Graph

insert

# config.yaml
method: graph_insert
species: CO
spectators: [C, O]
sites:
    - cn: 1
      group:
          - "symbol Cu"
          - "region cube 0. 0. 0. -100. -100. 6. 100. 100. 8."
      radius: 3
      ads:
          mode: "atop"
          distance: 2.0
    - cn: 2
      group:
          - "symbol Cu"
          - "region cube 0. 0. 0. -100. -100. 6. 100. 100. 8."
      radius: 3
      ads:
          mode: "atop"
          distance: 2.0
    - cn: 3
      group:
          - "symbol Cu"
          - "region cube 0. 0. 0. -100. -100. 6. 100. 100. 8."
      radius: 3
      ads:
          mode: "atop"
          distance: 2.0
graph:
    pbc_grid: [2, 2, 0]
    graph_radius: 2
    neigh_params:
        covalent_ratio: 1.1
        skin: 0.25

remove

# config.yaml
method: graph_remove
species: O
graph:
    pbc_grid: [2, 2, 0]
    graph_radius: 2
    neigh_params:
        covalent_ratio: 1.1
        skin: 0.25
spectators: [O]
target_group:
    - "symbol O"
    - "region surface_lattice 0.0 0.0 8.0 9.8431 0.0 0.0 0.0 10.5534 0.0 0.0 0.0 8.0"

exchange

# config.yaml
method: graph_exchange
species: Zn
target: Cr
graph:
    pbc_grid: [2, 2, 0]
    graph_radius: 2
    neigh_params:
        # AssertionError: Single atoms group into one adsorbate.
        # Try reducing the covalent radii. if it sets 1.1.
        covalent_ratio: 1.0
        skin: 0.25
spectators: [Zn, Cr]
target_group:
    - "symbol Zn Cr"
    - "region surface_lattice 0.0 0.0 8.0 9.8431 0.0 0.0 0.0 10.5534 0.0 0.0 0.0 8.0"