Use the van der Waals radius optimized by Stefan Grimme in J. Comput. Chem. 27: 1787-1799, 2006,
except for C, N and O, reported in J. Chem. Phys. 120, 3893 (2004).
- pcm_vdw_species:
The vdW radii are set from the share/pseudopotentials/elements file. These values are obtained from
Alvarez S., Dalton Trans., 2013, 42, 8617-8636. Values can be changed in the Species block.
Name PDBCoordinates
Section System::Coordinates
Type string
If this variable is present, the program tries to read the atomic coordinates
from the file specified by its value. The PDB (Protein Data Bank)
format is quite complicated, and it goes
well beyond the scope of this manual. You can find a comprehensive
description here.
From the plethora of instructions defined in the PDB standard, Octopus
only reads two, ATOM and HETATOM. From these fields, it reads:
- columns 13-16: The species; in fact Octopus only cares about the first letter - CA and CB will both refer to carbon - so elements whose chemical symbol has more than one letter cannot be represented in this way. So, if you want to run mercury (Hg), please use one of the other methods to input the coordinates.
- columns 18-21: The residue. Ignored.
- columns 31-54: The Cartesian coordinates. The Fortran format is (3f8.3).
- columns 61-65: Classical charge of the atom. Required if reading classical atoms, ignored otherwise. The Fortran format is (f6.2).
Name PDBGOConstrains
Section Calculation Modes::Geometry Optimization
Type string
Like XYZGOConstrains but in PDB format, as in PDBCoordinates.
Name PDBVelocities
Section System::Velocities
Type string
Like XYZVelocities but in PDB format, as in PDBCoordinates.
Name PeriodicBoundaryMask
Section Mesh
Type block
(Experimental) Defines a mask for which periodic boundaries are replaced by zero boundary conditions.
Name PeriodicDimensions
Section System
Type integer
Default 0
Define how many directions are to be considered periodic. It has to be a number
between zero and Dimensions.
Options:
- 0:
No direction is periodic (molecule).
- 1:
The x direction is periodic.
- 2:
The x and y directions are periodic.
- 3:
The x, y, and z directions are periodic.
Name PES_Flux_AnisotropyCorrection
Section Time-Dependent::PhotoElectronSpectrum
Type logical
Apply anisotropy correction.
Name PES_Flux_ARPES_grid
Section Time-Dependent::PhotoElectronSpectrum
Type logical
Use a curvilinear momentum space grid that compensates the transformation
used to obtain ARPES. With this choice ARPES data is laid out on a Cartesian
regular grid.
By default true when PES_Flux_Shape = pln and a KPointsPath
is specified.
Name PES_Flux_DeltaK
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default 0.02
Spacing of the the photoelectron momentum grid.
Name PES_Flux_EnergyGrid
Section Time-Dependent::PhotoElectronSpectrum
Type block
The block PES_Flux_EnergyGrid specifies the energy grid
in momentum space.
%PES_Flux_EnergyGrid
Emin | Emax | DeltaE
%
Name PES_Flux_Face_Dens
Section Time-Dependent::PhotoElectronSpectrum
Type block
Define the number of points density per unit of area (in au) on the
face of the ‘cub’ surface.
Name PES_Flux_GridTransformMatrix
Section Time-Dependent::PhotoElectronSpectrum
Type block
Define an optional transformation matrix for the momentum grid.
%PES_Flux_GridTransformMatrix
M_11 | M_12 | M_13
M_21 | M_22 | M_23
M_31 | M_32 | M_33
%
Name PES_Flux_Kmax
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default 1.0
The maximum value of the photoelectron momentum.
For cartesian momentum grids one can specify a value different
for cartesian direction using a block input.
Name PES_Flux_Kmin
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default 0.0
The minimum value of the photoelectron momentum.
For cartesian momentum grids one can specify a value different
for cartesian direction using a block input.
Name PES_Flux_Lmax
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default 80
Maximum order of the spherical harmonic to be integrated on an equidistant spherical
grid (to be changed to Gauss-Legendre quadrature).
Name PES_Flux_Lsize
Section Time-Dependent::PhotoElectronSpectrum
Type block
For PES_Flux_Shape = cub sets the dimensions along each direction. The syntax is:
%PES_Flux_Lsize
xsize | ysize | zsize
%
where xsize, ysize, and zsize are with respect to the origin. The surface can
be shifted with PES_Flux_Offset.
