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# coding: utf-8 

# Copyright (c) Pymatgen Development Team. 

# Distributed under the terms of the MIT License. 

 

from __future__ import division, unicode_literals, print_function 

 

""" 

Module implementing classes and functions to use Zeo++. 

Zeo++ can be obtained from http://www.maciejharanczyk.info/Zeopp/ 

""" 

 

from six.moves import map 

 

__author__ = "Bharat Medasani" 

__copyright = "Copyright 2013, The Materials Project" 

__version__ = "0.1" 

__maintainer__ = "Bharat Medasani" 

__email__ = "bkmedasani@lbl.gov" 

__data__ = "Aug 2, 2013" 

 

import os 

import re 

 

from monty.io import zopen 

from monty.dev import requires 

from monty.tempfile import ScratchDir 

 

from pymatgen.core.structure import Structure, Molecule 

from pymatgen.core.lattice import Lattice 

from pymatgen.io.cssr import Cssr 

from pymatgen.io.xyz import XYZ 

 

try: 

from zeo.netstorage import AtomNetwork, VoronoiNetwork 

from zeo.area_volume import volume, surface_area 

from zeo.cluster import get_nearest_largest_diameter_highaccuracy_vornode,\ 

generate_simplified_highaccuracy_voronoi_network, \ 

prune_voronoi_network_close_node 

zeo_found = True 

except ImportError: 

zeo_found = False 

 

 

class ZeoCssr(Cssr): 

""" 

ZeoCssr adds extra fields to CSSR sites to conform with Zeo++ 

input CSSR format. The coordinate system is rorated from xyz to zyx. 

This change aligns the pivot axis of pymatgen (z-axis) to pivot axis 

of Zeo++ (x-axis) for structurural modifications. 

 

Args: 

structure: A structure to create ZeoCssr object 

""" 

 

def __init__(self, structure): 

super(ZeoCssr, self).__init__(structure) 

 

def __str__(self): 

""" 

CSSR.__str__ method is modified to padd 0's to the CSSR site data. 

The padding is to conform with the CSSR format supported Zeo++. 

The oxidation state is stripped from site.specie 

Also coordinate system is rotated from xyz to zxy 

""" 

output = [ 

"{:.4f} {:.4f} {:.4f}" 

#.format(*self.structure.lattice.abc), 

.format(self.structure.lattice.c, 

self.structure.lattice.a, 

self.structure.lattice.b), 

"{:.2f} {:.2f} {:.2f} SPGR = 1 P 1 OPT = 1" 

#.format(*self.structure.lattice.angles), 

.format(self.structure.lattice.gamma, 

self.structure.lattice.alpha, 

self.structure.lattice.beta), 

"{} 0".format(len(self.structure)), 

"0 {}".format(self.structure.formula) 

] 

for i, site in enumerate(self.structure.sites): 

#if not hasattr(site, 'charge'): 

# charge = 0 

#else: 

# charge = site.charge 

charge = site.charge if hasattr(site, 'charge') else 0 

#specie = site.specie.symbol 

specie = site.species_string 

output.append( 

"{} {} {:.4f} {:.4f} {:.4f} 0 0 0 0 0 0 0 0 {:.4f}" 

.format( 

i+1, specie, site.c, site.a, site.b, charge 

#i+1, site.specie, site.a, site.b, site.c, site.charge 

) 

) 

 

return "\n".join(output) 

 

@staticmethod 

def from_string(string): 

""" 

Reads a string representation to a ZeoCssr object. 

 

Args: 

string: A string representation of a ZeoCSSR. 

 

Returns: 

ZeoCssr object. 

