input_geometry section

The input_geometry section defines the atomic structure used in the simulation.

The geometry is assumed in all cases to be in Angstrom.

There are three supported modes for declaring geometries:

Direct YAML string input
External .xyz file
Generation with GEOM interface

The input_geometry section is mandatory for atomistic simulations. For BEM, it can be used to construct new geometries (see Generation with GEOM interface)

1. YAML inline geometry

Geometry can be written directly in the YAML file as a multiline string, using the | character.

Important : Remember the first blank space at the beginning of each new line for YAML format.

Example

input_geometry: |
  Ag 0.0 0.0 0.0
  Ag 1.0 0.0 0.0
  Ag 0.0 1.0 0.0
  Ag 0.0 0.0 1.0

If you are running a FQ or FQFMu calculations, you can specify the molecule number using the [IMol=X] tag:

input_geometry: |
  O-OW[IMol= 1]      0.09543100      0.65652700      1.21555100
  H-HW[IMol= 1]      0.67989369      0.65652700      1.97965006
  H-HW[IMol= 1]      0.67989417      0.65652700      0.45145232
  O-OW[IMol= 2]     -0.09543100     -0.65652700     -1.21555100
  H-HW[IMol= 2]     -0.67989417     -0.65652700     -0.45145232
  H-HW[IMol= 2]     -0.67989369     -0.65652700     -1.97965006

Atom types must be defined in the atom_types section or defaulted.
IMol must be a positive integer.
Coordinates must be three floating-point numbers.

2. External .xyz file

You can reference an external geometry file in XYZ format using the keyword external xyz file.

Important : This is not recommended for FQ or FQFMu calculations, because all the atoms are assumed to constitute one molecule.

Example

input_geometry:
  external xyz file: my_structure.xyz

The file must be in standard XYZ format.
Atom types must match those used in atom_types.

3. Generation with GEOM

You can use plasmonX interface to GEOM to construct complex nanostructures directly.

The allowed shapes and related keywords are given in: geom_interface.