If PES_Flux_Shape = pln, specifies the position of two planes perpendicular to
the non-periodic dimension symmetrically placed at PES_Flux_Lsize distance from
the origin.
Name PES_Flux_Momenutum_Grid
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Decides how the grid in momentum space is generated.
Options:
- polar:
The grid is in polar coordinates with the zenith axis is along z.
The grid parameters are defined by PES_Flux_Kmax, PES_Flux_DeltaK,
PES_Flux_StepsThetaK, PES_Flux_StepsPhiK.
This is the default choice for PES_Flux_Shape = sph or cub.
- cartesian:
The grid is in cartesian coordinates with parameters defined by
PES_Flux_ARPES_grid, PES_Flux_EnergyGrid.
This is the default choice for PES_Flux_Shape = sph or cub.
Name PES_Flux_Offset
Section Time-Dependent::PhotoElectronSpectrum
Type block
Shifts the surface for PES_Flux_Shape = cub. The syntax is:
%PES_Flux_Offset
xshift | yshift | zshift
%
Name PES_Flux_Parallelization
Section Time-Dependent::PhotoElectronSpectrum
Type flag
The parallelization strategy to be used to calculate the PES spectrum
using the resources available in the domain parallelization pool.
This option is not available without domain parallelization.
Parallelization over k-points and states is always enabled when available.
Options:
- pf_none:
No parallelization.
- pf_time:
Parallelize time integration. This requires to store some quantities over a
number of time steps equal to the number of cores available.
- pf_momentum:
Parallelize over the final momentum grid. This strategy has a much lower
memory footprint than the one above (time) but seems to provide a smaller
speedup.
- pf_surface:
Parallelize over surface points.
Option pf_time and pf_surface can be combined: pf_time + pf_surface.
Name PES_Flux_PhiK
Section Time-Dependent::PhotoElectronSpectrum
Type block
Define the grid points on theta ($0 \le \theta \le 2\pi$) when
using a spherical grid in momentum.
The block defines the maximum and minimum values of theta and the number of
of points for the discretization.
%PES_Flux_PhiK
theta_min | theta_max | npoints
%
By default theta_min=0, theta_max = pi, npoints = 90.
Name PES_Flux_Radius
Section Time-Dependent::PhotoElectronSpectrum
Type float
The radius of the sphere, if PES_Flux_Shape == sph.
Name PES_Flux_RuntimeOutput
Section Time-Dependent::PhotoElectronSpectrum
Type logical
Write output in ascii format at runtime.
Name PES_Flux_Shape
Section Time-Dependent::PhotoElectronSpectrum
Type integer
The shape of the surface.
Options:
- cub:
Uses a parallelepiped as surface. All surface points are grid points.
Choose the location of the surface with variable PES_Flux_Lsize
(default for 1D and 2D).
- sph:
Constructs a sphere with radius PES_Flux_Radius. Points on the sphere
are interpolated by trilinear interpolation (default for 3D).
- pln:
This option is for periodic systems.
Constructs a plane perpendicular to the non-periodic dimension
at PES_Flux_Lsize.
Name PES_Flux_StepsPhiK
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default 90
Number of steps in $\phi$ ($0 \le \phi \le 2 \pi$) for the spherical grid in k.
Name PES_Flux_StepsPhiR
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default 2 PES_Flux_Lmax + 1
Number of steps in $\phi$ ($0 \le \phi \le 2 \pi$) for the spherical surface.
Name PES_Flux_StepsThetaK
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default 45
Number of steps in $\theta$ ($0 \le \theta \le \pi$) for the spherical grid in k.
Name PES_Flux_StepsThetaR
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default 2 PES_Flux_Lmax + 1
Number of steps in $\theta$ ($0 \le \theta \le \pi$) for the spherical surface.
Name PES_Flux_ThetaK
Section Time-Dependent::PhotoElectronSpectrum
Type block
Define the grid points on theta ($0 \le \theta \le \pi$) when
using a spherical grid in momentum.
The block defines the maximum and minimum values of theta and the number of
of points for the discretization.
%PES_Flux_ThetaK
theta_min | theta_max | npoints
%
By default theta_min=0, theta_max = pi, npoints = 45.