""" 

lines = string.split("\n") 

toks = lines[0].split() 

lengths = [float(i) for i in toks] 

toks = lines[1].split() 

angles = [float(i) for i in toks[0:3]] 

# Zeo++ takes x-axis along a and pymatgen takes z-axis along c 

a = lengths.pop(-1) 

lengths.insert(0, a) 

alpha = angles.pop(-1) 

angles.insert(0, alpha) 

latt = Lattice.from_lengths_and_angles(lengths, angles) 

sp = [] 

coords = [] 

chrg = [] 

for l in lines[4:]: 

m = re.match("\d+\s+(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+" + 

"([0-9\-\.]+)\s+(?:0\s+){8}([0-9\-\.]+)", l.strip()) 

if m: 

sp.append(m.group(1)) 

#coords.append([float(m.group(i)) for i in xrange(2, 5)]) 

# Zeo++ takes x-axis along a and pymatgen takes z-axis along c 

coords.append([float(m.group(i)) for i in [3, 4, 2]]) 

chrg.append(m.group(5)) 

return ZeoCssr( 

Structure(latt, sp, coords, site_properties={'charge': chrg}) 

) 

 

@staticmethod 

def from_file(filename): 

""" 

Reads a CSSR file to a ZeoCssr object. 

 

Args: 

filename: Filename to read from. 

 

Returns: 

ZeoCssr object. 

""" 

with zopen(filename, "r") as f: 

return ZeoCssr.from_string(f.read()) 

 

 

class ZeoVoronoiXYZ(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. 

 

Args: 

mol: Input molecule holding the voronoi node information 

""" 

 

def __init__(self, mol): 

super(ZeoVoronoiXYZ, self).__init__(mol) 

 

@staticmethod 

def from_string(contents): 

""" 

Creates Zeo++ Voronoi XYZ object from a string. 

from_string method of XYZ class is being redefined. 

 

Args: 

contents: String representing Zeo++ Voronoi XYZ file. 

 

Returns: 

ZeoVoronoiXYZ object 

""" 

lines = contents.split("\n") 

num_sites = int(lines[0]) 

coords = [] 

sp = [] 

prop = [] 

coord_patt = re.compile( 

"(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+" + 

"([0-9\-\.]+)" 

) 

for i in range(2, 2 + num_sites): 

m = coord_patt.search(lines[i]) 

if m: 

sp.append(m.group(1)) # this is 1-indexed 

#coords.append(map(float, m.groups()[1:4])) # this is 0-indexed 

coords.append([float(j) 

for j in [m.group(i) for i in [3, 4, 2]]]) 

prop.append(float(m.group(5))) 

return ZeoVoronoiXYZ( 

Molecule(sp, coords, site_properties={'voronoi_radius': prop}) 

) 

 

@staticmethod 

def from_file(filename): 

""" 

Creates XYZ object from a file. 

 

Args: 

filename: XYZ filename 

 

Returns: 

XYZ object 

""" 

with zopen(filename) as f: 

return ZeoVoronoiXYZ.from_string(f.read()) 

 

def __str__(self): 

output = [str(len(self._mol)), self._mol.composition.formula] 

fmtstr = "{{}} {{:.{0}f}} {{:.{0}f}} {{:.{0}f}} {{:.{0}f}}".format( 

self.precision 

) 

for site in self._mol: 

output.append(fmtstr.format( 

site.specie.symbol, site.z, site.x, site.y, 

#site.specie, site.x, site.y, site.z, 

site.properties['voronoi_radius'] 

)) 

return "\n".join(output) 

 

@requires(zeo_found, 

"get_voronoi_nodes requires Zeo++ cython extension to be " 

"installed. Please contact developers of Zeo++ to obtain it.") 

def get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1): 

""" 

Analyze the void space in the input structure using voronoi decomposition 

Calls Zeo++ for Voronoi decomposition. 

