Output

Name BandStructureComputeProjections
Section Output
Type logical
Default false

Determines if projections of wavefunctions on the atomic orbitals are computed or not for obtaining the orbital resolved band-structure.

Name CurrentThroughPlane
Section Output
Type block

The code can calculate current traversing a user-defined portion of a plane, as specified by this block. A small plain-text file current-flow will be written containing this information. Only available for 1D, 2D, or 3D. In the format below, origin is a point in the plane. u and v are the (dimensionless) vectors defining the plane; they will be normalized. spacing is the fineness of the mesh on the plane. Integers nu and mu are the length and width of the portion of the plane, in units of spacing. Thus, the grid points included in the plane are x_ij = origin + ispacingu + jspacingv, for nu <= i <= mu and nv <= j <= mv. Analogously, in the 2D case, the current flow is calculated through a line; in the 1D case, the current flow is calculated through a point. Note that the spacing can differ from the one used in the main calculation; an interpolation will be performed.

Example (3D):

%CurrentThroughPlane
   0.0 | 0.0 | 0.0 # origin
   0.0 | 1.0 | 0.0 # u
   0.0 | 0.0 | 1.0 # v
   0.2 # spacing
   0 | 50 # nu | mu
   -50 | 50 # nv | mv
%

Example (2D):

%CurrentThroughPlane
   0.0 | 0.0 # origin
   1.0 | 0.0 # u
   0.2 # spacing
   0 | 50 # nu | mu
%

Example (1D):

%CurrentThroughPlane
   0.0 # origin
%

Name DOSComputePDOS
Section Output
Type logical
Default false

Determines if projected dos are computed or not. At the moment, the PDOS is computed from the bare pseudo-atomic orbitals, directly taken from the pseudopotentials. The orbitals are not orthonormalized, in order to preserve their atomic orbitals character. As a consequence, the sum of the different PDOS does not integrate to the total DOS.

The radii of the orbitals are controled by the threshold defined by AOThreshold, and the fact that they are normalized or not by AONormalize.

Name DOSEnergyMax
Section Output
Type float

Upper bound for the energy mesh of the DOS. The default is the highest eigenvalue, plus a quarter of the total range of eigenvalues.

Name DOSEnergyMin
Section Output
Type float

Lower bound for the energy mesh of the DOS. The default is the lowest eigenvalue, minus a quarter of the total range of eigenvalues.

Name DOSEnergyPoints
Section Output
Type integer
Default 500

Determines how many energy points Octopus should use for the DOS energy grid.

Name DOSGamma
Section Output
Type float
Default 0.008 Ha

Determines the width of the Lorentzian which is used for the DOS sum.

Name ELFWithCurrentTerm
Section Output
Type logical
Default true

The ELF, when calculated for complex wavefunctions, should contain a term dependent on the current. This term is properly calculated by default; however, for research purposes it may be useful not to add it. If this feature proves to be useless, this option should go away.

Name LinearMediumOutput
Section Output
Type block
Default none

Specifies what to print. The output files are written at the beginning of the run into the output directory for the linear medium. Each option must be in a separate row. Optionally individual output formats can be defined for each row (VTK format is supported) or they can be read separately from OutputFormat in the input file.

Example:

%LinearMediumOutput
  permittivity
  permeability
%
This block supports all the formats of the Output block. See Output.

Options:

• points:
  Outputs 1 if the a given point is inside the medium, and 0 otherwise. This can be used to check the grid points of the medium region.
  
• permittivity:
  Output of the (static) space-dependent relative permittivity
  
• permeability:
  Output of the (static) space-dependent relative permeability
  
• speed_of_light:
  Output of the speed of light in atomic units
  

Name LinearMediumOutputDir
Section Output
Type string
Default “output_iter”

The name of the directory where Octopus stores the information about the linear medium system, as required by the LinearMediumOutput variable.

Name LocalMagneticMomentsSphereRadius
Section Output
Type float

The local magnetic moments are calculated by integrating the magnetization density in spheres centered around each atom. This variable controls the radius of the spheres. The default is half the minimum distance between two atoms in the input coordinates, or 100 a.u. if there is only one atom (for isolated systems).

Name MaxwellOutput
Section Output
Type block
Default none

Specifies what to print. The output files are written at the end of the run into the output directory for the Maxwell run. Time-dependent simulations print only per iteration, including always the last. The frequency of output per iteration is set by OutputInterval and the directory is set by OutputIterDir. Each option must be in a separate row. Optionally individual output formats and output intervals can be defined for each row or they can be read separately from OutputFormat and MaxwellOutputInterval variables in the input file.

