pymatgen.io.xr module

This module provides input and output mechanisms for the xr file format, which is a modified CSSR file format and, for example, used in GULP. In particular, the module makes it easy to remove shell positions from relaxations that employed core-shell models.

class Xr(structure)

Bases: object

Basic object for working with xr files.

Parameters

structure (Structure/IStructure) – Structure object to create the Xr object.

static from_file(filename, use_cores=True, thresh=0.0001)

Reads an xr-formatted file to create an Xr object.

Parameters

• filename (str) – name of file to read from.

• use_cores (bool) – use core positions and discard shell positions if set to True (default). Otherwise, use shell positions and discard core positions.

• thresh (float) – relative threshold for consistency check between cell parameters (lengths and angles) from header information and cell vectors, respectively.

Returns

Xr object corresponding to the input

file.

Return type

xr (Xr)

static from_string(string, use_cores=True, thresh=0.0001)

Creates an Xr object from a string representation.

Parameters

• string (str) – string representation of an Xr object.

• use_cores (bool) – use core positions and discard shell positions if set to True (default). Otherwise, use shell positions and discard core positions.

• thresh (float) – relative threshold for consistency check between cell parameters (lengths and angles) from header information and cell vectors, respectively.

Returns

Xr object corresponding to the input

string representation.

Return type

xr (Xr)

write_file(filename)

Write out an xr file.

Parameters

filename (str) – name of the file to write to.