Load trajectory — OVITO User Manual 3.15.3-dev-HEAD-b1e9512d documentation

# Load trajectory

This modifier loads atomic trajectories and other time-dependent data from a separate trajectory file and merges them with static information loaded from the primary data file (e.g. atom types and bond connectivity). The Load trajectory modifier may be used several times in the same pipeline to load different types of time-varying data from separate files and merge them all into a single dataset (e.g. atomic trajectories + reactive bond topologies + angular interactions).

Some molecular dynamics codes work with separate topology and trajectory files. The topology file typically serves as a starting point of the MD simulation and contains the initial atomic positions and the definitions of static structures like the atom types, bonds, etc., which do not change throughout the simulation. The trajectories of the particles computed by the MD code are then written to an output file, which stores just the time-dependent coordinates and sometimes other varying information such as the atomic energies.

LAMMPS is a simulation code that employs this topology-trajectory file philosophy. LAMMPS uses the data file format for input files, which define the atom types and bonds in the simulation, whereas the dump file format serves as the output format storing the computed atom trajectories and other time-varying information.

To load such a pair of topology and trajectory files in OVITO, first open the topology file using the regular File ‣ Load File menu function. Then insert the Load trajectory modifier into the data pipeline and use the button highlighted in this screenshot to also load the corresponding trajectory file. Make sure you perform the last step in the user interface panel of the selected Load trajectory modifier and not in the original External file panel, which looks very similar and manages the initial topology file.

After loading the trajectory file in the Load trajectory panel, the modifier will subsequently replace the initial particle positions with the time-dependent positions read from the trajectory file. The same is done for the simulation cell geometry as well as any other auxiliary particle properties found in the trajectory file. Furthermore, the OVITO timeline will now display the animation frames found in the trajectory file.

## Particle ordering

The modifier needs to assign the coordinates read from the trajectory file to the corresponding particles from the topology dataset. In order to do this mapping correctly, the modifier uses the unique identifiers of particles (`Particle Identifier` property) if available. Otherwise, the modifier simply assumes that the storage order of particles in the topology and in the trajectory file is the same.

## Loading dynamic bonds/angles/dihedrals/impropers

The LAMMPS code supports reactive molecular dynamics simulations, in which the bond topology dynamically changes during the course of the simulation as bonds break or newly form. The changing bond connectivity in such simulations can be dumped to an output file using the dump local command of LAMMPS in combination with the compute property/local command, see the example below. In simulations using the ReaxFF potential, the fix reaxff/bonds command may be used to write the bonds list (including bond orders) to a text-based output file at regular time intervals.

OVITO’s Load trajectory modifier can read the varying bond topology from dump local or reaxff/bonds files and merge it with the molecular dataset. The loaded bonds list will replace any static connectivity that may have already been present in the initial LAMMPS data file. Typically, you will use two instances of the Load trajectory modifier in the same pipeline to load the atomic trajectories as well as the time-varying bond information from a reactive MD simulation:

Caution

Make sure that you dump the atomic trajectories and the bonds information at the exact same MD timesteps when running an MD simulation. OVITO does not use LAMMPS timesteps as a common time basis. It simply assumes that the atomic trajectory file and the bond topology file both contain snapshots taken at the exact same times, and each Load Trajectory modifier maps them sequentially to the program’s animation timeline without checking the consistency of the timestep information.

LAMMPS is able to output the changing bond topology at regular time intervals and also additional per-bond quantities such as the bond lengths, bond forces or bond energies. Consider, for example, the following LAMMPS commands, which dump the current bonds list to an output file in regular timestep intervals:

    compute 1 all property/local btype batom1 batom2
    compute 2 all bond/local dist engpot
    dump 1 all local 100 bonds.dump index c_1[*] c_2[*]

The `dump local` command generates a file named `bonds.dump` with six data columns:

    ITEM: ENTRIES index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
    1 10 24 33 1.02482 0.158356
    2 10 24 34 1.01407 0.0298494
    3  7 21 22 1.53167 0.000836934
    ...

When importing the file into OVITO using the Load trajectory modifier, you need to map these data columns to the correct bond properties so that the program can interpret the values in the LAMMPS dump file correctly. The following table shows what that mapping should look like:

Column | LAMMPS name | File column identifier | OVITO bond property
--- | --- | --- | ---
1 | index | index | (ignore)
2 | btype | c_1[1] | `Bond Type`
3 | batom1 | c_1[2] | `Particle Identifiers.1`
4 | batom2 | c_1[3] | `Particle Identifiers.2`
5 | dist | c_2[1] | `Length`
6 | engpot | c_2[2] | `Energy`

Tip

It is highly recommended to use the dump_modify colname command in LAMMPS to give the columns in your dump file meaningful names that can be automatically recognized by OVITO’s LAMMPS dump local file reader. The steps for this are described in the section Automatic column mapping.

In the previous example, the third and the fourth file column were mapped to the `Particle Identifiers` bond property, which signals OVITO that the dump local file contains a new set of bonds, replacing the initial (static) bond topology previously loaded from the LAMMPS data file.

If the dump local file doesn’t contain the batom1 and batom2 columns, then OVITO assumes that it doesn’t define a new bond topology. The Load trajectory will then simply add the stored values to the existing bonds in OVITO as new properties. The number of records in the dump local file must exactly match the number of existing bonds in this case.

Files written by the fix reaxff/bonds command have a different, fully specified format. OVITO can automatically map the information from such ReaxFF files to the right bond and particle properties, see the ReaxFF file reader documentation.

See also

- `ovito.modifiers.LoadTrajectoryModifier` (Python API)

- LAMMPS dump local file reader

- ReaxFF file reader