User Guide
Command Line Interface
The PQAnalysis package does not only provide an API but also a number of different command line tools. These tools can be categorized into two groups primary groups: pure command line tools and tools that are based on an input file.
Input file based tools
For more details on the grammar and syntax of the input file see Input File.
RDF input files
Basic RDF calculations only need a trajectory, selections, bin settings, and an output file. A restart file is not required for this case:
reference_selection = H
target_selection = O
delta_r = 0.05
out_file = rdf.out
traj_files = trajectory.xyz
Restart files and moldescriptor files are only needed when the calculation
requires molecular topology information. For example,
no_intra_molecular = True excludes pairs from the same molecule.
If the files are not given explicitly, PQAnalysis tries to infer
trajectory.rst from trajectory.xyz and
moldescriptor.dat from the trajectory directory:
reference_selection = H
target_selection = O
delta_r = 0.05
out_file = rdf_inter.out
traj_files = trajectory.xyz
no_intra_molecular = True
Explicit restart_file and moldescriptor_file values are used
as-is. If both files are given and no_intra_molecular is omitted,
no_intra_molecular defaults to True. If
no_intra_molecular is set to False, intra molecular pairs are
included. Inferred and defaulted values are written to the normal PQAnalysis
log output.