| Key | Purpose | Options |
|---|
checkpoint | Allows the current sequence of DFT-raMO to begin using the specified basis set typically obtained partway through the analysis. | Blank – starts with the basis set generated from DFT inputs |
| | Path to the .chkpt file containing the starting basis set for the analysis |
mode | Specifies if DFT-raMO evaluates the raMO and how the basis set is updated. | default – keeps all generated raMOs regardless of $P_{sphere}$ value and updates the basis set accordingly. |
| | auto_psphere – automatically returns raMOs with $P_{sphere}$ values <15% of the maximum $P_{sphere}$ value to the basis set. Subsequent raMOs that do meet the criteria are automatically rerun. |
| | discard – all raMOs are returned to the basis set. Typically used for testing raMOs at different sites. |
software | Indicates which DFT package is used to calculate wavefunction information | vasp (abinit is currently not supported but will be implemented in a future update) |
emin and emax | Specifies the lower and upper limit of energy for wavefunctions used in the basis set | Blank – by default, will start at the lowest energy |
| | (Number) eV – Energy in eV |
| | (Number) Ha – Energy in Ha |
runs | Indicates the list of raMO sequences will follow | The list of raMO sequences and corresponding keys. See table. |
| Key | Purpose | Options |
|---|
name | Names the directory that stores output files corresponding to the raMO analysis. Also prepends files within that directory with this name. | Blank – (not recommended) by default, starts with run_1 and continues numbering. |
| | A string. It is recommended to use a descriptive yet concise string with no whitespace (e.g. 1_Sc_dxy to indicate it is the first sequence and corresponds to reconstruction of the Sc dxy atomic orbitals). |
type | Specifies which type of target raMO to generate | Atomic orbitals (s, px, py, pz, dx2y2 or dx2-y2, dz2, dxy, dxz, dyz) |
| | sp - Molecular orbital-like targets built from s- and p-based orbitals based on distance to a specified central site. |
| | lcao - Builds targets based on user-specified linear combination of atomic orbitals. |
| | displaced (AO) - Creates targets that are displaced off the central site by some specified direction and distance. |
site_file | Specifies the .xyz (sp type) or .yaml (lcao type) file for the sequence | For sp type runs, the path to an .xyz file |
| | For lcao type runs, the path to a .yaml file |
sites | Specifies which sites in the periodic atom list/.xyz/.yaml to build targets for | For atomic orbital type runs, a list of atomic sites in the supercell based on the periodic atom list (e.g. 1, 2, 4:12) or specific elements (e.g. Sc for all Sc sites, or Sc 1, 2, 4:12 for the 1st, 2nd, and 4th through 12th sites of Sc) |
| | For sp and lcao type runs, all builds targets for all sites listed in the .xyz or .yaml file, or a list of sites based on the .xyz or .yaml file (e.g. 1, 2, 4:12) |
direction | For displaced (AO) type runs only, specifies a directional vector in fractional coordinates for the displacement | [a, b, c] – where a, b, and c correspond to the displacement direction in the fractional coordinate system. The directional vector is automatically normalized. |
radius | For sp type runs, indicates the maximum distance from the site to search for atoms whose s and p orbitals are used in generating the target. For displaced (AO) type runs, indicates the distance of the displacement. | (Number) - distance in Å |
rsphere | Specifies $r_{sphere}$ used for $P_{sphere}$ analysis | Blank - a default value of 3 Å will be applied |
| | (Number) - distance in Å |