httk.io

Submodules

• httk.io.cif
• httk.io.vasp

Functions

read_cif(fs[, pragmatic, allow_cif2, use_types])	Generic cif reader, given a filename / ioadapter it places all data in a python dictionary.
read_poscar(→ dict[str, Any])	Parse a VASP POSCAR/CONTCAR into a neutral, string-preserving mapping.

Package Contents

httk.io.read_cif(fs, pragmatic=True, allow_cif2=False, use_types=False)

Generic cif reader, given a filename / ioadapter it places all data in a python dictionary.

It returns a tuple: (header, list) Where list are pairs of data blocks names and data blocks

Each data block is a dictionary with tag_name:value

For loops, value is another dictionary with format column_name:value

The optional parameter pragmatic regulates handling of some counter-intuitive aspects of the cif specification, where the default pragmatic=True handles these features the way people usually use them, whereas pragmatic=False means to read the cif file precisely according to the spec. For example, in a multiline text field:

;
some text
;

Means the string ‘nsome text’. For this specific case pragmatic=True removes the leading newline.

set use_types to True to convert things that look like floats and integers to those respective types

A filename (str or os.PathLike) is opened through httk.core.TextstreamFileView, so a compressed file (.cif.bz2, .cif.gz, …) is decompressed transparently. An already-open text stream or a plain iterable of lines is consumed as-is and left open for the caller.

httk.io.read_poscar(source: Any) → dict[str, Any]

Parse a VASP POSCAR/CONTCAR into a neutral, string-preserving mapping.

source may be a filename (str or os.PathLike, opened through httk.core.TextstreamFileView so compressed files such as CONTCAR.bz2 are decompressed transparently) or an already-open text stream / iterable of lines.

The returned mapping has the keys format (always "vasp-poscar"), comment, scale and volume (exactly one is a string, the other None), cell (a 3x3 list of coordinate strings), symbols (list[str] for VASP-5, None for VASP-4), counts (list[int]), cartesian (bool), coords (an N``x3 list of strings), and ``selective_dynamics (an N``x3 list of booleans when the file declares selective dynamics, else ``None). Malformed input raises a clear ValueError naming the offending line.