Name PES_Flux_UseSymmetries
Section Time-Dependent::PhotoElectronSpectrum
Type logical
Use surface and momentum grid symmetries to speed up calculation and
lower memory footprint.
By default available only when the surface shape matches the grid symmetry i.e.:
PES_Flux_Shape = m_cub or m_pln and PES_Flux_Momenutum_Grid = m_cartesian
or
PES_Flux_Shape = m_sph and PES_Flux_Momenutum_Grid = m_polar
Name PES_spm_DeltaOmega
Section Time-Dependent::PhotoElectronSpectrum
Type float
The spacing in frequency domain for the photoelectron spectrum (if PES_spm_OmegaMax > 0).
The default is PES_spm_OmegaMax/500.
Name PES_spm_OmegaMax
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default 0.0
If PES_spm_OmegaMax > 0, the photoelectron spectrum is directly calculated during
time-propagation, evaluated by the PES_spm method. PES_spm_OmegaMax is then the maximum frequency
(approximate kinetic energy) and PES_spm_DeltaOmega the spacing in frequency domain of the spectrum.
Name PES_spm_points
Section Time-Dependent::PhotoElectronSpectrum
Type block
List of points at which to calculate the photoelectron spectrum by the sample point
method. If no points are given, a spherical grid is generated automatically.
The exact syntax is:
%PES_spm_points
x1 | y1 | z1
%
Name PES_spm_Radius
Section Time-Dependent::PhotoElectronSpectrum
Type float
The radius of the sphere for the spherical grid (if no PES_spm_points
are given).
Name PES_spm_recipe
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default phase
The type for calculating the photoelectron spectrum in the sample point method.
Options:
- raw:
Calculate the photoelectron spectrum according to A. Pohl, P.-G. Reinhard, and
E. Suraud, Phys. Rev. Lett. 84, 5090 (2000).
- phase:
Calculate the photoelectron spectrum by including the Volkov phase (approximately), see
P. M. Dinh, P. Romaniello, P.-G. Reinhard, and E. Suraud, Phys. Rev. A. 87, 032514 (2013).
Name PES_spm_StepsPhiR
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default 90
Number of steps in $\phi$ ($0 \le \phi \le 2 \pi$) for the spherical grid (if no
PES_spm_points are given).
Name PES_spm_StepsThetaR
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default 45
Number of steps in $\theta$ ($0 \le \theta \le \pi$) for the spherical grid (if no
PES_spm_points are given).
Name PESMask2PEnlargeFactor
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default 1.0
Mask two points enlargement factor. Enlarges the mask box by adding two
points at the edges of the box in each direction (x,y,z) at a distance
L=Lb*PESMask2PEnlargeFactor where Lb is the box size.
This allows to run simulations with an additional void space at a price of
adding few points. The Fourier space associated with the new box is restricted
by the same factor.
Note: needs PESMaskPlaneWaveProjection = nfft_map or pnfft_map .
Name PESMaskEnlargeFactor
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default 1
Mask box enlargement level. Enlarges the mask bounding box by a PESMaskEnlargeFactor.
This helps to avoid wavefunction wrapping at the boundaries.
Name PESMaskFilterCutOff
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default -1
In calculation with PESMaskMode = fullmask_mode and NFFT, spurious frequencies
may lead to numerical instability of the algorithm. This option gives the possibility
to filter out the unwanted components by setting an energy cut-off.
If PESMaskFilterCutOff = -1 no filter is applied.
Name PESMaskIncludePsiA
Section Time-Dependent::PhotoElectronSpectrum
Type logical
Default false
Add the contribution of $\Psi_A$ in the mask region to the photo-electron spectrum.
Literally adds the Fourier components of:
$\Theta(r-R1) \Psi_A(r)$
with $\Theta$ being the Heaviside step function.
With this option PES will contain all the contributions starting from the inner
radius $R1$. Use this option to improve convergence with respect to the box size
and total simulation time.
Note: Carefully choose $R1$ in order to avoid contributions from returning electrons.
Name PESMaskMode
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default mask_mode
PES calculation mode.
Options:
- mask_mode:
Mask method.
- fullmask_mode:
Full mask method. This includes a back action of the momentum-space states on the
interaction region. This enables electrons to come back from the continuum.
