Command line interface

dynasor can be run via the command line and expects a number of input parameters. To show all available options run:

dynasor --help

Trajectory options

You need to specify the format of your trajectory via the –trajectory-format flag, for example,

dynasor dump.xyz --trajectory-format=extxyz

would use the internal xyz reader (for more info see the workflow page).

q-point sampling options

For example, to sample along a specific path in \(\boldsymbol{q}\)-space, one can run

dynasor dump.xyz --trajectory-format=extxyz --q-sampling="line" --q-direction=10,0,0 --q-points=100 --q-bins=100

or, to conduct a spherical average over \(\boldsymbol{q}\)-points, one can run

dynasor dump.xyz --trajectory-format=extxyz --q-sampling="isotropic" --q-max=10 --q-bins=100 --max_q_points=20000

Time sampling options

For example, the command

dynasor ... --nt=500 --max-frames=2000

implies that correlation functions are calculated for frames separated by up to 500 frames. This window is moved over the trajectory until it reaches frame number max-frames.

The examples section contains more examples for how to use dynasor via the command line.

Output options

The output files can be written in the form of numpy npy-files. For example use as

dynasor -f dump.atom --outfile=output.npy

These output functions can be easily read in python using the read_sample_from_npz function or numpy directly.

Incoherent intermediate scattering function and current correlations

The incoherent intermediate scattering function is not evaluated by default but can be calculated by adding the --calculate-incoherent option

dynasor ... --calculate-incoherent

Similarly the current (velocity) correlation functions are calculated by

dynasor ... --calculate-currents