atom-ops

To add or delete single atoms on a surface model in the CatGo viewer, use one-shot single-atom edits that directly issue the catgo_structure action. This skips the discovery loop and applies to adding, deleting, moving, and replacing individual atoms including coordinate-based placements.

Yes, you can place a hydrogen atom at specific coordinates on a surface structure by providing the exact placement location in Ångströms. The skill processes coordinate-based placements directly, such as adding a hydrogen at (1.5, 2.0, 6.3) Å, using a single catgo_structure action.

The fastest way to replace or swap one atom for another on a site is using one-shot single-atom edits. It directly targets the matching catgo_structure action for substitutions, such as replacing H with Li or swapping an oxygen at site 3 for fluorine, avoiding multiple tool queries.

Editing a single atom takes long with default structure tools because the default exploration path lists structure-tool actions, reads several docs, and queries the viewer state, requiring 4–8 MCP calls. One-shot single-atom edits collapse every common operation to a single call to avoid this delay.

Yes, the CatGo viewer supports batch deletion of atoms by index range through single-atom edit commands. You can delete a specific range of atoms, such as deleting atoms 5–9, directly via the catgo_structure action without checking adsorption sites first.

You should use one-shot atom editing instead of a full discovery loop whenever you need to add, delete, move, or replace individual atoms on a surface model. It skips listing structure tools and checking adsorption sites, using at most one get_info call when locating sites.