- passive_mode:
Passive analysis of the wf. Simply analyze the plane-wave components of the
wavefunctions on the region r > R1. This mode employs a step masking function by default.
Name PESMaskPlaneWaveProjection
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default fft_map
With the mask method, wavefunctions in the continuum are treated as plane waves.
This variable sets how to calculate the plane-wave projection in the buffer
region. We perform discrete Fourier transforms (DFT) in order to approximate
a continuous Fourier transform. The major drawback of this approach is the built-in
periodic boundary condition of DFT. Choosing an appropriate plane-wave projection
for a given simulation in addition to PESMaskEnlargeFactor and
PESMask2PEnlargeFactorwill help to converge the results.
NOTE: depending on the value of PESMaskMode PESMaskPlaneWaveProjection,
may affect not only performance but also the time evolution of the density.
Options:
- fft_out:
FFT filtered in order to keep only outgoing waves. 1D only.
- fft_map:
FFT transform.
- nfft_map:
Non-equispaced FFT map.
- pfft_map:
Use PFFT library.
- pnfft_map:
Use PNFFT library.
Name PESMaskShape
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default m_sin2
The mask function shape.
Options:
- m_sin2:
sin2 mask.
- m_step:
- m_erf:
Name PESMaskSize
Section Time-Dependent::PhotoElectronSpectrum
Type block
Set the size of the mask function.
Here you can set the inner (R1) and outer (R2) radius by setting
the block as follows:
%PESMaskSize
R1 | R2 | "user-defined"
%
The optional 3rd column is a user-defined expression for the mask
function. For example, r creates a spherical mask (which is the
default for BoxShape = sphere). Note, values R2 larger than
the box size may lead in this case to unexpected reflection
behaviours.
Name PESMaskSpectEnergyMax
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default maxval(mask%Lk)
The maximum energy for the PES spectrum.
Name PESMaskSpectEnergyStep
Section Time-Dependent::PhotoElectronSpectrum
Type float
The PES spectrum energy step.
Name PESMaskStartTime
Section Time-Dependent::PhotoElectronSpectrum
Type float
Default -1.0
The time photoelectrons start to be recorded. In pump-probe simulations, this allows
getting rid of an unwanted ionization signal coming from the pump.
NOTE: This will enforce the mask boundary conditions for all times.
Name PhotoDopingBand
Section States
Type integer
Default 1
This variable specifies where the minium (starting) conduction band index for the photodoping electrons.
Name PhotoDopingNumElectrons
Section States
Type float
Default 0
This variable allows to set the number of valence electrons taken out to put
into the conduction bands. The method follows Marini and Calandra, PRB 104, 144103 (2021).
Name PhotoDopingSmearing
Section States
Type float
Default 0.1 eV
If Occupations is not set, PhotoDopingSmearing is the
smearing width used in the SmearingFunction to distribute the electrons in conduction bands
among the existing states.
Name PhotoElectronSpectrum
Section Time-Dependent::PhotoElectronSpectrum
Type integer
Default none
This variable controls the method used for the calculation of
the photoelectron spectrum. You can specify more than one value
by giving them as a sum, for example:
PhotoElectronSpectrum = pes_spm + pes_mask
Options:
- none:
The photoelectron spectrum is not calculated. This is the default.
- pes_spm:
Store the wavefunctions at specific points in order to
calculate the photoelectron spectrum at a point far in the box as proposed in
A. Pohl, P.-G. Reinhard, and E. Suraud, Phys. Rev. Lett. 84, 5090 (2000).
- pes_mask:
Calculate the photo-electron spectrum using the mask method.
U. De Giovannini, D. Varsano, M. A. L. Marques, H. Appel, E. K. U. Gross, and A. Rubio,
Phys. Rev. A 85, 062515 (2012).
- pes_flux:
Calculate the photo-electron spectrum using the t-surff technique, i.e.,
spectra are computed from the electron flux through a surface close to the absorbing
boundaries of the box. (Experimental.)
L. Tao and A. Scrinzi, New Journal of Physics 14, 013021 (2012).
Name PhotoelectronSpectrumOutput
Section Utilities::oct-photoelectron_spectrum
Type block
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).
Each option must be in a separate row. Optionally individual output formats can be defined
for each row or they can be read separately from OutputFormat variable
in the input file.
