D

Name Debug
Section Execution::Debug
Type flag
Default no

This variable controls the amount of debugging information generated by Octopus. You can use include more than one option with the + operator.

Options:

• no:
  (default) Octopus does not enter debug mode.
  
• info:
  Octopus prints additional information to the terminal.
  
• trace:
  Octopus generates a stack trace as it enters end exits subroutines. This information is reported if Octopus stops with an error.
  
• trace_term:
  The trace is printed to the terminal as Octopus enters or exits subroutines. This slows down execution considerably.
  
• trace_file:
  The trace is written to files in the debug directory. For each node (when running in parallel) there is a file called debug_trace.<rank>. Writing these files slows down the code by a huge factor and it is usually only necessary for parallel runs.
  
• extra_checks:
  This enables Octopus to perform some extra checks, to ensure code correctness, that might be too costly for regular runs.
  
• interaction_graph:
  Octopus generates a dot file containing the graph for a multisystem run.
  
• interaction_graph_full:
  Octopus generates a dot file containing the graph for a multisystem run including ghost interactions.
  
• propagation_graph:
  Octopus generates a file with information for the propagation diagram.
  
• instrument:
  Octopus adds instrumentation to functions specified in an InstrumentFunctions block.
  

Name DebugTrapSignals
Section Execution::Debug
Type logical
Default yes

If true, trap signals to handle them in octopus itself and print a custom backtrace. If false, do not trap signals; then, core dumps can be produced or gdb can be used to stop at the point a signal was produced (e.g. a segmentation fault).

Name DegeneracyThreshold
Section States
Type float
Default 1e-5

States with energy $E_i$ and $E_j$ will be considered degenerate if $ \left| E_i - E_j \right| < $DegeneracyThreshold.

Name DensitytoCalc
Section States::ModelMB
Type block

Choice of which particle density (event. matrices) will be calculated and output, in the modelmb particles scheme.

%DensitytoCalc
   "proton" | 1 | 10
   "electron" | 2 | 15
%

would ask octopus to calculate the density matrix corresponding to the 1st particle (whose coordinates correspond to dimensions 1 to ndim_modelmb), which is an proton, then that corresponding to the 2nd particle (electron with dimensions ndim_modelmb+1 to 2*ndim_modelmb), printing 10 natural orbitals for the first and 15 for the second.

%DensitytoCalc
   "proton" | 1 | -1
   "electron" | 2 | -1
%

would ask octopus to print out just the densities for particles 1 and 2 without any density matrix output.

Name DerivativesOrder
Section Mesh::Derivatives
Type integer
Default 4

This variable gives the discretization order for the approximation of the differential operators. This means, basically, that DerivativesOrder points are used in each positive/negative spatial direction, e.g. DerivativesOrder = 1 would give the well-known three-point formula in 1D. The number of points actually used for the Laplacian depends on the stencil used. Let $O$ = DerivativesOrder, and $d$ = Dimensions.

• stencil_star: $2 O d + 1$
• stencil_cube: $(2 O + 1)^d$
• stencil_starplus: $2 O d + 1 + n$ with n being 8 in 2D and 24 in 3D.

Name DerivativesStencil
Section Mesh::Derivatives
Type integer
Default stencil_star

Decides what kind of stencil is used, i.e. which points, around each point in the mesh, are the neighboring points used in the expression of the differential operator.

If curvilinear coordinates are to be used, then only the stencil_starplus or the stencil_cube may be used. We only recommend the stencil_starplus, since the cube typically needs far too much memory.

Options:

• stencil_star:
  A star around each point (i.e., only points on the axis).
  
• stencil_variational:
  Same as the star, but with coefficients built in a different way.
  
• stencil_cube:
  A cube of points around each point.
  
• stencil_starplus:
  The star, plus a number of off-axis points.
  
• stencil_stargeneral:
  The general star. Default for non-orthogonal grids.
  

Name DescribeParticlesModelmb
Section States::ModelMB
Type block

Characterization of different modelmb particles in space%dim dimensional space.

%DescribeParticlesModelmb
   "proton" | 1 | 1800. | 1. | fermion
   "proton" | 1 | 1800. | 1. | fermion
   "electron" | 2 | 1. | 1. | fermion
%

would tell Octopus that there are presently 3 particles, called proton, proton, and electron, with types 1, 1, and 2, and corresponding masses and charges. All particles should be fermions, and this can be later enforced on the spatial part of the wavefunctions. The label and charge are presently only for informational purposes and are not checked or used in Octopus. The interaction has to take the actual charge into account.

