Source code for pymatgen.io.exciting.inputs

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

"""
Classes for reading/manipulating/writing exciting input files.
"""

import numpy as np

from monty.io import zopen

import xml.etree.cElementTree as ET

import scipy.constants as const

from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.core.periodic_table import Element
from monty.json import MSONable

from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.symmetry.bandstructure import HighSymmKpath

__author__ = "Christian Vorwerk"
__copyright__ = "Copyright 2016"
__version__ = "1.0"
__maintainer__ = "Christian Vorwerk"
__email__ = "vorwerk@physik.hu-berlin.de"
__status__ = "Development"
__date__ = "Nov 28, 2016"


[docs]class ExcitingInput(MSONable): """ Object for representing the data stored in the structure part of the exciting input. .. attribute:: structure Associated Structure. .. attribute:: title Optional title string. .. attribute:: lockxyz Lockxyz attribute for each site if available. A Nx3 array of booleans. """ def __init__(self, structure, title=None, lockxyz=None): """ Args: structure (Structure): Structure object. title (str): Optional title for exciting input. Defaults to unit cell formula of structure. Defaults to None. lockxyz (Nx3 array): bool values for selective dynamics, where N is number of sites. Defaults to None. """ if structure.is_ordered: site_properties = {} if lockxyz: site_properties["selective_dynamics"] = lockxyz self.structure = structure.copy(site_properties=site_properties) self.title = structure.formula if title is None else title else: raise ValueError("Structure with partial occupancies cannot be " "converted into exciting input!") # define conversion factor between Bohr radius and Angstrom bohr2ang = const.value('Bohr radius') / const.value('Angstrom star') @property def lockxyz(self): """ :return: Selective dynamics site properties. """ return self.structure.site_properties.get("selective_dynamics") @lockxyz.setter def lockxyz(self, lockxyz): self.structure.add_site_property("selective_dynamics", lockxyz)
[docs] @staticmethod def from_string(data): """ Reads the exciting input from a string """ root = ET.fromstring(data) speciesnode = root.find('structure').iter('species') elements = [] positions = [] vectors = [] lockxyz = [] # get title title_in = str(root.find('title').text) # Read elements and coordinates for nodes in speciesnode: symbol = nodes.get('speciesfile').split('.')[0] if len(symbol.split('_')) == 2: symbol = symbol.split('_')[0] if Element.is_valid_symbol(symbol): # Try to recognize the element symbol element = symbol else: raise ValueError("Unknown element!") for atom in nodes.iter('atom'): x, y, z = atom.get('coord').split() positions.append([float(x), float(y), float(z)]) elements.append(element) # Obtain lockxyz for each atom if atom.get('lockxyz') is not None: lxyz = [] for l in atom.get('lockxyz').split(): if l == 'True' or l == 'true': lxyz.append(True) else: lxyz.append(False) lockxyz.append(lxyz) else: lockxyz.append([False, False, False]) # check the atomic positions type if 'cartesian' in root.find('structure').attrib.keys(): if root.find('structure').attrib['cartesian']: cartesian = True for i in range(len(positions)): for j in range(3): positions[i][j] = positions[i][j] * ExcitingInput.bohr2ang print(positions) else: cartesian = False # get the scale attribute scale_in = root.find('structure').find('crystal').get('scale') if scale_in: scale = float(scale_in) * ExcitingInput.bohr2ang else: scale = ExcitingInput.bohr2ang # get the stretch attribute stretch_in = root.find('structure').find('crystal').get('stretch') if stretch_in: stretch = np.array([float(a) for a in stretch_in]) else: stretch = np.array([1.0, 1.0, 1.0]) # get basis vectors and scale them accordingly basisnode = root.find('structure').find('crystal').iter('basevect') for vect in basisnode: x, y, z = vect.text.split() vectors.append([float(x) * stretch[0] * scale, float(y) * stretch[1] * scale, float(z) * stretch[2] * scale]) # create lattice and structure object lattice_in = Lattice(vectors) structure_in = Structure(lattice_in, elements, positions, coords_are_cartesian=cartesian) return ExcitingInput(structure_in, title_in, lockxyz)
[docs] @staticmethod def from_file(filename): """ :param filename: Filename :return: ExcitingInput """ with zopen(filename, 'rt') as f: data = f.read().replace('\n', '') return ExcitingInput.from_string(data)