Example (minimal):
%PhotoelectronSpectrumOutput
energy_tot
velocity_map
%
Example (with OutputFormat):
%PhotoelectronSpectrumOutput
arpes | vtk
velocity_map | ncdf
%
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, ncdf or ascii.
- arpes:
Full ARPES for semi-periodic systems (vtk).
- arpes_cut:
ARPES cut on a plane following a zero-weight path in reciprocal space.
Name 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
%
Name PhotonEta
Section Linear Response::Sternheimer
Type float
Default 0.0000367
This variable provides the value for the broadening of the photonic spectra
when the coupling of electrons to photons is enabled in the frequency-dependent Sternheimer equation
Name PhotonModes
Section Hamiltonian::XC
Type block
Each line of the block should specify one photon mode. The syntax is the following:
%PhotonModes omega1 | lambda1| PolX1 | PolY1 | PolZ1 … %
The first column is the mode frequency, in units of energy.
The second column is the coupling strength, in units of energy.
The remaining columns specify the polarization direction of the mode.
If the polarization vector should be normalized to one. If that is not the case
the code will normalize it.
Name PhotonmodesFilename
Section Linear Response::Casida
Type string
Default “photonmodes”
Filename for photon modes in text format
- first line contains 2 integers: number of photon modes and number of columns
- each further line contains the given number of floats for one photon
mode
Name PhotonXCEnergyMethod
Section Hamiltonian::XC
Type integer
Default 1
There are different ways to calculate the energy,
Options:
- virial:
(modified) virial approach
$
(E_{\rm{px}}^{\rm{virial}} = \frac{1}{2}\int d\mathbf{r}\ \mathbf{r}\cdot[
-\rho(\mathbf{r})\nabla v_{\rm{px}}(\mathbf{r})])
$
- expectation_value:
expectation value w.tr.t. the wave functions (valid only for 1 electron)
$
E_{\rm{px}}[\rho] = -\sum_{\alpha=1}^{M_{p}}\frac{\tilde{\lambda}_{\alpha}^{2}}{2\tilde{\omega}_{\alpha}^{2}}
\langle (\tilde{\mathbf{{\varepsilon}}}_{\alpha}\cdot\hat{\mathbf{J}}_{\rm{p}})\Phi[\rho]
| (\tilde{\mathbf{{\varepsilon}}}_{\alpha}\cdot\hat{\mathbf{J}}_{\rm{p}})\Phi[\rho] \rangle
$
This option only works for the wave function based electron-photon functionals
- LDA:
energy from electron density
$
E_{\rm pxLDA}[\rho] = \frac{-2\pi^{2}}{(d+2)({2V_{d}})^{\frac{2}{d}}}
\sum_{\alpha=1}^{M_{p}}\frac{\tilde{\lambda}_{\alpha}^{2}}{\tilde{\omega}_{\alpha}^{2}}
\int d\mathbf{r}\ \rho^{\frac{2+d}{d}}(\mathbf{r})
$
This option only works with LDA electron-photon functionals.
Name PhotonXCEtaC
Section Hamiltonian::XC
Type float
Default 1.0
The scaling factor for the px potential to reduce the weak coupling perturbation regime
Name PhotonXCLambShift
Section Hamiltonian::XC
Type logical
Default .false.
to deal with the photon free exchange potential for continuum mode in free space
Name PhotonXCLambShiftOmegaCutoff
Section Hamiltonian::XC
Type float
Default 0.0
the cutoff frequency (Ha) for Lamb shift
Name PhotonXCLambShiftRenormalizeMass
Section Hamiltonian::XC
Type logical
Default .false.
to deal with the photon free exchange potential for continuum mode in free space
Name PhotonXCLDAKappa
Section Hamiltonian::XC
Type float
Default 1.0
the scaling factor for px-LDA potential
Name PNFFTCutoff
Section Mesh::FFTs
Type integer
Default 6
Cut-off parameter of the window function.
Name PNFFTOversampling
Section Mesh::FFTs
Type float
Default 2.0
PNFFT oversampling factor (sigma). This will rule the size of the FFT under the hood.
Name Poisson1DSoftCoulombParam
Section Hamiltonian::Poisson
Type float
Default 1.0 bohr
When Dimensions = 1, to prevent divergence, the Coulomb interaction treated by the Poisson
solver is not $1/r$ but $1/\sqrt{a^2 + r^2}$, where this variable sets the value of $a$.
