Molecules
A handfull of variables are used to customize prebuilt POSCARs (see tags for more info):
- MOLECULE_CELL_SIZE_$structure sets the base cell size for the cell in which the molecule is placed (in Angstrom).
- MOLECULE_ASYMETRY_$structure adds a distortion to the base cell to make it cuboidal. (in Angstrom).
For example, if MOLECULE_CELL_SIZE_$structure = 15, MOLECULE_ASYMETRY_$structure = 2.5, then the molecule is placed in a 12.5 x 15 x 17.5 Angstrom cell.
- POSITION_ATOM_$n_$structure for $n=1,2,... sets the positions of the atoms within the molecule (array of type "x y z" in cartesian coordinates (Angstrom)) .
$structure refers to the name of the molecular structure in question. Typing $structure (after sourcing 23vaspAS) builds its POSCAR so you can easily inspect it.
Currently available molecules (as of v.0.1.0):
| Name |
Molecule type | Prototypes |
|---|---|---|
| monatomic_mol | AX0En | He |
| diatomic_mol | AX1En | CO, O2, H2 |
| linear_mol | AX2E0, AX2E3 | CO2, HCN, N2O |
| bent_mol | AX2E1, AX2E2 | H2O, SO2, O3 |
| trigonalplanar_mol | AX3E0 | BF3 |
| trigonalpyramidal_mol | AX3E1 | NH3 |
| tshaped_mol | AX3E2 | ClF3 |
| tetrahedral_mol | AX4E0 | CH4 |
| disphoreal_mol | AX4E1 | SF4 |
| squareplanar_mol | AX4E2 | XeF4 |
...