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Edit atoms and cell geometry

Select, move, add, substitute, delete, and measure atoms in the viewport. Keep geometry changes deliberate and inspect the result before rerunning a calculation.

Complete guide

Atom tools

ToolUse
Select (V)Select an atom and inspect its properties.
Move (G)Move a selection; choose an axis or plane, then apply or cancel the move.
Add atom (A)Open the element selection flow and place the intended species.
Measure (M)Select the atoms required by the distance or angle mode.
Focus (F)Center the viewport on the selected atom.
Delete / BackspaceDelete the selected atom when the viewport has focus.

Constrained movement

In Move mode, X, Y, or Z constrains motion to that Cartesian axis. Shift+X, Shift+Y, or Shift+Z uses the perpendicular YZ, XZ, or XY plane. Enter applies the move; Escape cancels it.

Use coordinate fields when you need an exact displacement. Numeric editors allow an intermediate draft such as a minus sign or exponent; commit with Enter or by leaving the field. Escape restores the previous value.

Cell edits and visual appearance

  • Cell metric edits change the actual lattice. Inspect whether the resulting geometry represents the strain or model you intend.
  • The vacuum action increases separation normal to the a-b plane and preserves Cartesian atomic distances; it is not a general arbitrary-axis slab builder.
  • Atom size, bond size, labels, neighbor cutoff, and displayed repeat count affect visualization.
  • Undo/redo applies to supported editor actions in the current editing session. Keep explicit structure copies for scientific variants you want to retain permanently.

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