Name PoissonCutoffRadius
Section Hamiltonian::Poisson
Type float
When PoissonSolver = fft and PoissonFFTKernel is neither multipole_corrections
nor fft_nocut,
this variable controls the distance after which the electron-electron interaction goes to zero.
A warning will be written if the value is too large and will cause spurious interactions between images.
The default is half of the FFT box max dimension in a finite direction.
Name PoissonFFTKernel
Section Hamiltonian::Poisson
Type integer
Defines which kernel is used to impose the correct boundary
conditions when using FFTs to solve the Poisson equation. The
default is selected depending on the dimensionality and
periodicity of the system:
In 1D, spherical if finite, fft_nocut if periodic.
In 2D, spherical if finite, cylindrical if 1D-periodic, fft_nocut if 2D-periodic.
In 3D, spherical if finite, cylindrical if 1D-periodic, planar if 2D-periodic,
fft_nocut if 3D-periodic.
See C. A. Rozzi et al., Phys. Rev. B 73, 205119 (2006) for 3D implementation and
A. Castro et al., Phys. Rev. B 80, 033102 (2009) for 2D implementation.
Options:
- spherical:
FFTs using spherical cutoff (in 2D or 3D).
- cylindrical:
FFTs using cylindrical cutoff (in 2D or 3D).
- planar:
FFTs using planar cutoff (in 3D).
- fft_nocut:
FFTs without using a cutoff (for fully periodic systems).
- multipole_correction:
The boundary conditions are imposed by using a multipole expansion. Only appropriate for finite systems.
Further specification occurs with variables PoissonSolverBoundaries and PoissonSolverMaxMultipole.
Name PoissonMultigridCycle
Section Hamiltonian::Poisson::Multigrid
Type integer
The flavor of multigrid cycle
Options:
- v_shape:
V-shape cycle
- w_shape:
W-shape cycle
- fmg:
Full multigrid solver
Name PoissonSolver
Section Hamiltonian::Poisson
Type integer
Defines which method to use to solve the Poisson equation. Some incompatibilities apply depending on
dimensionality, periodicity, etc.
For a comparison of the accuracy and performance of the methods in Octopus, see P Garcia-Risueño,
J Alberdi-Rodriguez et al., J. Comp. Chem. 35, 427-444 (2014)
or arXiV.
Defaults:
1D and 2D: fft.
3D: cg_corrected if curvilinear, isf if not periodic, fft if periodic.
Dressed orbitals: direct_sum.
Options:
- NoPoisson:
Do not use a Poisson solver at all.
- direct_sum:
Direct evaluation of the Hartree potential (only for finite systems).
- fft:
The Poisson equation is solved using FFTs. A cutoff technique
for the Poisson kernel is selected so the proper boundary
conditions are imposed according to the periodicity of the
system. This can be overridden by the PoissonFFTKernel
variable. To choose the FFT library use FFTLibrary
- cg:
Conjugate gradients (only for finite systems).
- cg_corrected:
Conjugate gradients, corrected for boundary conditions (only for finite systems).
- multigrid:
Multigrid method (only for finite systems).
- isf:
Interpolating Scaling Functions Poisson solver (only for finite systems).
- psolver:
Solver based on Interpolating Scaling Functions as implemented in the PSolver library.
Parallelization in k-points requires PoissonSolverPSolverParallelData = no.
Requires the PSolver external library.
Name PoissonSolverBoundaries
Section Hamiltonian::Poisson
Type integer
Default multipole
For finite systems, some Poisson solvers (multigrid,
cg_corrected, and fft with PoissonFFTKernel = multipole_correction)
require the calculation of the
boundary conditions with an auxiliary method. This variable selects that method.
Options:
- multipole:
A multipole expansion of the density is used to approximate the potential on the boundaries.
- exact:
An exact integration of the Poisson equation is done over the boundaries. This option is
experimental, and not implemented for domain parallelization.
Name PoissonSolverMaxIter
Section Hamiltonian::Poisson
Type integer
Default 500
The maximum number of iterations for conjugate-gradient
Poisson solvers.
Name PoissonSolverMaxMultipole
Section Hamiltonian::Poisson
Type integer
Order of the multipolar expansion for boundary corrections.
