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Section System::Species
Type block

A species is by definition either an "ion" (nucleus + core electrons) described through a pseudopotential, or a model potential.

Note that some sets of pseudopotentials are distributed with the code. To use these pseudopotentials, you do not need to define them explicitly in the Species block, as default parameters are provided. You can select the set for default pseudopotentials using the PseudopotentialSet variable.

Additional pseudopotentials can be downloaded from the octopus homepage or from other sources. Supported norm-conserving pseudopotential formats are detected by the file extension: UPF (.upf), PSF (SIESTA, .psf), FHI (ABINIT 6, .fhi), CPI (Fritz-Haber, .cpi), QSO (quantum-simulation.org, for Qbox, .xml), HGH (Hartwigsen-Goedecker-Hutter, .hgh). PSPIO format can also be used via species_pspio if that library is linked. Note: pseudopotentials may only be used in 3D.

Note that not all pseudopotential format are supporting spin-orbit coupling (SOC). At the moment, only HGH, UPF1 and UPF2 formats are supporting SOC. Some fully-relativistic pseudopotentials can still be used, but only without SOC.

The format of this block is the following: The first field is a string that defines the name of the species. The second field defines the type of species (the valid options are detailed below).

Then a list of parameters follows. The parameters are specified by a first field with the parameter name and the field that follows with the value of the parameter. Some parameters are specific to a certain species while others are accepted by all species. These are mass, max_spacing, and min_radius.

These are examples of possible species:

  ‘O’ | species_pseudo | file | ‘O.psf’ | lmax | 1 | lloc | 1
  ‘H’ | species_pseudo | file | ‘../H.hgh’
  ‘Xe’ | species_pseudo | set | pseudojo_pbe_stringent
  ‘C’ | species_pseudo | file | "carbon.xml"
  ‘jlm’ | species_jellium | jellium_radius | 5.0
  ‘rho’ | species_charge_density | density_formula | "exp(-r/a)" | mass | 17.0 | valence | 6
  ‘udf’ | species_user_defined | potential_formula | "1/2*r^2" | valence | 8
  ‘He_all’ | species_full_delta
  ‘H_all’ | species_full_gaussian | gaussian_width | 0.2
  ‘Li1D’ | species_soft_coulomb | softening | 1.5 | valence | 3
  ‘H_all’ | species_full_anc | anc_a | 4


Source information

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