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)[source]
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)[source]
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)[source]
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)