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 -f dump.xyz --trajectory-format=extxyz --outfile=output.npz

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 -f dump.xyz --trajectory-format=extxyz --q-sampling="line" --q-direction=10,0,0 --q-points=100 --outfile=output.npz

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

dynasor -f dump.xyz --trajectory-format=extxyz --q-sampling="isotropic" --q-max=10 --q-bins=100 --max-q-points=20000 --outfile=output.npz

Time sampling options

For example, the command

dynasor ... --time-window=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 tutorials section contains more examples for how to use dynasor via the command line.

Output options

The output files are written as NumPy NPZ files. For example, use:

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

These output files 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