Example:

%MaxwellOutput
  electric_field
  magnetic_field
%
This block supports all the formats of the Output block. See Output.

Options:

• electric_field:
  Output of the electric field
  
• magnetic_field:
  Output of the magnetic field
  
• trans_electric_field:
  Output of the transversal electric field
  
• trans_magnetic_field:
  Output of the transversal magnetic field
  
• long_electric_field:
  Output of the longitudinal electric field
  
• long_magnetic_field:
  Output of the longitudinal magnetic field
  
• div_electric_field:
  Output of the divergence of the electric field
  
• div_magnetic_field:
  Output of the divergence of the magnetic field
  
• poynting_vector:
  Output of the Maxwell Poynting vector
  
• maxwell_energy_density:
  Output of the electromagnetic density
  
• external_current:
  Output of the external Maxwell current
  
• charge_density:
  Output of the charge density calculated by the divergence of the electric field.
  
• orbital_angular_momentum:
  Output of the orbital angular momentum
  

Name MaxwellOutputInterval
Section Output
Type integer
Default 50

The output requested by variable MaxwellOutput is written to the directory MaxwellOutputIterDir when the iteration number is a multiple of the MaxwellOutputInterval variable. Subdirectories are named Y.X, where Y is td, scf, or unocc, and X is the iteration number. To use the working directory, specify "." (Output of restart files is instead controlled by MaxwellRestartWriteInterval.) Must be >= 0. If it is 0, then no output is written. This variable can also be defined inside the MaxwellOutput block. See MaxwellOutput.

Name MaxwellOutputIterDir
Section Output
Type string
Default “output_iter”

The name of the directory where Octopus stores information such as the density, forces, etc. requested by variable MaxwellOutput in the format specified by OutputHow. This information is written while iterating CalculationMode = maxwell according to OutputInterval, and has nothing to do with the restart information.

Name MomentumTransfer
Section Output
Type block

Momentum-transfer vector $\vec{q}$ to be used when calculating matrix elements $\left< f \left| e^{i \vec{q} \cdot \vec{r}} \right| i \right>$. This enables the calculation of the dynamical structure factor, which is closely related to generalized oscillator strengths. If the vector is not given, but TPA output is requested (Output = TPA), only the oscillator strengths are written in the output file. For example, to use $\vec{q}$ = (0.1, 0.2, 0.3), set

%MomentumTransfer
   0.1 | 0.2 | 0.3
%

Name Output
Section Output
Type block
Default none

Specifies what to print. Each output must be in a separate row. Optionally individual output formats and output intervals can be defined for each row or they can be read separately from OutputFormat and OutputInterval variables in the input file. The output files are written at the end of the run into the output directory for the relevant kind of run (e.g. static for CalculationMode = gs). Time-dependent simulations print only per iteration, including always the last. The frequency of output per iteration (available for CalculationMode = gs, unocc, td, and opt_control) is set by OutputInterval and the directory is set by OutputIterDir. For linear-response run modes, the derivatives of many quantities can be printed, as listed in the options below. Indices in the filename are labelled as follows: sp = spin (or spinor component), k = k-point, st = state/band. There is no tag for directions, given as a letter. The perturbation direction is always the last direction for linear-response quantities, and a following +/- indicates the sign of the frequency.

Example (minimal):

%Output
  density
  potential
%

Example (with OutputFormat):

%Output
  density | cube + axis_z
  potential | cube
%

Example (with OutputFormat, incomplete):

%Output
  density | cube + axis_z
  potential
%

Example (tagged):

%Output
  density | "output_format" | cube + axis_z | "output_interval" | 50
  potential | "output_format" | cube | "output_interval" | 20
%

Example (tagged, incomplete):

%Output
  density | "output_format" | cube + axis_z
  potential | "output_interval" | 20
%
Missing information for the incomplete blocks will be parsed form the out-of-block definitions. It is also possible to mix the order of columns in the tagged format. See OutputFormat, and OutputInterval.

Options:

• potential:
  Outputs Kohn-Sham potential, separated by parts. File names are v0 for the local part of the ionic potential, vc for the classical potential (if it exists), vh for the Hartree potential, vks for the local part of the Kohn-Sham potential, and vxc- for the exchange-correlation potentials. For vks and vxc, a suffix for spin is added in the spin-polarized case.
  
• density:
  Outputs density. The output file is called density-, or lr_density- in linear response.
  
• wfs:
  Outputs wavefunctions. Which wavefunctions are to be printed is specified by the variable OutputWfsNumber -- see below. The output file is called wf-, or lr_wf- in linear response.
  
