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 xml.etree.cElementTree as ET

import numpy as np
import scipy.constants as const
from monty.io import zopen
from monty.json import MSONable

from pymatgen.core.lattice import Lattice
from pymatgen.core.periodic_table import Element
from pymatgen.core.structure import Structure
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 in ("True", "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, p in enumerate(positions): for j in range(3): p[j] = p[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, **kwargs): """ Writes the exciting input parameters to an xml object. Args: celltype (str): Choice of unit cell. Can be either the unit cell from self.structure ("unchanged"), the conventional cell ("conventional"), or the primitive unit cell ("primitive"). cartesian (bool): Whether the atomic positions are provided in Cartesian or unit-cell coordinates. Default is False. bandstr (bool): Whether the bandstructure path along the HighSymmKpath is included in the input file. Only supported if the celltype is set to "primitive". Default is False. symprec (float): Tolerance for the symmetry finding. Default is 0.4. angle_tolerance (float): Angle tolerance for the symmetry finding. Default is 5. **kwargs: Additional parameters for the input file. Returns: ET.Element containing the input XML structure """ 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_species, 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!" ) # write extra parameters from kwargs if provided self._dicttoxml(kwargs, root) return root
[docs] def write_string(self, celltype, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5, **kwargs): """ Writes exciting input.xml as a string. Args: celltype (str): Choice of unit cell. Can be either the unit cell from self.structure ("unchanged"), the conventional cell ("conventional"), or the primitive unit cell ("primitive"). cartesian (bool): Whether the atomic positions are provided in Cartesian or unit-cell coordinates. Default is False. bandstr (bool): Whether the bandstructure path along the HighSymmKpath is included in the input file. Only supported if the celltype is set to "primitive". Default is False. symprec (float): Tolerance for the symmetry finding. Default is 0.4. angle_tolerance (float): Angle tolerance for the symmetry finding. Default is 5. **kwargs: Additional parameters for the input file. Returns: String """ try: root = self.write_etree(celltype, cartesian, bandstr, symprec, angle_tolerance, **kwargs) 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, **kwargs): """ Writes exciting input file. Args: celltype (str): Choice of unit cell. Can be either the unit cell from self.structure ("unchanged"), the conventional cell ("conventional"), or the primitive unit cell ("primitive"). filename (str): Filename for exciting input. cartesian (bool): Whether the atomic positions are provided in Cartesian or unit-cell coordinates. Default is False. bandstr (bool): Whether the bandstructure path along the HighSymmKpath is included in the input file. Only supported if the celltype is set to "primitive". Default is False. symprec (float): Tolerance for the symmetry finding. Default is 0.4. angle_tolerance (float): Angle tolerance for the symmetry finding. Default is 5. **kwargs: Additional parameters for the input file. """ try: root = self.write_etree(celltype, cartesian, bandstr, symprec, angle_tolerance, **kwargs) self._indent(root) tree = ET.ElementTree(root) tree.write(filename) except Exception: raise ValueError("Incorrect celltype!")
# Missing PrettyPrint option in the current version of xml.etree.cElementTree @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 el in elem: ExcitingInput._indent(el, 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 def _dicttoxml(self, paramdict_, element): for key, value in paramdict_.items(): if isinstance(value, str) and key == "text()": element.text = value elif isinstance(value, str): element.attrib[key] = value elif isinstance(value, list): for item in value: self._dicttoxml(item, ET.SubElement(element, key)) elif isinstance(value, dict): if element.findall(key) == []: self._dicttoxml(value, ET.SubElement(element, key)) else: self._dicttoxml(value, element.findall(key)[0]) else: print("cannot deal with", key, "=", value)