Atom Architect

Atom Architect is a tool for loading, visualizing, and analyzing atomistic structures from electronic structure calculations performed in VASP.

Philosophy

Atom Architect is built around a simple, but fundamental idea:

There is no “up” in space.

In chemistry and physics, atomic systems are inherently translationally and rotationally invariant. A molecule does not become a different molecule because it is shifted, rotated, or placed at another point in space. Any coordinate system we impose is therefore arbitrary — useful for computation, but meaningless from a physical perspective.

Traditional modeling tools often require users to position atoms or fragments by entering absolute Cartesian coordinates with respect to a fixed origin. While mathematically valid, this approach forces users to think in terms of an artificial reference frame rather than in terms of chemical structure.

Atom Architect takes a different approach.

Instead of asking “Where is this atom in space?”, Atom Architect asks:

“How is this fragment positioned relative to the atoms that already exist?”

Fragments are positioned by selecting atoms, typically chemically relevant sites such as metal atoms on a catalyst surface. Rotations are performed around axes defined by existing atoms, not around abstract coordinate directions. In this way, every transformation is expressed in terms of chemically meaningful relationships.

This design has two important consequences:

• Structures remain intuitive and reproducible, independent of their absolute orientation.

• User interactions closely mirror how chemists think about bonding, coordination, and geometry.

By eliminating the notion of a privileged origin or direction, Atom Architect keeps the focus on chemistry, not coordinates.