• wfs_sqmod:
  Outputs modulus squared of the wavefunctions. The output file is called sqm-wf-. For linear response, the filename is sqm_lr_wf-.
  
• geometry:
  Outputs file containing the coordinates of the atoms treated within quantum mechanics. If OutputFormat = xyz, the file is called geometry.xyz; a file crystal.xyz is written with a supercell geometry if the system is periodic; if point charges were defined in the PDB file (see PDBCoordinates), they will be output in the file geometry_classical.xyz. If OutputFormat = xcrysden, a file called geometry.xsf is written.
  
• current:
  Outputs the total current density. The output file is called current-. For linear response, the filename is lr_current-.
  
• ELF:
  Outputs electron localization function (ELF). The output file is called elf-, or lr_elf- in linear response, in which case the associated function D is also written, as lr_elf_D-. Only in 2D and 3D.
  
• ELF_basins:
  Outputs basins of attraction of the ELF. The output file is called elf_rs_basins.info. Only in 2D and 3D.
  
• Bader:
  Outputs Laplacian of the density which shows lone pairs, bonded charge concentrations and regions subject to electrophilic or nucleophilic attack. See RF Bader, Atoms in Molecules: A Quantum Theory (Oxford Univ. Press, Oxford, 1990).
  
• el_pressure:
  Outputs electronic pressure. See Tao, Vignale, and Tokatly, Phys Rev Lett 100, 206405 (2008).
  
• matrix_elements:
  Outputs a series of matrix elements of the Kohn-Sham states. What is output can be controlled by the OutputMatrixElements variable.
  
• pol_density:
  Outputs dipole-moment density dipole_density-, or polarizability density alpha_density- in linear response. If ResponseMethod = finite_differences, the hyperpolarizability density beta_density- is also printed.
  
• mesh_r:
  Outputs values of the coordinates over the grid. Files will be called mesh_r- followed by the direction.
  
• kinetic_energy_density:
  Outputs kinetic-energy density, defined as:

  $\tau_\sigma(\vec{r}) = \sum_{i=1}^{N_\sigma} \left| \vec{\nabla} \phi_{i\sigma}(\vec{r}) \right|^2,. $

  The index $\sigma$ is the spin index for the spin-polarized case, or if you are using spinors. For spin-unpolarized calculations, you get the total kinetic-energy density. The previous expression assumes full or null occupations. If fractional occupation numbers, each term in the sum is weighted by the occupation. Also, if we are working with an infinite system, all k-points are summed up, with their corresponding weights. The files will be called tau-sp1 and tau-sp2, if the spin-resolved kinetic energy density is produced (runs in spin-polarized and spinors mode), or only tau if the run is in spin-unpolarized mode.
  

• dos:
  Outputs density of states. See DOSEnergyMax, DOSEnergyMin, DOSEnergyPoints, and DOSGamma.
  
• tpa:
  Outputs transition-potential approximation (TPA) matrix elements, using $\vec{q}$-vector specified by MomentumTransfer.
  
• forces:
  Outputs file forces.xsf containing structure and forces on the atoms as a vector associated with each atom, which can be visualized with XCrySDen.
  
• wfs_fourier:
  (Experimental) Outputs wavefunctions in Fourier space. This is only implemented for the ETSF file format output. The file will be called wfs-pw-etsf.nc.
  
• xc_density:
  Outputs the XC density, which is the charge density that generates the XC potential. (This is $-1/4\pi$ times the Laplacian of the XC potential). The files are called nxc.
  
• PES_wfs:
  Outputs the photoelectron wavefunctions. The file name is pes_wfs- plus the orbital number.
  
• PES_density:
  Outputs the photolectron density. Output file is pes_dens- plus spin species if spin-polarized calculation is performed.
  
• PES:
  Outputs the time-dependent photoelectron spectrum.
  
• BerkeleyGW:
  Output for a run with BerkeleyGW. See Output::BerkeleyGW for further specification.
  
• delta_perturbation:
  Outputs the "kick", or time-delta perturbation applied to compute optical response in real time.
  
• external_td_potential:
  Outputs the (scalar) time-dependent potential.
  
• mmb_wfs:
  Triggers the ModelMB wavefunctions to be output for each state.
  
• mmb_den:
  Triggers the ModelMB density matrix to be output for each state, and the particles specified by the DensitytoCalc block. Calculates, and outputs, the reduced density matrix. For the moment the trace is made over the second dimension, and the code is limited to 2D. The idea is to model N particles in 1D as an N-dimensional non-interacting problem, then to trace out N-1 coordinates.
  