The Poisson solvers multigrid, cg, and cg_corrected (and fft with PoissonFFTKernel = multipole_correction) do a multipolar expansion of the given charge density, such that $\rho = \rho_{multip.expansion}+\Delta \rho$. The Hartree potential due to the $\rho_{multip.expansion}$ is calculated analytically, while the Hartree potential due to $\Delta \rho$ is calculated with either a multigrid or cg solver. The order of the multipolar expansion is set by this variable.
Default is 4 for PoissonSolver = cg_corrected and multigrid, and 2
for fft with PoissonFFTKernel = multipole_correction.
Name PoissonSolverNodes
Section Hamiltonian::Poisson
Type integer
Default 0
How many nodes to use to solve the Poisson equation. A value of
0, the default, implies that all available nodes are used.
Name PoissonSolverPSolverParallelData
Section Hamiltonian::Poisson::PSolver
Type logical
Default yes
Indicates whether data is partitioned within the PSolver library.
If data is distributed among processes, Octopus uses parallel data-structures
and, thus, less memory.
If "yes", data is parallelized. The z-axis of the input vector
is split among the MPI processes.
If "no", entire input and output vector is saved in all the MPI processes.
If k-points parallelization is used, "no" must be selected.
Name PoissonSolverThreshold
Section Hamiltonian::Poisson
Type float
Default 1e-6
The tolerance for the Poisson solution, used by the cg,
cg_corrected, and multigrid solvers.
Name PoissonTestPeriodicThreshold
Section Hamiltonian::Poisson
Type float
Default 1e-5
This threshold determines the accuracy of the periodic copies of
the Gaussian charge distribution that are taken into account when
computing the analytical solution for periodic systems.
Be aware that the default leads to good results for systems
that are periodic in 1D - for 3D it is very costly because of the
large number of copies needed.
Name Preconditioner
Section SCF::Eigensolver
Type integer
Which preconditioner to use in order to solve the Kohn-Sham
equations or the linear-response equations. The default is
pre_filter, except for curvilinear coordinates, where no
preconditioner is applied by default.
Options:
- no:
Do not apply preconditioner.
- pre_filter:
Filter preconditioner.
- pre_jacobi:
Jacobi preconditioner. Only the local part of the pseudopotential is used.
Not very helpful.
- pre_poisson:
Uses the full Laplacian as preconditioner. The inverse is calculated through
the solution of the Poisson equation. This is, of course, very slow.
- pre_multigrid:
Multigrid preconditioner.
Name PreconditionerFilterFactor
Section SCF::Eigensolver
Type float
This variable controls how much filter preconditioner is
applied. A value of 1.0 means no preconditioning, 0.5 is the
standard.
The default is 0.5, except for periodic systems where the default is 0.6.
If you observe that the first eigenvectors are not converging properly, especially for periodic systems, you should increment this value.
The allowed range for this parameter is between 0.5 and 1.0.
For other values, the SCF may converge to wrong results.
Name PreconditionerIterationsMiddle
Section SCF::Eigensolver
Type integer
This variable is the number of smoothing iterations on the coarsest grid for the multigrid
preconditioner. The default is 1.
Name PreconditionerIterationsPost
Section SCF::Eigensolver
Type integer
This variable is the number of post-smoothing iterations for the multigrid
preconditioner. The default is 2.
Name PreconditionerIterationsPre
Section SCF::Eigensolver
Type integer
This variable is the number of pre-smoothing iterations for the multigrid
preconditioner. The default is 1.
Name Preorthogonalization
Section Linear Response::Sternheimer
Type logical
Whether initial linear-response wavefunctions should be orthogonalized
or not against the occupied states, at the start of each SCF cycle.
Default is true only if SmearingFunction = semiconducting,
or if the Occupations block specifies all full or empty states,
and we are not solving for linear response in the occupied subspace too.
Name ProfilingAllNodes
Section Execution::Optimization
Type logical
Default no
This variable controls whether all nodes print the time
profiling output. If set to no, the default, only the root node
will write the profile. If set to yes, all nodes will print it.
Name ProfilingMode
Section Execution::Optimization
Type integer
Default no
Use this variable to run Octopus in profiling mode. In this mode
Octopus records the time spent in certain areas of the code and
the number of times this code is executed. These numbers
are written in ./profiling.NNN/profiling.nnn with nnn being the
node number (000 in serial) and NNN the number of processors.