 

Args: 

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.Strucutre within the 

unit cell defined by the lattice of input structure 

voronoi face centers as pymatgen.core.structure.Strucutre within the 

unit cell defined by the lattice of input structure 

""" 

 

with ScratchDir('.'): 

name = "temp_zeo1" 

zeo_inp_filename = name + ".cssr" 

ZeoCssr(structure).write_file(zeo_inp_filename) 

rad_file = None 

rad_flag = False 

 

if rad_dict: 

rad_file = name + ".rad" 

rad_flag = True 

with open(rad_file, 'w+') as fp: 

for el in rad_dict.keys(): 

fp.write("{} {}\n".format(el, rad_dict[el].real)) 

 

atmnet = AtomNetwork.read_from_CSSR( 

zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file) 

vornet, vor_edge_centers, vor_face_centers = \ 

atmnet.perform_voronoi_decomposition() 

vornet.analyze_writeto_XYZ(name, probe_rad, atmnet) 

voro_out_filename = name + '_voro.xyz' 

voro_node_mol = ZeoVoronoiXYZ.from_file(voro_out_filename).molecule 

 

species = ["X"] * len(voro_node_mol.sites) 

coords = [] 

prop = [] 

for site in voro_node_mol.sites: 

coords.append(list(site.coords)) 

prop.append(site.properties['voronoi_radius']) 

 

lattice = Lattice.from_lengths_and_angles( 

structure.lattice.abc, structure.lattice.angles) 

vor_node_struct = Structure( 

lattice, species, coords, coords_are_cartesian=True, 

to_unit_cell=True, site_properties={"voronoi_radius": prop}) 

 

 

#PMG-Zeo c<->a transformation for voronoi face centers 

rot_face_centers = [(center[1],center[2],center[0]) for center in 

vor_face_centers] 

rot_edge_centers = [(center[1],center[2],center[0]) for center in 

vor_edge_centers] 

 

species = ["X"] * len(rot_face_centers) 

prop = [0.0] * len(rot_face_centers) # Vor radius not evaluated for fc 

vor_facecenter_struct = Structure( 

lattice, species, rot_face_centers, coords_are_cartesian=True, 

to_unit_cell=True, site_properties={"voronoi_radius": prop}) 

 

species = ["X"] * len(rot_edge_centers) 

prop = [0.0] * len(rot_edge_centers) # Vor radius not evaluated for fc 

vor_edgecenter_struct = Structure( 

lattice, species, rot_edge_centers, coords_are_cartesian=True, 

to_unit_cell=True, site_properties={"voronoi_radius": prop}) 

 

return vor_node_struct, vor_edgecenter_struct, vor_facecenter_struct 

 

def get_high_accuracy_voronoi_nodes(structure, rad_dict, probe_rad=0.1): 

""" 

Analyze the void space in the input structure using high accuracy 

voronoi decomposition. 

Calls Zeo++ for Voronoi decomposition. 

 

Args: 

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.Strucutre within the 

unit cell defined by the lattice of input structure 

voronoi face centers as pymatgen.core.structure.Strucutre within the 

unit cell defined by the lattice of input structure 

""" 

 

with ScratchDir('.'): 

name = "temp_zeo1" 

zeo_inp_filename = name + ".cssr" 

ZeoCssr(structure).write_file(zeo_inp_filename) 

rad_flag = True 

rad_file = name + ".rad" 

with open(rad_file, 'w+') as fp: 

for el in rad_dict.keys(): 

print("{} {}".format(el, rad_dict[el].real), file=fp) 

 

atmnet = AtomNetwork.read_from_CSSR( 

zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file) 

#vornet, vor_edge_centers, vor_face_centers = \ 

# atmnet.perform_voronoi_decomposition() 

red_ha_vornet = \ 

prune_voronoi_network_close_node(atmnet) 

#generate_simplified_highaccuracy_voronoi_network(atmnet) 

#get_nearest_largest_diameter_highaccuracy_vornode(atmnet) 

red_ha_vornet.analyze_writeto_XYZ(name, probe_rad, atmnet) 

voro_out_filename = name + '_voro.xyz' 

voro_node_mol = ZeoVoronoiXYZ.from_file(voro_out_filename).molecule 

 

species = ["X"] * len(voro_node_mol.sites) 

coords = [] 

prop = [] 

for site in voro_node_mol.sites: 

coords.append(list(site.coords)) 

prop.append(site.properties['voronoi_radius']) 

