Apply Atomic Constraints

Prevent selected atoms or Cartesian components from moving during supported calculations, such as holding a host or slab fixed while relaxing a guest or adsorbate.

Before you begin

Distinguish three controls:

• A layer lock prevents interactive editing.
• Layer visibility controls display.
• An atomic constraint changes the calculation degrees of freedom.

Only the third is a scientific constraint.

Procedure

1. Switch to Edit and select the intended atoms.
2. Open the Constraints tool.
3. Enable Fix X, Fix Y, and/or Fix Z.
4. Apply the constraint and inspect the selected atoms or property table.
5. Save the constrained structure so its selective flags are preserved.
6. Run a short test optimization and inspect the trajectory before starting a long workflow.

Use all three axes to hold atoms completely fixed. Use partial Cartesian constraints only when the coordinate system and physical rationale are explicit.

Verify the result

Note that convergence behavior can differ by operation. In some optimization paths, forces on constrained atoms may still influence the reported maximum-force criterion even though their coordinates do not move. Inspect both trajectory and force diagnostics.

Variants

• In Tako Script, use tako.structure.fix(structure, indices) for fully fixed atoms and documented selective-coordinate helpers for partial constraints.
• For surfaces, constrain physically justified bottom layers rather than every substrate atom by default.
• For host–guest screening, report clearly that a rigid-host energy excludes induced fit.

Troubleshooting