Trajectory analysis

PQViewer keeps trajectory inspection next to the molecular view. Pair distribution and coordination calculations run through PQAnalysis; interactive selection geometry and measurements are evaluated in the viewer.

Measurements over time

Select two, three, or four atoms in order, then choose Plot. The resulting distance, angle, or dihedral curve loads incrementally and follows the displayed frame.

Exports are available after the curve is complete:

  • CSV for numeric values

  • SVG for an editable vector plot

  • PDF for a vector publication plot

Choose Pin to retain a measurement. Two or more compatible pinned measurements can be compared in one plot. Distance measurements compare with distance measurements; angular measurements compare together.

Periodic measurements use minimum-image geometry by default. A plot preserves the measurement mode used when it was created.

Bookmarks and reference frames

Use the timeline menu or M to bookmark a frame. A bookmark retains stable source, segment, step, and time identity when available.

Choose Set as reference to compare the current structure with another frame. Select atoms and choose Show displacement to draw their motion from the reference. If the source changes and the saved frame identity no longer matches, the stale reference is cleared.

Atom trails

Select atoms and choose Track to draw their positions over the previous 50 frames plus the current position. Tracking uses unwrapped motion where available and is limited to sixteen selected atom images.

Scalar properties

Numeric frame properties from trajectory metadata or energy/info companions appear under Plot in the timeline menu. Opening one does not change the structural display. The plot cursor follows playback, and selecting a point navigates to that frame.

Pair distribution and coordination

Pair analysis requires a multi-frame, file-backed trajectory with a full three-dimensional periodic cell.

Open Pair distribution or Coordination from the timeline menu, selection bar, or command search. In the setup:

  • From is the reference population around which neighbors are counted.

  • To is the target population being counted.

  • Frames selects all frames, the last 100, or the last 1,000 when available. All samples automatically when the trajectory exceeds 10,000 frames.

  • Bins controls radial resolution.

  • r max · Å sets the maximum radius; leave it automatic to use the safe periodic range.

The result switches between g(r) and integrated coordination N(r). It exports CSV, SVG, and vector PDF.

The calculation is intentionally bounded:

  • at most 4,096 atoms in each population

  • at most 10,000 sampled frames

  • 20–2,000 bins in the interface

  • at most 50 million frame/reference/target pair evaluations

  • at most 5 million reconstructed atom-frames for sliced, ASE, and other non-native sources

Choose a shorter frame preset or smaller populations if the requested calculation exceeds a work limit. Pair-analysis curves aggregate the selected frames and do not follow one current-frame cursor.

For a custom interval or stride, open a sliced source such as trajectory.xyz@100:1000:10 before starting the analysis.