This is mainly for development purposes. Note, however, that
Octopus should be compiled with –disable-debug to do proper
profiling. Warning: you may encounter strange results with OpenMP.
Options:
- no:
No profiling information is generated.
- prof_time:
Profile the time spent in defined profiling regions.
- prof_memory:
As well as the time, summary information on memory usage and the largest arrays are reported.
- prof_memory_full:
As well as the time and summary memory information, a
log is reported of every allocation and deallocation.
- likwid:
Enable instrumentation using LIKWID.
- prof_io:
Count the number of file open and close.
Name ProfilingOutputTree
Section Execution::Optimization
Type logical
Default yes
This variable controls whether the profiling output is additionally
written as a tree.
Name ProfilingOutputYAML
Section Execution::Optimization
Type logical
Default no
This variable controls whether the profiling output is additionally
written to a YAML file.
Name PropagateSpatialMaxwellField
Section Maxwell::TD Propagation
Type logical
Default yes
Allow for numerical propagation of Maxwells equations of spatially constant field.
If set to no, do only analytic evaluation of the field inside the box.
Name 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.
Name 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.
Name 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.
Name 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.
Name PropagationSpectrumMaxEnergy
Section Utilities::oct-propagation_spectrum
Type float
Default 20 eV
The Fourier transform is calculated for energies smaller than this value.
Name PropagationSpectrumMinEnergy
Section Utilities::oct-propagation_spectrum
Type float
Default 0
The Fourier transform is calculated for energies larger than this value.
Name 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.
Name 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.
Name 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.
Name PropagationSpectrumTransform
Section Utilities::oct-propagation_spectrum
Type integer
Default sine
Decides which transform to perform, if SpectrumMethod = fourier.
Options:
- 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.
- 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.
Name 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.
Name PseudopotentialSet
Section System::Species
Type integer
Default standard
Selects the set of pseudopotentials used by default for species
not defined in the Species block.
These sets of pseudopotentials come from different sources. Octopus developers have not validated them. We include them with the code for convenience of the users, but you are expected to check the quality and suitability of the pseudopotential for your application.
Options:
- none:
Do not load any pseudopotential by default. All species must be
specified in the Species block.
- standard:
The standard set of Octopus that provides LDA pseudopotentials
in the PSF format for some elements: H, Li, C, N, O, Na, Si, S, Ti, Se, Cd.
- sg15:
The set of Optimized Norm-Conserving Vanderbilt
PBE pseudopotentials. Ref: M. Schlipf and F. Gygi, Comp. Phys. Commun. 196, 36 (2015).
This set provides pseudopotentials for elements up to Z = 83
(Bi), excluding Lanthanides.
Current version of the set is 1.2.
- hgh_lda:
The set of Hartwigsen-Goedecker-Hutter LDA pseudopotentials for elements from H to Rn.
Ref: C. Hartwigsen, S. Goedecker, and J. Hutter, Phys. Rev. B 58, 3641 (1998).
- hgh_lda_sc:
The semicore set of Hartwigsen-Goedecker-Hutter LDA pseudopotentials.
Ref: C. Hartwigsen, S. Goedecker, and J. Hutter, Phys. Rev. B 58, 3641 (1998).
- hscv_lda:
The set of Hamann-Schlueter-Chiang-Vanderbilt (HSCV) potentials
for LDA exchange and correlation downloaded from http://fpmd.ucdavis.edu/potentials/index.htm.
These pseudopotentials were originally intended for the QBox
code. They were generated using the method of Hamann, Schluter
and Chiang. Ref: D. Vanderbilt, Phys. Rev. B 32, 8412 (1985).
Warning from the original site: The potentials provided in this
site are distributed without warranty. In most cases,
potentials were not tested. Potentials should be thoroughly
tested before being used in simulations.
- hscv_pbe:
PBE version of the HSCV pseudopotentials. Check the
documentation of the option hscv_lda for details and warnings.
- pseudodojo_pbe:
PBE version of the pseudopotentials of http://pseudo-dojo.org. Version 0.4.
- pseudodojo_lda:
LDA pseudopotentials of http://pseudo-dojo.org. Version 0.4.
- pseudodojo_pbesol:
PBEsol version of the pseudopotentials of http://pseudo-dojo.org. Version 0.3.