Output
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.
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.
DOSEnergyPoints
Section: Output
Type: integer
Default: 500
Determines how many energy points Octopus should use for
the DOS energy grid.
DOSGamma
Section: Output
Type: float
Default: 0.008 Ha
Determines the width of the Lorentzian which is used for the DOS sum.
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.
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.
Output
Section: Output
Type: flag
Default: no
Specifies what to print. The output files go into the static directory, except when
running a time-dependent simulation, when the directory td.XXXXXXX is used. For
linear-response run modes, the derivatives of many quantities can be printed, as listed in
the options below; the files will be printed in the directory
for the run mode. Indices in the filename are labelled as follows:
sp = spin, 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: density + potential
Options:
- el_pressure: Outputs electronic pressure. See Tao, Vignale, and Tokatly, Phys Rev Lett 100, 206405 (2008).
- xc_density: Outputs the XC density, which is the charge density that
generates the XC potential. (This is times
the Laplacian of the XC potential). The files are called nxc.
- ELF_basins: Outputs basins of attraction of the ELF. The output file is called
elf_rs_basins.info. Only in 2D and 3D.
- tpa: Outputs transition-potential approximation (TPA) matrix elements.
- mmb: This flag turns on the output for model many-body calculations, for
particles described in the DescribeParticlesModelMB block.
- kinetic_energy_density: Outputs kinetic-energy density, defined as:
The index 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.
- BerkeleyGW: Output for a run with BerkeleyGW (www.berkeleygw.org). See Output::BerkeleyGW for further specification.
- geometry: Outputs file containing the coordinates of the atoms treated within quantum mechanics.
If OutputHow = 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 OutputHow = xcrysden, a file called geometry.xsf is written.
- potential: Outputs Kohn-Sham potential, separated by parts. File names are v0 for
the local part, vc for the classical potential (if it exists), vh for the
Hartree potential, and vxc- for the exchange-correlation potentials.
- matrix_elements: Outputs a series of matrix elements of the Kohn-Sham states. What is output can
be controlled by the OutputMatrixElements variable.
- PES_wfs: Outputs the photoelectron wavefunctions. The file name is pes_wfs-
plus the orbital number.
- ELF_FS: Outputs electron localization function in Fourier space (experimental). The output file is called
elf_FS-. Only in 2D and 3D.
- 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.
- mmb_wfs: Triggers the ModelMB wavefunctions to be output for each state
- density: Outputs density. The output file is called density-, or lr_density- in linear response.
- current: Outputs paramagnetic current density. The output file is called current-.
For linear response, the filename is lr_current-.
- delta_perturbation: Outputs the "kick", or time-delta perturbation applied to compute linear response in real time.
- 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.
- PES_density: Outputs the photolectron density. Output file is pes_dens- plus spin species if
spin-polarized calculation is performed.
- 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.
- 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).
- wfs_fourier: (Experimental) Outputs wavefunctions in Fourier space. This is
only implemented for the ETSF file format output. The file will
be called static/wfs-pw-etsf.nc.
- mmb_den: triggers the ModeMB density or density matrix to be output for each state, and the particles
speficied by the DensitytoCalc block. In the latter case, 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.
- 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.
- dos: Outputs density of states.
- external_td_potential: Outputs the (scalar) time-dependent potential.
- mesh_r: Outputs values of the coordinates over the grid. Files
will be in the exec/ directory.
- PES: Outputs the time-dependent photoelectron spectrum.
- wfs_sqmod: Outputs modulus squared of the wavefunctions.
The output file is called sqm-wf-. For linear response, the filename is sqm_lr_wf-.
OutputBandsGnuplotMode
Section: Output
Type: logical
Default: no
The band file will be written in Gnuplot-friendly format to bands-gp.dat
(or band-gp-is.dat if spin-polarized).
OutputBandsGraceMode
Section: Output
Type: logical
Default: no
The band file will be written in Grace-friendly format to bands-grace.dat
(or bands-grace-is.dat if spin-polarized).
OutputDuringSCF
Section: Output
Type: logical
Default: no
If this variable is set to yes, during a ground-state run,
Octopus output will be written after every self-consistent
iteration to a directory called scf.nnnn/ (with
nnnn the iteration number).
