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.

Three further keys report how precisely the file wrote its numbers, each the coarsest claim among the tokens it covers, or None when none of them claim anything: cell_precision, scale_precision, and coordinate_precision. They are the precisions of the tokens as written, deliberately not converted: the cell vectors are still to be multiplied by the scaling factor, and the coordinates may be Cartesian or fractional depending on cartesian. Doing that conversion needs the assembled cell, so it belongs to whoever builds the structure — httk.atomistic.structure_from_poscar() — not to the reader.