Crystals & Periodic Structures

Qemica 0.5 preserves crystallographic meaning instead of flattening a crystal into an isolated molecule. Import a CIF or create a cell, edit lattice and site data, expand symmetry, control the periodic view, and run the supported periodic PySCF calculation without losing the source structure.

Import or create a unit cell

  • Import .cif from Model → Import. The cell, space group, fractional sites, occupancies, symmetry operations, and available crystallographic metadata travel with the molecule.
  • For a structure you built yourself, open the PBC tab and choose Create 10 Å cubic cell, then edit a, b, c and α, β, γ. Keep fractional positions preserves fractional coordinates while the cell changes; turn it off to preserve Cartesian positions.
  • Show unit-cell edges controls only the display. Periodic calculation is a separate switch, so you can inspect a cell without accidentally enabling periodic electronic structure.

Space groups, symmetry, and sites

  • Load any of the 230 space groups by International Tables number or Hermann–Mauguin symbol; setting choices and the stored x,y,z operations remain visible and editable.
  • An asymmetric unit can be expanded into a new explicit unit cell with Apply symmetry to sites. Special-position duplicates are removed; the original crystallographic provenance remains recorded.
  • The site table edits fractional coordinates, labels, elements, and occupancy. Advanced fields include oxidation state, Wyckoff letter, site symmetry, isotropic displacement, and the anisotropic displacement tensor.
  • Split site creates two coincident disorder sites with divided occupancy. The occupancy audit detects overfilled disorder groups before you proceed.
  • Explicit three-dimensional cells can be standardized to primitive or conventional form with spglib.

Periodic display and bonding

  • Display 1×1×1, 2×2×2, or 3×3×3 replicas; extend along one axis; use a centred ±1 neighborhood; or enter exact fractional bounds. These are view settings and do not duplicate the stored canonical sites.
  • Choose whether to draw the home cell or all displayed cell edges, show a/b/c axes, complete bonded molecules across boundaries, and complete nearby coordination shells.
  • Periodic bond perception uses minimum-image distances. Adjust its radius allowance or add element-pair rules with an explicit distance range, bond order, or a suppression rule.
  • Wrap atoms moves canonical sites into the home cell. Make explicit supercell creates a separate P1 structure with the requested a×b×c repeats when you need real duplicated atoms rather than a display expansion.
Periodic calculation limits.
  • Periodic electronic-structure calculations currently run only on Classical · PySCF as closed-shell HF or DFT single points for fully 3D cells.
  • Configure exposes the Monkhorst–Pack k-point mesh. The engine uses pyscf.pbc with a GTH-SZV basis and GTH-PADE pseudopotentials and records that choice in the result.
  • ORCA, MACE, and quantum backends refuse a PBC-enabled structure instead of silently dropping the cell. Slabs and wires can be displayed, but the current calculation path requires all three periodic axes.
  • Turn off Periodic calculation in the PBC tab when you intentionally want to treat the current coordinates as a finite molecular cluster.