Note that the number of columns is always the same for cores and shells. Similarly, if charges and occupancies are defined, then the radius for breathing shells (rad) may also be written. As stated in the GULP documentation, if electric charges are written, then the site occupancies (occ) may also be written (if they are defined). So, if the electric charges of ions (q) are defined, they will be written. Values in square brackets will be written by Atomsk only if they are defined, either by being read from an input file or thanks to the option -properties. core ]] Īs shown in this example, if an atom is made of a core and a shell, the coordinates of the shell appear right after the ones of the core. This is not recognized here, and only the positions of the 1st NEB image will be read and converted by Atomsk.Ītomsk can only write a basic GIN file, containing the cell parameters and the positions of the cores (and shells if any) with the following format: And second, since NEB was implemented in GULP (>3.4) the restart files (res or grs) can contain all atomic positions for all images of NEB. Symmetry is a whole other story to implement, so it was not done in this program. So, if coordinates of a primitive lattice are used, only atoms in that primitive cell will be read and output. First, symmetry operations are not taken into account. The reading of GULP files come essentially with two restrictions. If the charges appear after each particle coordinate, then they will override the ones defined in the "species" section. If the electric charges of cores (and shells) are defined in the section "species" then Atomsk will store them as auxiliary properties. if cores and shells are written in any other arbitrary order) one can use the option -bind-shells. For Atomsk to associate cores and shells correctly, the position of each shell should always appear right after the position of the corresponding core (like in the example below), or all core positions should be contiguous and followed by all shells positions in a matching order. If electronic shells are present (in the sense of an ionic core-shell model potential) their positions are also read, but beware that they will be transferred for output only to formats that support it (like GULP files themselves, or DL_POLY CONFIG files). If velocities are present, they are saved as auxiliary properties. It may be appened by any string or characters (e.g. The "atom names" in the first column should always start with the species symbol (one or two letters) for Atomsk to recognize it. When reading GULP input files (gin, res or grs), Atomsk will always read the positions of atom cores. Visualization programs: gdis Restrictions Name: General Utility Lattice Package (GULP) input file
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