Simulation cells
The simulation box VOLT records for every frame, and the listing that shows them across a team.
A simulation cell is the box a frame was simulated in: its three edge vectors, its origin and which axes are periodic. VOLT records one per frame when a trajectory is uploaded, read from the frame's header. The canvas uses it to draw the box and its periodic images.
What a record holds
| Field | Content |
|---|---|
| Trajectory | The trajectory the frame belongs to |
| Timestep | The frame's timestep |
| Cell vectors | The edge vectors a, b and c, in ångströms |
| Cell origin | The corner the vectors start from |
| Periodic boundary conditions | Whether X, Y and Z are periodic |
| Bounding box | Width (the x component of a), Length (the y component of b) and Height (the z component of c) |
For an orthogonal box the bounding box is the box's size. For a triclinic cell it holds only the diagonal components; the full shape is in the cell vectors.
Records are created when the upload is committed, before the frames are processed, and they are deleted with their trajectory. You can't edit them.
The listing
Simulation cells in the trajectories section of the sidebar opens /dashboard/simulation-cells/list, the
cells of every frame of every trajectory in the team.
| Column | Content |
|---|---|
| Trajectory | The trajectory's name. Click it for the trajectory's details. |
| Timestep | The frame |
| Width (Å), Height (Å), Length (Å) | The bounding box, to three decimals |
| Boundary Conditions | Periodic · X Y Z for a fully periodic box, otherwise one chip per axis, such as Z: Open |
| Created At | When the record was made |
Sort by any column except Boundary Conditions and Created At by clicking its header. Right-click a row for Copy Document ID.
In the canvas
The canvas shows the cell of the frame on screen in two places:
- Simulation cell under Visual elements in the pipeline panel draws the box. Its checkbox shows or hides it, and selecting it lets you set its opacity. See Canvas.
- The Simulation Cell tab of the timeline lists the Bounding Box, Boundary Conditions, Cell Vectors and Cell Origin of the current frame.
The Simulation Cell tab also has Show PBC images, which outlines the neighboring copies of the box along each periodic axis, and Edit Cell, which lets you change the a/b/c vectors and the periodic axes and Apply them. The edit only changes how the canvas draws the cell in your browser; the stored record stays as it is. Reset Cell returns to the stored cell.