• potential_gradient:
  Prints the gradient of the potential.
  
• energy_density:
  Outputs the total energy density to a file called energy_density.
  
• heat_current:
  Outputs the total heat current density. The output file is called heat_current-.
  
• photon_correlator:
  Outputs the electron-photon correlation function. The output file is called photon_correlator.
  
• J_flow:
  todo: document J_flow option!
  
• current_kpt:
  Outputs the current density resolved in momentum space. The output file is called current_kpt-.
  
• density_kpt:
  Outputs the electronic density resolved in momentum space.
  
• occ_matrices:
  Only for DFT+U calculations. Outputs the occupation matrices of LDA+U
  
• effectiveU:
  Only for DFT+U calculations. Outputs the value of the effectiveU for each atoms
  
• magnetization:
  Only for DFT+U calculations. Outputs file containing structure and magnetization of the localized subspace on the atoms as a vector associated with each atom, which can be visualized. For the moment, it only works if a +U is added on one type of orbital per atom.
  
• local_orbitals:
  Only for DFT+U calculations. Outputs the localized orbitals that form the correlated subspace
  
• kanamoriU:
  Only for DFT+U calculations. Outputs the Kanamori interaction parameters U, U`, and J. These parameters are not determined self-consistently, but are taken from the occupation matrices and Coulomb integrals comming from a standard +U calculation.
  
• xc_torque:
  Outputs the exchange-correlation torque. Only for the spinor case and in the 3D case.
  
• eigenval_kpt:
  Outputs the eigenvalues resolved in momentum space, with one file for each band.
  

Name OutputDuringSCF
Section Output
Type logical
Default no

During gs and unocc runs, if this variable is set to yes, output will be written after every OutputInterval iterations.

Name OutputFormat
Section Output
Type flag
Default 0

Describes the format of the output files. This variable can also be defined inside the Output block. See Output. Example: axis_x + plane_x + dx

Options:

• axis_x:
  The values of the function on the x axis are printed. The string .y=0,z=0 is appended to previous file names.
  
• axis_y:
  The values of the function on the y axis are printed. The string .x=0,z=0 is appended to previous file names.
  
• axis_z:
  The values of the function on the z axis are printed. The string .x=0,y=0 is appended to previous file names.
  
• plane_x:
  A plane slice at x = 0 is printed. The string .x=0 is appended to previous file names.
  
• plane_y:
  A plane slice at y = 0 is printed. The string .y=0 is appended to previous file names.
  
• plane_z:
  A plane slice at z = 0 is printed. The string .z=0 is appended to previous file names.
  
• dx:
  For printing three-dimensional information, the open-source program visualization tool OpenDX can be used. The string .dx is appended to previous file names. Available only in 3D.
  
• netcdf:
  Outputs in NetCDF format. This file can then be read, for example, by OpenDX. The string .ncdf is appended to previous file names. Requires the NetCDF library. Only writes the real part of complex functions.
  
• mesh_index:
  Generates output files of a given quantity (density, wavefunctions, ...) which include the internal numbering of mesh points. Since this mode produces large datafiles this is only useful for small meshes and debugging purposes. The output can also be used to display the mesh directly. A Gnuplot script for mesh visualization can be found under PREFIX/share/octopus/util/display_mesh_index.gp.
  
• xcrysden:
  A format for printing structures and three-dimensional information, which can be visualized by the free open-source program XCrySDen and others. The string .xsf is appended to previous file names. Note that lattice vectors and coordinates are as specified by UnitsOutput. Available in 2D and 3D.
  
• matlab:
  In combination with plane_x, plane_y and plane_z, this option produces output files which are suitable for 2D Matlab functions like mesh(), surf(), or waterfall(). To load these files into Matlab you can use, e.g. >> density = load('static/density-1.x=0.matlab.abs'); >> mesh(density);
  
• meshgrid:
  Outputs in Matlab mode the internal mesh in a format similar to >> [x,y] = meshgrid(-2:.2:2,-1:.15:1) The x meshgrid is contained in a file *.meshgrid.x and the y-grid can be found in *.meshgrid.y.
  
• boundary_points:
  This option includes the output of the mesh enlargement. Default is without. Supported only by binary, axis, plane, mesh_index, and matlab formats. Not all types of Output will have this information available. Not supported when parallel in domains.
  
• binary:
  Plain binary, new format.
  
• etsf:
  ETSF file format. Requires the ETSF_IO library. Applies only to Output = density, geometry, wfs, and/or wfs_fourier.
  
