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.