[docs] def write_etree(self, celltype, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5): """ :param celltype: :param cartesian: :param bandstr: :param symprec: :param angle_tolerance: :return: """ root = ET.Element('input') root.set('{http://www.w3.org/2001/XMLSchema-instance}noNamespaceSchemaLocation', 'http://xml.exciting-code.org/excitinginput.xsd') title = ET.SubElement(root, 'title') title.text = self.title if cartesian: structure = ET.SubElement(root, 'structure', cartesian="true", speciespath="./") else: structure = ET.SubElement(root, 'structure', speciespath="./") crystal = ET.SubElement(structure, 'crystal') # set scale such that lattice vector can be given in Angstrom ang2bohr = const.value('Angstrom star') / const.value('Bohr radius') crystal.set('scale', str(ang2bohr)) # determine which structure to use finder = SpacegroupAnalyzer(self.structure, symprec=symprec, angle_tolerance=angle_tolerance) if celltype == 'primitive': new_struct = finder.get_primitive_standard_structure(international_monoclinic=False) elif celltype == 'conventional': new_struct = finder.get_conventional_standard_structure(international_monoclinic=False) elif celltype == 'unchanged': new_struct = self.structure else: raise ValueError('Type of unit cell not recognized!') # write lattice basis = new_struct.lattice.matrix for i in range(3): basevect = ET.SubElement(crystal, 'basevect') basevect.text = "%16.8f %16.8f %16.8f" % (basis[i][0], basis[i][1], basis[i][2]) # write atomic positions for each species index = 0 for i in sorted(new_struct.types_of_specie, key=lambda el: el.X): species = ET.SubElement(structure, 'species', speciesfile=i.symbol + '.xml') sites = new_struct.indices_from_symbol(i.symbol) for j in sites: coord = "%16.8f %16.8f %16.8f" % (new_struct[j].frac_coords[0], new_struct[j].frac_coords[1], new_struct[j].frac_coords[2]) # obtain cartesian coords from fractional ones if needed if cartesian: coord2 = [] for k in range(3): inter = (new_struct[j].frac_coords[k] * basis[0][k] + new_struct[j].frac_coords[k] * basis[1][k] + new_struct[j].frac_coords[k] * basis[2][k]) * ang2bohr coord2.append(inter) coord = "%16.8f %16.8f %16.8f" % (coord2[0], coord2[1], coord2[2]) # write atomic positions index = index + 1 _ = ET.SubElement(species, 'atom', coord=coord) # write bandstructure if needed if bandstr and celltype == 'primitive': kpath = HighSymmKpath(new_struct, symprec=symprec, angle_tolerance=angle_tolerance) prop = ET.SubElement(root, 'properties') bandstrct = ET.SubElement(prop, 'bandstructure') for i in range(len(kpath.kpath['path'])): plot = ET.SubElement(bandstrct, 'plot1d') path = ET.SubElement(plot, 'path', steps='100') for j in range(len(kpath.kpath['path'][i])): symbol = kpath.kpath['path'][i][j] coords = kpath.kpath['kpoints'][symbol] coord = "%16.8f %16.8f %16.8f" % (coords[0], coords[1], coords[2]) if symbol == '\\Gamma': symbol = 'GAMMA' _ = ET.SubElement(path, 'point', coord=coord, label=symbol) elif bandstr and celltype != 'primitive': raise ValueError("Bandstructure is only implemented for the \ standard primitive unit cell!") return root
[docs] def write_string(self, celltype, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5): """ Writes to a string. :param celltype: :param cartesian: :param bandstr: :param symprec: :param angle_tolerance: :return: """ try: root = self.write_etree(celltype, cartesian, bandstr, symprec, angle_tolerance) self.indent(root) # output should be a string not a bytes object string = ET.tostring(root).decode('UTF-8') except Exception: raise ValueError('Incorrect celltype!') return string
[docs] def write_file(self, celltype, filename, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5): """ Write to a file. :param celltype: :param filename: :param cartesian: :param bandstr: :param symprec: :param angle_tolerance: :return: """ try: root = self.write_etree(celltype, cartesian, bandstr, symprec, angle_tolerance) self.indent(root) tree = ET.ElementTree(root) tree.write(filename) except Exception: raise ValueError('Incorrect celltype!') return
# Missing PrerryPrint option in the current version of xml.etree.cElementTree
[docs] @staticmethod def indent(elem, level=0): """ Helper method to indent elements. :param elem: :param level: :return: """ i = "\n" + level * " " if len(elem): if not elem.text or not elem.text.strip(): elem.text = i + " " if not elem.tail or not elem.tail.strip(): elem.tail = i for elem in elem: ExcitingInput.indent(elem, level + 1) if not elem.tail or not elem.tail.strip(): elem.tail = i else: if level and (not elem.tail or not elem.tail.strip()): elem.tail = i