MedeA SCI file reader

Added in version 3.15.5.

For loading molecular and crystalline structures stored in the native .sci file format of the MedeA® software suite by Materials Design, Inc. This section-based text format supports non-periodic molecular systems, periodic crystalline structures, and mesoscale coarse-grained models.

The file header must start with #MD System 2.0 or #SciCo System 1.0 (legacy). An optional @Title directive sets the SCI.Title global attribute.

The file reader processes the following table sections:

Atom

Reads all atoms in a non-periodic or periodically-expanded system (Cartesian coordinates) and imports:

  • Position (x, y, z)

  • Particle Type — the chemical element derived from the AtomicNumber column. OVITO assigns standard CPK colors for each element.

  • Particle Identifier — from the Point column (1-based atom index).

  • Force-Field Type — SYBYL/CHARMM force-field atom type (FFAtomType column), if present.

  • Charge — partial charge from the FFCharge column, if present.

  • Mass — atomic mass from the Mass column, if present.

Atom names will be read by OVITO 3.16.0 and later, but are currently ignored in OVITO 3.15.5.

AsymmetricAtom

Present in periodic systems that have not been expanded to the full unit cell. Contains fractional coordinates and the same optional columns as Atom above, plus:

  • Spin — magnetic spin value from the Spin column, if present.

When an AsymmetricAtom table is found without a corresponding expanded Atom table, OVITO uses the gemmi crystallography library to generate the full P1 unit cell by applying all symmetry operations of the space group.

Note

Bond topology of symmetry-reduced files with centred lattices. When a structure is stored with reduced symmetry (only an AsymmetricAtom table) and the space group has a centred Bravais lattice (lattice symbol A, B, C, I, F or R, e.g. the common monoclinic setting \(C2/c\)), OVITO may connect the wrong pairs of atoms when rebuilding the bond network after the symmetry expansion. The atomic positions, the simulation cell, and the number of bonds are correct, but individual bonds can be attached to symmetry-equivalent atoms other than the intended ones.

The reason is that the Bond table references atoms by MedeA’s internal enumeration order, which OVITO must reproduce in order to remap the bonds onto its own atom ordering. For primitive lattices this order can be reconstructed reliably, but for centred lattices MedeA derives it from proprietary internal tables (and from a canonical site representative that need not match the coordinate stored in the file), so it cannot be reproduced from the file alone.

If you need correct bond topology for such a structure, export it from MedeA in its fully expanded (P1) form, in which all atoms and bonds are listed explicitly and no symmetry expansion is required.

Cell

Reads the unit cell parameters and sets up a periodic simulation cell:

  • Lattice parameters (a, b, c, α, β, γ) are converted to a triclinic cell matrix.

  • Periodic boundary conditions are enabled in all three directions.

  • The space group name and number are stored as the global attributes SCI.SpaceGroup and SCI.SpaceGroupNumber.

Bond

Reads all bonds and creates:

  • Bond Topology — the two connected atom indices.

  • Bond Type — named types Single, Aromatic, Double, and Triple, corresponding to the SCI bond-order integers 0, 1, 2, and 3.

  • Bond Order — a numeric value: single→1.0, aromatic→1.5, double→2.0, triple→3.0. This property is used by the Bonds visual element to render double/triple bonds as parallel cylinders and aromatic bonds as dashed cylinders.

  • Periodic Image — integer cell-offset vector for bonds across periodic boundaries (from the CellOffset2 column), present in periodic systems.

AsymmetricBond

Present alongside Bond in periodic systems. Stores the bond order (Order column) which is looked up when processing expanded Bond rows.

Bead

Present in mesoscale coarse-grained systems. Each row defines one bead type and provides:

  • Name — bead type label (e.g. C1, Qa), used as the particle type name.

  • Mass — bead mass in g/mol, stored as the type mass.

  • Radius — bead radius in Å, stored as the type display radius.

  • Color — RGB color in [0, 1] range, stored as the type display color.

  • Charge — bead charge.

When a Bead table is present and the Atom table (non-periodic systems) or the AsymmetricAtom table (periodic systems) contains a Bead reference column, the system is treated as a mesoscale model: particle types are taken from bead type names instead of chemical element symbols.

Properties

Reads molecule-level scalar quantities (non-periodic systems only):

All other table sections are silently ignored.

Options

Generate bounding box if needed

If this option is enabled and the SCI file contains no Cell table, OVITO will generate an axis-aligned bounding box enclosing all atoms. This bounding box has open boundary conditions and serves as an approximate simulation cell.

Center simulation cell on coordinate origin

If enabled, OVITO shifts the simulation cell and all atom coordinates so that the geometric center of the cell coincides with the coordinate origin.

Python parameters

The file reader accepts the following optional keyword parameters in a call to the import_file() or load() Python functions.

import_file(location, bounding_box=False, centering=False)
Parameters:

  • bounding_box (bool) – Generate an ad-hoc simulation cell as a bounding box around the imported atoms when the file contains no Cell table.

  • centering (bool) – Translate atom coordinates and simulation cell to center them at the coordinate origin.