OutputEvery
Section: Output
Type: integer
Default: 50
The output is saved when the iteration number is a multiple of the
OutputEvery variable. For CalculationMode = gs or unocc,
this variable controls writing of restart files. For td and opt_control,
this variable also controls the writing of the output requested by the variable Output.
OutputHow
Section: Output
Type: flag
Describes the format of the output files (see Output).
Example: axis_x + plane_x + dx
Options:
- xcrysden: A format for printing structures and three-dimensional information, which can be visualized by
the free open-source program XCrySDen (http://www.xcrysden.org/). The string
.xsf is appended to previous file names. Note that lattice vectors and coordinates are as
specified by UnitsOutput.
- netcdf: Outputs in NetCDF (http://www.unidata.ucar.edu/packages/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.
- cube: Generates output in the cube file format (http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/)
Available only in 3D. Only writes the real part of complex functions.
- binary: Plain binary, new format.
- plane_y: A plane slice at y = 0 is printed. The string .y=0 is appended
to previous file names.
- 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.
- 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);
- 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.
- etsf: ETSF file format (http://www.etsf.eu/resources/software/standardization_project).
Requires the ETSF_IO library.
- plane_z: A plane slice at z = 0 is printed. The string .z=0 is appended to
previous file names.
- 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.
- 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.
- 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 vizualization
can be found under PREFIX/share/octopus/util/display_mesh_index.gp.
- dx: For printing three-dimensional information, the open-source program
visualization tool OpenDX (http://www.opendx.org/) can be used. The string
.dx is appended to previous file names.
- xyz: Geometry will be output in XYZ format. Does not affect other outputs.
- boundary_points: This option includes the output of the mesh enlargement. Default is without.
- plane_x: A plane slice at x = 0 is printed. The string .x=0 is appended
to previous file names.
OutputMEMultipoles
Section: Output
Type: integer
Default: 1
This variable decides which multipole moments
are printed out: e.g., if 1, then the
program will print three files, ks_multipoles.x (x=1,2,3), containing
respectively the (1,-1), (1,0) and (1,1) multipole matrix elements
between Kohn-Sham states.
OutputMatrixElements
Section: Output
Type: flag
Default: no
Specifies what matrix elements to print.
The output files go into the static directory, except when
running a time-dependent simulation, when the directory td.XXXXXXX is used.
Example: "momentum + ks_multipoles"
Options:
- ks_multipoles: TODO
- momentum: TODO
- ang_momentum: TODO
- one_body:
- two_body:
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.
Output::BerkeleyGW
BerkeleyGW_CalcExchange
Section: Output::BerkeleyGW
Type: logical
Default: false
Whether to calculate exchange matrix elements to be written in x.dat.
These will be calculated anyway by BerkeleyGW Sigma, so this is useful
mainly for comparison and testing.
BerkeleyGW_Complex
Section: Output::BerkeleyGW
Type: logical
Default: false
Even when wavefunctions, density, and XC potential could be real in reciprocal space,
they will be output as complex.
BerkeleyGW_NumberBands
Section: Output::BerkeleyGW
Type: integer
Default: all states
Wavefunctions for bands up to this number will be output.
BerkeleyGW_Vxc_diag_nmax
Section: Output::BerkeleyGW
Type: integer
Default: nst
Highest band for which to write diagonal exchange-correlation matrix elements.
BerkeleyGW_Vxc_diag_nmin
Section: Output::BerkeleyGW
Type: integer
Default: 1
Lowest band for which to write diagonal exchange-correlation matrix elements.
BerkeleyGW_Vxc_offdiag_nmax
Section: Output::BerkeleyGW
Type: integer
Default: nst
Highest band for which to write off-diagonal exchange-correlation matrix elements.
If < 1, off-diagonals will be skipped.
BerkeleyGW_Vxc_offdiag_nmin
Section: Output::BerkeleyGW
Type: integer
Default: 1
Lowest band for which to write off-diagonal exchange-correlation matrix elements.
If < 1, off-diagonals will be skipped.
BerkeleyGW_WFN_filename
Section: Output::BerkeleyGW
Type: string
Default: WFN
Filename for the wavefunctions.