Skip to content

xmolout file — Atomic trajectory output

The xmolout file contains the atomic trajectory generated during a ReaxFF MD run or MM minimization.
It is generally the most useful output file for visualization and post‑processing.

Many molecular visualization programs can read xmolout directly, including: - Icarus - Xmol - Molden - Jmol

These programs can display animated trajectories of the simulation.

Purpose of the xmolout file

  • Store atomic positions over time
  • Visualize molecular motion and reactions
  • Analyze trajectories frame‑by‑frame
  • Interface ReaxFF with external viewers and analysis tools

Output behavior

MD simulations

  • Frame output frequency is controlled by the iout2 keyword in the control file
  • One frame is written every iout2 MD iterations

MM minimizations

  • Frame output frequency is controlled by iout4 in the control file

Appending behavior

  • xmolout is always appended, never overwritten
  • If a previous xmolout exists in the run directory, new frames are added to the end
  • The exe script may delete old xmolout files before a run
  • If not deleted, trajectories from multiple runs or geometries accumulate

When running ReaxFF on: - multiple geometries in a single geo file, or - multiple geometries listed in models.in

the xmolout file will contain frames from all geometries in sequence.

File format

The xmolout file follows an extended XYZ-style format.

Each frame consists of:

  1. Number of atoms
  2. Structure identifier
  3. One line per atom: atom type and Cartesian coordinates

Per‑frame layout

<N_atoms>
<Structure_identifier>
<Atom>  x  y  z
...

Coordinates are in Ångström.

Example 3.1: xmolout file

The following example shows three frames from an MD simulation of an ethyl radical.

7
Ethyl_radical
C 39.19924 40.08333 39.66585
H 40.88239 40.79608 40.81249
C 40.61413 39.91227 40.24250
H 38.86032 41.06389 39.38266
H 38.59716 39.25081 39.41763
H 41.33155 39.78117 39.45850
H 40.65892 39.04746 40.86980

7
Ethyl_radical
C 39.20278 40.09024 39.65697
H 40.80762 40.70179 40.96412
C 40.61564 39.90857 40.24468
H 38.93202 40.97423 39.12611
H 38.47436 39.29665 39.73567
H 41.35468 39.98863 39.43895
H 40.70164 38.93982 40.75604

7
Ethyl_radical
C 39.20278 40.09024 39.65697
H 40.80762 40.70179 40.96412
C 40.61564 39.90857 40.24468
H 38.93202 40.97423 39.12611
H 38.47436 39.29665 39.73567
H 41.35468 39.98863 39.43895
H 40.70164 38.93982 40.75604

Optional extended output (ixmolo)

If the ixmolo keyword in the control file is set to 1, additional information is written to xmolout, including:

  • Atomic velocities
  • Molecule numbers

Higher ixmolo values may include: - Strain energy per atom - Total bond order per atom

(See the control file documentation for details.)

Practical notes

  • xmolout is the primary trajectory file for ReaxFF
  • Ideal for visualization, diffusion analysis, and reaction tracking
  • Can grow very large for long simulations — periodic cleanup may be needed
  • Compatible with most XYZ‑based analysis tools

Summary

  • xmolout stores ReaxFF trajectories
  • Written during MD and MM runs
  • Appended continuously
  • Directly readable by common molecular viewers
  • Central to visualization and trajectory analysis workflows