Options:

• fermion:
  Particle is a fermion.
  
• boson:
  Particle is a boson.
  
• anyon:
  Particle is neither fermion nor boson.
  

Name DFTUBasisFromStates
Section Hamiltonian::DFT+U
Type logical
Default no

If set to yes, Octopus will construct the localized basis from user-defined states. The states are taken at the Gamma point (or the first k-point of the states in the restart_proj folder. The states are defined via the block DFTUBasisStates

Name DFTUBasisStates
Section Hamiltonian::DFT+U
Type block
Default none

This block starts by a line containing a single integer describing the number of orbital sets. One orbital set is a group of orbitals on which one adds a Hubbard U. Each following line of this block contains the index of a state to be used to construct the localized basis, followed by the index of the corresponding orbital set. See DFTUBasisFromStates for details.

Name DFTUDoubleCounting
Section Hamiltonian::DFT+U
Type integer
Default dft_u_fll

This variable selects which DFT+U double counting term is used.

Options:

• dft_u_fll:
  (Default) The Fully Localized Limit (FLL)
  
• dft_u_amf:
  (Experimental) Around mean field double counting, as defined in PRB 44, 943 (1991) and PRB 49, 14211 (1994).
  
• dft_u_mix:
  (Experimental) Mixed double countind term as introduced by Petukhov et al., PRB 67, 153106 (2003). This recovers the FLL and AMF as limiting cases.
  

Name DFTULevel
Section Hamiltonian::XC
Type integer
Default no

This variable selects which DFT+U expression is added to the Hamiltonian.

Options:

• dft_u_none:
  No +U term is not applied.
  
• dft_u_empirical:
  An empiricial Hubbard U is added on the orbitals specified in the block species with hubbard_l and hubbard_u
  
• dft_u_acbn0:
  Octopus determines the effective U term using the ACBN0 functional as defined in PRX 5, 011006 (2015)
  

Name DFTUPoissonSolver
Section Hamiltonian::DFT+U
Type integer

This variable selects which Poisson solver is used to compute the Coulomb integrals over a submesh. These are non-periodic Poisson solvers. The FFT Poisson solver with spherical cutoff is used by default.

Options:

• dft_u_poisson_direct:
  Direct Poisson solver. Slow but working in all cases.
  
• dft_u_poisson_isf:
  (Experimental) ISF Poisson solver on a submesh. This does not work for non-orthogonal cells nor domain parallelization.
  
• dft_u_poisson_psolver:
  (Experimental) PSolver Poisson solver on a submesh. This does not work for non-orthogonal cells nor domain parallelization. Requires the PSolver external library.
  
• dft_u_poisson_fft:
  (Default) FFT Poisson solver on a submesh. This uses the 0D periodic version of the FFT kernels.
  

Name Dimensions
Section System
Type integer
Default 3

Octopus can run in 1, 2 or 3 or more dimensions, depending on the value of this variable. Note that not all input variables may be available in all cases.

Name DisableAccel
Section Execution::Accel
Type logical
Default yes

If Octopus was compiled with OpenCL or CUDA support, it will try to initialize and use an accelerator device. By setting this variable to yes you force Octopus not to use an accelerator even it is available.

Name Displacement
Section Linear Response::Vibrational Modes
Type float
Default 0.01 a.u.

When calculating phonon properties by finite differences (CalculationMode = vib_modes, ResponseMethod = finite_differences), Displacement controls how much the atoms are to be moved in order to calculate the dynamical matrix.

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. This is ignored for the joint density of states, and the minimal energy is always set to zero.

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 DoubleFFTParameter
Section Mesh::FFTs
Type float
Default 2.0

For solving the Poisson equation in Fourier space, and for applying the local potential in Fourier space, an auxiliary cubic mesh is built. This mesh will be larger than the circumscribed cube of the usual mesh by a factor DoubleFFTParameter. See the section that refers to Poisson equation, and to the local potential for details [the default value of two is typically good].

Name DressedOrbitals
Section Hamiltonian::Poisson
Type logical
Default false

Allows for the calculation of coupled elecron-photon problems by applying the dressed orbital approach. Details can be found in https://arxiv.org/abs/1812.05562 At the moment, N electrons in d (<=3) spatial dimensions, coupled to one photon mode can be described. The photon mode is included by raising the orbital dimension to d+1 and changing the particle interaction kernel and the local potential, where the former is included automatically, but the latter needs to by added by hand as a user_defined_potential! Coordinate 1-d: electron; coordinate d+1: photon.