MedeA SLI file reader — OVITO User Manual 3.16.0 documentation

# MedeA SLI file reader

Added in version 3.15.5.

For loading structure lists and molecular dynamics trajectories stored in the native `.sli` file format (Structures LIst) of the MedeA® software suite by Materials Design, Inc.

## Loading modes

Depending on the file contents, OVITO selects one of two loading modes:

Structure-list mode

  Each structure stored in the SLI file becomes one OVITO animation frame. The frame label is taken from the structure name, or from its molecular formula if no name is assigned. The atomic structure of each frame is read from the SCI data embedded in the file — see the MedeA SCI file reader for a description of the per-particle data imported in this step.

Trajectory mode

  When the SLI file contains trajectory data (a sequence of simulation frames), OVITO activates trajectory mode. Each simulation frame becomes one OVITO animation frame, labelled with its simulation time as available.

  Loading proceeds in two steps per frame:

  1. The base topology (atom types, bonds, charges, etc.) is read from the first structure in the file, exactly as in structure-list mode.

  2. The particle coordinates and the simulation cell are then updated with the current-frame values, overriding the static structure data. Periodic boundary conditions are kept as defined by the static structure.

## Global attributes

In trajectory mode, OVITO imports the following scalar thermodynamic quantities as time-dependent global attributes when they are present in the file.

OVITO attribute | SLI property name(s) | Description
--- | --- | ---
`SLI.Energy` | `E` / `Energy` | Total energy per frame (unit as stored, typically kJ/mol).
`SLI.Temperature` | `T` / `Temperature` | Instantaneous temperature.
`SLI.Volume` | `V` / `Volume` | Simulation cell volume.
`SLI.Pressure` | `P` / `Pressure` | Instantaneous pressure.
`SLI.PotentialEnergy` | `Epot` / `PotentialEnergy` | Potential energy contribution.
`SLI.KineticEnergy` | `Ekin` / `KineticEnergy` | Kinetic energy contribution.

## Options

Generate bounding box if needed

  If this option is enabled and a frame contains no periodic cell information, 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.

## 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)
  Parameters:

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