`dump_observer`¶

Writes atomistic properties such as positions, velocities and forces for each of the supplied NEP potentials in the extended XYZ format. Takes the same arguments as dump_exyz keyword, and additionally a keyword mode. mode can either be set to observe or average.

If set to observe, the first of the supplied NEP potentials will be used to propagate the molecular dynamics run, and the remaining potentials will be evaluated every interval_thermo and interval_exyz time steps. Every interval_thermo timesteps files in the style of thermo.out will be written, and every interval_exyz timesteps extended XYZ-files will be written. The files are named according to the following convention:

.out: observer0.out, observer1.out, …, observer(N-1).out for N supplied potentials.
.xyz: observer0.xyz, observer1.xyz, …, observer(N-1).xyz for N supplied potentials.

The index of these observer(index) files correspond to the index of each potential in the run.in file. Thus, observer0 corresponds to the first potential, observer1 to the second and so on. In this mode, observer0 corresponds to the main potential.

If set to average, all supplied NEP potentials will be evaluated at every timestep, with the average of all potentials used to propagate the molecular dynamics. In this case, two files will be written: observer.out every interval_thermo timesteps, and observer.xyz every interval_exyz timesteps. These files contains the thermo and atomistic properties as calculated with the average potential.

Note that the supplied potentials must have their atomic species written in the same order, i.e. the line nep* n_species species0 species1 must be the same in all potential files.

Syntax¶

dump_observer <mode> <interval_thermo> <interval_exyz> <has_velocity> <has_force>

mode corresponds to the two cases described above, and can be either observe or average. interval_thermo parameter is the output interval (number of steps) for writing thermo files. interval_exyz parameter is the output interval (number of steps) of writing exyz files. has_velocity can be 1 or 0, which means the velocities will or will not be included in the exyz output. has_force can be 1 or 0, which means the forces will or will not be included in the exyz output.

Examples¶

Example 1¶

To use one NEP potential to propagate the MD (nep0), and another (nep1) to observe thermo properties every 100 steps and write exyz files every 1000 steps, write:

potential nep0
potential nep1
...
dump_observer observe 100 1000 1 1

before the run keyword. This will generate four output files, observer0.xyz, observer0.out, observer1.xyz and observer1.out, containing thermo properties and positions, velocities and forces as calculated with nep0 and nep1 respectively.

Example 2¶

To run MD with an average of two NEP potentials, nep0 and nep1, and dump the positions, velocities and forces every 1000 steps, write:

potential nep0
potential nep1
...
dump_observer average 100 1000 1 1

before the run keyword. This will generate two output files, observer.out containing thermo properties and observer.xyz, containing positions, velocities and forces as calculated with the average of nep0 and nep1. observer.out will be written every 100 timesteps, and observer.xyz every 1000 timesteps.

Caveats¶

This keyword is not propagating. That means, its effect will not be passed from one run to the next.
If mode is set to observe, then the output file has an appending behavior and will result in two files, observer(index).out and observer(index).xyz file for each potential no matter how many times the simulation is run.
If mode is set to average, then the output file has an appending behavior and will result in a single observer.xyz file no matter how many times the simulation is run.

dump_observer¶