 

lattice = Lattice.from_lengths_and_angles( 

structure.lattice.abc, structure.lattice.angles) 

vor_node_struct = Structure( 

lattice, species, coords, coords_are_cartesian=True, 

to_unit_cell=True, site_properties={"voronoi_radius": prop}) 

 

return vor_node_struct 

 

@requires(zeo_found, 

"get_voronoi_nodes requires Zeo++ cython extension to be " 

"installed. Please contact developers of Zeo++ to obtain it.") 

def get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1): 

""" 

Analyze the void space in the input structure using voronoi decomposition 

Calls Zeo++ for Voronoi decomposition. 

 

Args: 

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.Strucutre within the 

unit cell defined by the lattice of input structure 

voronoi face centers as pymatgen.core.structure.Strucutre within the 

unit cell defined by the lattice of input structure 

""" 

 

with ScratchDir('.'): 

name = "temp_zeo1" 

zeo_inp_filename = name + ".cssr" 

ZeoCssr(structure).write_file(zeo_inp_filename) 

rad_file = None 

rad_flag = False 

 

if rad_dict: 

rad_file = name + ".rad" 

rad_flag = True 

with open(rad_file, 'w+') as fp: 

for el in rad_dict.keys(): 

fp.write("{} {}\n".format(el, rad_dict[el].real)) 

 

atmnet = AtomNetwork.read_from_CSSR( 

zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file) 

out_file = "temp.res" 

atmnet.calculate_free_sphere_parameters(out_file) 

if os.path.isfile(out_file) and os.path.getsize(out_file) > 0: 

with open(out_file) as fp: 

output = fp.readline() 

else: 

output = "" 

fields = [val.strip() for val in output.split()][1:4] 

if len(fields) == 3: 

fields = [float(field) for field in fields] 

free_sphere_params = {'inc_sph_max_dia':fields[0], 

'free_sph_max_dia':fields[1], 

'inc_sph_along_free_sph_path_max_dia':fields[2]} 

return free_sphere_params 

 

 

# Deprecated. Not needed anymore 

def get_void_volume_surfarea(structure, rad_dict=None, chan_rad=0.3, 

probe_rad=0.1): 

""" 

Computes the volume and surface area of isolated void using Zeo++. 

Useful to compute the volume and surface area of vacant site. 

 

Args: 

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: 

volume: floating number representing the volume of void 

""" 

with ScratchDir('.'): 

name = "temp_zeo" 

zeo_inp_filename = name + ".cssr" 

ZeoCssr(structure).write_file(zeo_inp_filename) 

 

rad_file = None 

if rad_dict: 

rad_file = name + ".rad" 

with open(rad_file, 'w') as fp: 

for el in rad_dict.keys(): 

fp.write("{0} {1}".format(el, rad_dict[el])) 

 

atmnet = AtomNetwork.read_from_CSSR(zeo_inp_filename, True, rad_file) 

vol_str = volume(atmnet, 0.3, probe_rad, 10000) 

sa_str = surface_area(atmnet, 0.3, probe_rad, 10000) 

vol = None 

sa = None 

for line in vol_str.split("\n"): 

if "Number_of_pockets" in line: 

fields = line.split() 

if float(fields[1]) > 1: 

vol = -1.0 

break 

if float(fields[1]) == 0: 

vol = -1.0 

break 

vol = float(fields[3]) 

for line in sa_str.split("\n"): 

if "Number_of_pockets" in line: 

fields = line.split() 

if float(fields[1]) > 1: 

#raise ValueError("Too many voids") 

sa = -1.0 

break 

if float(fields[1]) == 0: 

sa = -1.0 

break 

sa = float(fields[3]) 

 

if not vol or not sa: 

raise ValueError("Error in zeo++ output stream") 

return vol, sa