Analysis Input Files¶

RDF, MSD, VACF and vibrational analyses use a compact key-value format parsed with Lark. Each analysis documents its required and optional keys in the generated command and input-reader reference.

Inline statements¶

An inline statement assigns one value to one key:

key = value

Several assignments may share a line when separated by commas:

window = 1000, gap = 10, time_step = 0.001

Use separate lines for scientific input files unless a compact generated file is required; one assignment per line is easier to review and diff.

Multiline lists¶

A key followed by values on subsequent lines creates a list. Terminate the list with END:

traj_files
trajectory-001.xyz
trajectory-002.xyz
trajectory-003.xyz
END

Multiline syntax always produces a list-like value. Use inline syntax for keys that accept only a scalar.

Comments and case¶

Keys are case-insensitive. The closing END token must be uppercase. Values remain case-sensitive because they may contain filenames or selection expressions. Leading and trailing whitespace is ignored. # starts a comment, including at the end of a statement:

target_selection = O  # oxygen atoms

Value conversion¶

The parser converts strings to the type required by each documented key. Common forms include:

Input	Parsed form	Notes
`True` or `False`	Boolean	Case-insensitive
`1`	Integer	May also satisfy a real-valued key
`1.0`	Floating-point number	Scientific notation is accepted where numeric keys permit it
`[1, 2, 3]`	List	Elements must have compatible types
`1..4` or `1-4`	`range(1, 4)`	The stop value follows Python’s exclusive convention
`1..3..10` or `1-3-10`	`range(1, 10, 3)`	The middle value is the step
`frame-*.xyz`	Matching file list	Expanded with Python glob semantics

Filenames¶

Relative filenames in an input file, including outputs and glob patterns, are interpreted from the directory that contains the input file, so pqanalysis rdf runs/water/rdf.in reads runs/water/trajectory.xyz and writes runs/water/rdf.dat whatever the working directory is. Absolute filenames are used as written. Command-line arguments such as --export are resolved from the working directory, as in any shell command. The ordinary filename grammar accepts letters, digits, _, -, . and /; * provides glob matching.

Complete example¶

# oxygen-hydrogen radial distribution
traj_files
run-001.xyz
run-002.xyz
END

reference_selection = O
target_selection = H
delta_r = 0.05
r_max = 8.0
out_file = rdf.dat

Run it with:

$ pqanalysis rdf rdf.in

See Analyses for analysis-specific examples and Analysis Output Files for output formats and scientific schemas.