pymatgen.io.zeopp module

Module implementing classes and functions to use Zeo++ by Maciej Haranczyk.

If using this module, cite the following paper on Zeo++: T.F. Willems, C.H. Rycroft, M. Kazi, J.C. Meza, and M. Haranczyk, Algorithms and tools for high-throughput geometry-based analysis of crystalline porous materials, Microporous and Mesoporous Materials, 149 (2012) 134-141.

Zeo++ Installation Steps:

A stable version of Zeo++ can be obtained from http://zeoplusplus.org. Instructions can be found at http://www.zeoplusplus.org/download.html

Zeo++ Post-Installation Checking:

  1. Go to pymatgen/io/tests and run “python test_zeoio.py” If Zeo++ python bindings are properly installed, the tests should pass. One or two tests will be skipped.

  1. Go to pymatgen/analysis/defects/tests and run “python test_point_defects.py”. Lots of tests will be skipped if GULP is not installed. But there should be no errors.

class ZeoCssr(structure)[source]

Bases: Cssr

ZeoCssr adds extra fields to CSSR sites to conform with Zeo++ input CSSR format. The coordinate system is rotated from xyz to zyx. This change aligns the pivot axis of pymatgen (z-axis) to pivot axis of Zeo++ (x-axis) for structurural modifications.

Parameters:

structure – A structure to create ZeoCssr object

static from_file(filename)[source]

Reads a CSSR file to a ZeoCssr object.

Parameters:

filename – Filename to read from.

Returns:

ZeoCssr object.

static from_string(string)[source]

Reads a string representation to a ZeoCssr object.

Parameters:

string – A string representation of a ZeoCSSR.

Returns:

ZeoCssr object.

class ZeoVoronoiXYZ(mol)[source]

Bases: XYZ

Class to read Voronoi Nodes from XYZ file written by Zeo++. The sites have an additional column representing the voronoi node radius. The voronoi node radius is represented by the site property voronoi_radius.

Parameters:

mol – Input molecule holding the voronoi node information

static from_file(filename)[source]

Creates XYZ object from a file.

Parameters:

filename – XYZ filename

Returns:

XYZ object

static from_string(contents)[source]

Creates Zeo++ Voronoi XYZ object from a string. from_string method of XYZ class is being redefined.

Parameters:

contents – String representing Zeo++ Voronoi XYZ file.

Returns:

ZeoVoronoiXYZ object

get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1)[source]

Analyze the void space in the input structure using voronoi decomposition Calls Zeo++ for Voronoi decomposition.

Parameters:

  • structure – pymatgen.core.structure.Structure

  • rad_dict (optional) – Dictionary of radii of elements in structure. If not given, Zeo++ default values are used. Note: Zeo++ uses atomic radii of elements. For ionic structures, pass rad_dict with ionic radii

  • probe_rad (optional) – Sampling probe radius in Angstroms. Default is 0.1 A

Returns:

voronoi nodes as pymatgen.core.structure.Structure within the unit cell defined by the lattice of input structure voronoi face centers as pymatgen.core.structure.Structure within the unit cell defined by the lattice of input structure

get_high_accuracy_voronoi_nodes(structure, rad_dict, probe_rad=0.1)[source]

Analyze the void space in the input structure using high accuracy voronoi decomposition. Calls Zeo++ for Voronoi decomposition.

Parameters:

  • structure – pymatgen.core.structure.Structure

  • rad_dict (optional) – Dictionary of radii of elements in structure. If not given, Zeo++ default values are used. Note: Zeo++ uses atomic radii of elements. For ionic structures, pass rad_dict with ionic radii

  • probe_rad (optional) – Sampling probe radius in Angstroms. Default is 0.1 A

Returns:

voronoi nodes as pymatgen.core.structure.Structure within the unit cell defined by the lattice of input structure voronoi face centers as pymatgen.core.structure.Structure within the unit cell defined by the lattice of input structure

get_void_volume_surfarea(structure, rad_dict=None, chan_rad=0.3, probe_rad=0.1)[source]

Computes the volume and surface area of isolated void using Zeo++. Useful to compute the volume and surface area of vacant site.

Parameters:

  • structure – pymatgen Structure containing vacancy

  • rad_dict (optional) – Dictionary with short name of elements and their radii.

  • chan_rad (optional) – Minimum channel Radius.

  • probe_rad (optional) – Probe radius for Monte Carlo sampling.

Returns:

floating number representing the volume of void

Return type:

volume

get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1)[source]

Analyze the void space in the input structure using voronoi decomposition Calls Zeo++ for Voronoi decomposition.

Parameters:

  • structure – pymatgen.core.structure.Structure

  • rad_dict (optional) – Dictionary of radii of elements in structure. If not given, Zeo++ default values are used. Note: Zeo++ uses atomic radii of elements. For ionic structures, pass rad_dict with ionic radii

  • probe_rad (optional) – Sampling probe radius in Angstroms. Default is 0.1 A

Returns:

voronoi nodes as pymatgen.core.structure.Structure within the unit cell defined by the lattice of input structure voronoi face centers as pymatgen.core.structure.Structure within the unit cell defined by the lattice of input structure