• xyz:
  Geometry will be output in XYZ format. Does not affect other outputs.
  
• cube:
  Generates output in the cube file format. Available only in 3D. Only writes the real part of complex functions.
  
• bild:
  Generates output in BILD format.
  
• vtk:
  Generates output in VTK legacy format.
  
• integrate_xy:
  Integrates the function in the x-y plane and the result on the z axis is printed.
  
• integrate_xz:
  Integrates the function in the x-z plane and the result on the y axis is printed
  
• integrate_yz:
  Integrates the function in the y-z plane and the result on the x axis is printed
  
• ascii:
  Plain text format regardless of dimensionality. For the moment only employed by the oct-phototoelectron_spectrum post-processing utility.
  

Name OutputInterval
Section Output
Type integer
Default 50

The output requested by variable Output is written to the directory OutputIterDir when the iteration number is a multiple of the OutputInterval variable. Subdirectories are named Y.X, where Y is td, scf, or unocc, and X is the iteration number. To use the working directory, specify "." (Output of restart files is instead controlled by RestartWriteInterval.) Must be >= 0. If it is 0, then no output is written. For gs and unocc calculations, OutputDuringSCF must be set too for this output to be produced. This variable can also be defined inside the Output block. See Output.

Name OutputIterDir
Section Output
Type string
Default “output_iter”

The name of the directory where Octopus stores information such as the density, forces, etc. requested by variable Output in the format specified by OutputFormat. This information is written while iterating CalculationMode = gs, unocc, or td, according to OutputInterval, and has nothing to do with the restart information.

Name OutputMatrixElements
Section Output
Type block
Default none

Specifies what matrix elements to print. Enabled only if Output block includes matrix_elements. The output files go into the static directory, except when running a time-dependent simulation, when the directory td.XXXXXXX is used.

Example:

%OutputMatrixElements
  momentum
  ks_multipoles
%

It is possible to specify only compute the matrix elements for some of the states using the variables OutptMEStart and OutputMEEnd.

Options:

• momentum:
  Momentum. Filename: ks_me_momentum.
  
• ang_momentum:
  Dimensionless angular momentum $\vec{r} \times \vec{k}$. Filename: ks_me_angular_momentum.
  
• one_body:
  $\left< i \left| \hat{T} + V_{ext} \right| j \right>$. Not available with states parallelization.
  
• two_body:
  $\left< ij \left| \frac{1}{\left|\vec{r}_1-\vec{r}_2\right|} \right| kl \right>$. Not available with states parallelization. Not available with states parallelization. For periodic system, this is not available for k-point parallelization neither.
  
• two_body_exc_k:
  $\left< n1-k1, n2-k2 \left| \frac{1}{\left|\vec{r}_1-\vec{r}_2\right|} \right| n2-k1 n1-k2 \right>$. Not available with states parallelization. For periodic system, this is not available for k-point parallelization neither.
  
• ks_multipoles:
  See OutputMEMultipoles. Not available with states parallelization.
  
• dipole:
  Prints the dipole matrix elements. Not available with states parallelization. For periodic systems, the intraband terms (dipole matrix elements between degenerated states) are set to zero, and only the absolute value of the dipole matrix element is printed. Not yet supported for spinors.
  

Name OutputMEEnd
Section Output
Type integer
Default 1

Specifies the highest state/band index used to compute the matrix element. So far, this is only used for dipole matrix elements.

Name OutputMEMultipoles
Section Output
Type integer
Default 1

This variable decides which multipole moments are printed out for OutputMatrixElements = ks_multipoles:

In 3D, if, for example, OutputMEMultipoles = 1, then the program will print three files, ks_me_multipoles.x (x=1,2,3), containing respectively the (1,-1), (1,0) and (1,1) multipole matrix elements between Kohn-Sham states.

In 2D, this variable is ignored: it will always print two files, ks_me_multipoles.i (i=1,2), containing the $x$ and $y$ dipole matrix elements.

In 1D, if, for example, OutputMEMultipoles = 2, the program will print two files, containing the $x$ and $x^2$ matrix elements between Kohn-Sham states.

Name OutputMEStart
Section Output
Type integer
Default 1

Specifies the state/band index for starting to compute the matrix element. So far, this is only used for dipole matrix elements.

Name OutputWfsNumber
Section Output
Type string
Default all states

Which wavefunctions to print, in list form: i.e., "1-5" to print the first five states, "2,3" to print the second and the third state, etc. If more states are specified than available, extra ones will be ignored.