RandomBuilders

This section is about builders that generate random structures under certain geometric restraints.

The builder parameters:

composition:

A dictionary of the chemical composition to insert. This can be atoms, molecules, or a mixture of them. For example, only atoms as {“Cu”: 13}, only molecules as {“H2O”: 3} and mixed atoms and molecules {“Cu”: 13, “H2O”: 3}. Moreover, if the exact number of molecules is unknwon, it can be automatically determined by the density as {“H2O”: “density 0.998”} with the unit of g/cm^3.
region:

Define the region where random atoms/molecules are put. See Regions for more details.
covalent_ratio:

The geometric restraints. The minimum and maximum multipliers for the covalent distance between atoms.
random_seed:

Random seed for the random generator. Use the same seed to reproduce results.

Note

Sometimes the builder will fail to generate new structures due to geometric restraints. Simply reduce the first element of covalent_ratio that allows structures with very close atomic distances. If this still does not work, set test_too_far to false, which allows sparse atomic positions to generate.

The YAML input file has the format of

Cluster

Use cell to define the box where the generated cluster is in even though it is not periodic. Here, a smaller region is set to put random atoms, which makes atoms more concentrated.

# - Genreate a cluster with 13 Cu and 3 H2O.
method: random_cluster
composition:
  Cu: 13
  H2O: 3
# pbc: True # Set this to True if periodic structures are desired.
cell: [30., 0., 0., 0., 30., 0., 0., 0., 30.]
region:
  method: lattice
  origin: [10., 10., 10.,]
  cell: [10., 0., 0., 0., 10., 0., 0., 0., 10.]
covalent_ratio: [0.6, 2.0]
test_too_far: false
random_seed: 1112

Note

The structures generated by random_cluster are not periodic (pbc=False) by default. This may fail the following calculations as some codes do not support non-periodic structures. Thus, set pbc: True to make generated structures periodic.

Surface

Generate random atoms on a substrate. This is useful to explore reconstructed (amorphous) surfaces or supported nanoparticles. The region defines the lattice vector in the x-axis and the y-axis but a cut in z-axis that has a range from 7.5 to 13.5 (7.5+6.0).

# - Genreate a surface with 8 Cu and 3 O.
method: random_surface
substrate: ./assets/slab.xyz
composition:
  Cu: 8
  O: 3
region:
  method: surface_lattice
  origin: [0., 0., 7.5]
  cell: [5.85, 0.0, 0.0, 0.0, 4.40, 0.0, 0.0, 0.0, 6.0]
covalent_ratio: [0.4, 2.0]
test_dist_to_slab: false
test_too_far: false
random_seed: 1112

Bulk

Bulks have random lattice parameters. Use cell_bounds to set the range of angles and lengths.

# - Genreate a bulk with 4 Cu and 2 O.
method: random_bulk
composition:
  Cu: 4
  O: 2
cell_bounds:
  phi: [35, 145]
  chi: [35, 145]
  psi: [35, 145]
  a: [3, 50]
  b: [3, 50]
  c: [3, 50]