Source code for pymatgen.io.exciting.inputs
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import re
import itertools
import warnings
import logging
import six
import numpy as np
from numpy.linalg import det
from collections import OrderedDict, namedtuple
from hashlib import md5
from monty.io import zopen
from monty.os.path import zpath
from monty.json import MontyDecoder
import xml.etree.cElementTree as ET
from enum import Enum
from tabulate import tabulate
import scipy.constants as const
from pymatgen import SETTINGS
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.core.periodic_table import Element, get_el_sp
from monty.design_patterns import cached_class
from pymatgen.util.string import str_delimited
from pymatgen.util.io_utils import clean_lines
from monty.json import MSONable
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.symmetry.bandstructure import HighSymmKpath
"""
Classes for reading/manipulating/writing exciting input files.
"""
__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.
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.
.. 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):
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 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 NLValueError("Unknown element!")
natoms = nodes.getiterator('atom')
for atom in natoms:
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:
lxy=[]
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):
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):
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 new_struct.types_of_specie:
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
atom=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'
pt=ET.SubElement(path,'point',coord=coord,label=symbol)
elif bandstr and celltype is not '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):
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:
raise ValueError('Incorrect celltype!')
return string
[docs] def write_file(self, celltype, filename, cartesian=False, bandstr=False, symprec=0.4, angle_tolerance=5):
try:
root=self.write_etree(celltype, cartesian, bandstr, symprec, angle_tolerance)
self.indent(root)
tree=ET.ElementTree(root)
tree.write(filename)
except:
raise ValueError('Incorrect celltype!')
return
# Missing PrerryPrint option in the current version of xml.etree.cElementTree
[docs] @staticmethod
def indent(elem,level=0):
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