GEOM interface

plasmonX provides an internal engine for building complex nanostructures (both atomistic and implicit) through an interface to GEOM

The geometry is defined by specifying shape-specific keywords in the input_geometry section.

GEOM supports two major geometry types:

Implicit geometries
Atomistic geometries

In both cases, all the length parameters can be specified in:

Ang or Angstrom : Default
nm
a.u. or au

Implicit Geometries

Implicit (continuum) shapes are used with BEM models. These are defined via simple parameters and meshed for surface integration.

The implicit shapes are required by: type: implicit (mandatory)

The only supported shapes in implicit mode are:

Shape	Required Parameters	Description
sphere	`radius`	Spherical nanoparticle
rod	`main_axis`, `length`, `width`	Cylindrical nanorod aligned along x/y/z

Notes

Supported shapes for type: implicit geometries are:

sphere : the allowed keywords are:
- radius: outer radius of the nanoparticle.
- mesh_size (optional): resolution of the mesh used to discretize the surface (default: 10.0 Angstrom).
rod : the allowed keywords are:
- main_axis: orientation of the rod, one of x, y, or z.
- length: total length of the rod.
- width: base diameter of the rod.
- mesh_size (optional): resolution of the mesh used to discretize the surface (default: 10.0 Angstrom).

Example

input_geometry:
  type: implicit
  shape: sphere
  radius: 15.0
  mesh_size: 12.5

Atomistic Geometries

Atomistic geometries can be created by specifying type: atomistic, which is optional (default).

GEOM supports many shapes with both single-material and core-shell configurations. Dimers can also be generated.

For single-material configurations, the keyword atomtype is mandatory.

For core-shell configurations (available only for shape: sphere or shape: rod) the keywords core_atomtype and shell_atomtype are mandatory.

Shape	Required Parameters	Description
sphere	`radius`	Spherical nanoparticle
rod	`main_axis`, `length`, `width`	Cylindrical nanorod
pyramid	`base_length`, `height`	Tip-like pyramids with square base
icosahedron	`radius`	Icosahedral nanoparticle (`ico` or `ih` are allowed)
cone	`radius`, `height`	Cone
tip	`a`, `b`, `height`	Paraboloid tip
microscope	`a`, `b`, `height`, `base_length`, `height_tip`	This is constructed by using a tip + base + pyramid, and resembles a TERS configuration
disk	`radius`	Graphene-based disk
ring	`radius`, `radius_in`,	Graphene-based ring
triangle	`side_length`, `edge_type`	Graphene-based triangle armchair or zigzag
ribbon	`length`, `width`, `edge_type`	Graphene nanoribbon armchair or zigzag

Notes

sphere : the allowed keywords are:
- radius: radius of the sphere
- atomtype: atomtype
- For core-shell spheres:
  - core_atomtype : core atomtype
  - shell_atomtype : shell atomtype
  - core_radius : radius of the core
  - shell_radius : radius of the shell
rod : the allowed keywords are:
- main_axis: the main axis of the rod (x, y, z)
- length: rod length
- width: cross-sectional width of the rod
- atomtype: atomtype
- For core-shell rods:
  - core_atomtype : core atomtype
  - shell_atomtype : shell atomtype
  - core_length : core length
  - shell_length : shell length
  - core_width : core width
  - shell_width : shell width
pyramid : the allowed keywords are:
- base_length : length of the square base
- height : total height of the pyramid
- atomtype : atomtype
icosahedron (or ico, ih) : the allowed keywords are:
- radius: radius
- atomtype: atomtype
cone : the allowed keywords are:
- radius: base radius
- height: height of the cone
- atomtype: atomtype
tip : the allowed keywords are:
- a, b: shape parameters controlling the paraboloid curvature \(z = a x^2 - b y^2\)
- height: height of the tip
- atomtype: atomtype
microscope : the allowed keywords are:
- a, b: shape parameters controlling the paraboloid curvature \(z = x^2 / a^2 + y^2 / b^2\)
- height: paraboloid height
- base_length: length of square base
- height_tip: height of the small pyramid at the top of the paraboloid
- atomtype: atomtype
disk : the allowed keywords are:
- radius: disk radius
- atomtype: must be C (graphene)
ring : the allowed keywords are:
- radius: outer radius
- radius_in or shell_radius: internal radius or shell thickness
- atomtype: must be C (graphene)
triangle : the allowed keywords are:
- side_length: triangle side length
- edge_type: edge type. Allowed keywords are: armchair or zigzag
- atomtype: must be C (graphene)
ribbon : the allowed keywords are:
- length: ribbon length
- width: ribbon width
- edge_type: edge type. Allowed keywords are: armchair or zigzag.
- atomtype: must be C (graphene)

Additional options:

dimer : if provided, creates a dimer of two structures. Allowed values are :
- default : the dimer is constructed as face-tip-face-tip configuration [optional if dimer_axis and distance are provided]
- bowtie : the dimer is constructeda as face-tip-tip-face configuration
distance : minimum distance between the two nanostructures
dimer_axis : specifying the direction in which the two objects are aligned:
- x, y, z : axis

Example

input_geometry:
  shape: rod
  atomtype: Au
  main_axis: z
  length: 20.0 nm
  width: 8.0 nm
  distance: 5.0
  dimer_axis: z