Source code for pymatgen.io.feff.inputs
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes for reading/manipulating/writing the main sections
of FEFF input file(feff.inp), namely HEADER, ATOMS, POTENTIAL and the program
control tags.
XANES and EXAFS input files, are available, for non-spin case at this time.
"""
import re
import warnings
from operator import itemgetter
from tabulate import tabulate
import numpy as np
from monty.io import zopen
from monty.json import MSONable
from pymatgen import Structure, Lattice, Element, Molecule
from pymatgen.io.cif import CifParser
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.io_utils import clean_lines
from pymatgen.util.string import str_delimited
__author__ = "Alan Dozier, Kiran Mathew"
__credits__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "1.0.3"
__maintainer__ = "Alan Dozier"
__email__ = "adozier@uky.edu"
__status__ = "Beta"
__date__ = "April 7, 2013"
# **Non-exhaustive** list of valid Feff.inp tags
VALID_FEFF_TAGS = ("CONTROL", "PRINT", "ATOMS", "POTENTIALS", "RECIPROCAL",
"REAL", "MARKER", "LATTICE", "TITLE", "RMULTIPLIER",
"SGROUP", "COORDINATES", "EQUIVALENCE", "CIF", "CGRID",
"CFAVERAGE", "OVERLAP", "EXAFS", "XANES", "ELNES", "EXELFS",
"LDOS", "ELLIPTICITY", "MULTIPOLE", "POLARIZATION",
"RHOZZP", "DANES", "FPRIME", "NRIXS", "XES", "XNCD",
"XMCD", "XNCDCONTROL", "END", "KMESH", "PRINT", "EGRID",
"DIMS", "AFOLP", "EDGE", "COMPTON", "DANES",
"FPRIME" "MDFF", "HOLE", "COREHOLE", "S02", "CHBROAD",
"EXCHANGE", "FOLP", "NOHOLE", "RGRID", "SCF",
"UNFREEZEF", "CHSHIFT", "DEBYE",
"INTERSTITIAL", "CHWIDTH", "EGAP", "EPS0", "EXTPOT",
"ION", "JUMPRM", "EXPOT", "SPIN", "LJMAX", "LDEC", "MPSE",
"PLASMON", "RPHASES", "RSIGMA", "PMBSE", "TDLDA", "FMS",
"DEBYA", "OPCONS", "PREP", "RESTART", "SCREEN", "SETE",
"STRFACTORS", "BANDSTRUCTURE", "RPATH", "NLEG", "PCRITERIA",
"SYMMETRY", "SS", "CRITERIA", "IORDER", "NSTAR", "ABSOLUTE",
"CORRECTIONS", "SIG2", "SIG3", "MBCONV", "SFCONV", "RCONV",
"SELF", "SFSE", "MAGIC", "TARGET", "STRFAC")
[docs]class Header(MSONable):
"""
Creates Header for the FEFF input file.
Has the following format::
* This feff.inp file generated by pymatgen, www.materialsproject.org
TITLE comment:
TITLE Source: CoO19128.cif
TITLE Structure Summary: (Co2 O2)
TITLE Reduced formula: CoO
TITLE space group: P1, space number: 1
TITLE abc: 3.297078 3.297078 5.254213
TITLE angles: 90.0 90.0 120.0
TITLE sites: 4
* 1 Co 0.666666 0.333332 0.496324
* 2 Co 0.333333 0.666667 0.996324
* 3 O 0.666666 0.333332 0.878676
* 4 O 0.333333 0.666667 0.378675
"""
def __init__(self, struct, source='', comment=''):
"""
Args:
struct: Structure object, See pymatgen.core.structure.Structure.
source: User supplied identifier, i.e. for Materials Project this
would be the material ID number
comment: Comment for first header line
"""
if struct.is_ordered:
self.struct = struct
self.source = source
sym = SpacegroupAnalyzer(struct)
data = sym.get_symmetry_dataset()
self.space_number = data["number"]
self.space_group = data["international"]
self.comment = comment or "None given"
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
[docs] @staticmethod
def from_cif_file(cif_file, source='', comment=''):
"""
Static method to create Header object from cif_file
Args:
cif_file: cif_file path and name
source: User supplied identifier, i.e. for Materials Project this
would be the material ID number
comment: User comment that goes in header
Returns:
Header Object
"""
r = CifParser(cif_file)
structure = r.get_structures()[0]
return Header(structure, source, comment)
@property
def structure_symmetry(self):
"""
Returns space number and space group
Returns:
Space number and space group list
"""
return self.space_group, self.space_number
@property
def formula(self):
"""
Formula of structure
"""
return self.struct.composition.formula
[docs] @staticmethod
def from_file(filename):
"""
Returns Header object from file
"""
hs = Header.header_string_from_file(filename)
return Header.from_string(hs)
[docs] @staticmethod
def header_string_from_file(filename='feff.inp'):
"""
Reads Header string from either a HEADER file or feff.inp file
Will also read a header from a non-pymatgen generated feff.inp file
Args:
filename: File name containing the Header data.
Returns:
Reads header string.
"""
with zopen(filename, "r") as fobject:
f = fobject.readlines()
feff_header_str = []
ln = 0
# Checks to see if generated by pymatgen
try:
feffpmg = f[0].find("pymatgen")
if feffpmg == -1:
feffpmg = False
except IndexError:
feffpmg = False
# Reads pymatgen generated header or feff.inp file
if feffpmg:
nsites = int(f[8].split()[2])
for line in f:
ln += 1
if ln <= nsites + 9:
feff_header_str.append(line)
else:
# Reads header from header from feff.inp file from unknown
# source
end = 0
for line in f:
if (line[0] == "*" or line[0] == "T") and end == 0:
feff_header_str.append(line.replace("\r", ""))
else:
end = 1
return ''.join(feff_header_str)
[docs] @staticmethod
def from_string(header_str):
"""
Reads Header string and returns Header object if header was
generated by pymatgen.
Note: Checks to see if generated by pymatgen, if not it is impossible
to generate structure object so it is not possible to generate
header object and routine ends
Args:
header_str: pymatgen generated feff.inp header
Returns:
Structure object.
"""
lines = tuple(clean_lines(header_str.split("\n"), False))
comment1 = lines[0]
feffpmg = comment1.find("pymatgen")
if feffpmg == -1:
feffpmg = False
if feffpmg:
comment2 = ' '.join(lines[1].split()[2:])
source = ' '.join(lines[2].split()[2:])
basis_vec = lines[6].split(":")[-1].split()
# a, b, c
a = float(basis_vec[0])
b = float(basis_vec[1])
c = float(basis_vec[2])
lengths = [a, b, c]
# alpha, beta, gamma
basis_ang = lines[7].split(":")[-1].split()
alpha = float(basis_ang[0])
beta = float(basis_ang[1])
gamma = float(basis_ang[2])
angles = [alpha, beta, gamma]
lattice = Lattice.from_parameters(*lengths, *angles)
natoms = int(lines[8].split(":")[-1].split()[0])
atomic_symbols = []
for i in range(9, 9 + natoms):
atomic_symbols.append(lines[i].split()[2])
# read the atomic coordinates
coords = []
for i in range(natoms):
toks = lines[i + 9].split()
coords.append([float(s) for s in toks[3:]])
struct = Structure(lattice, atomic_symbols, coords, False,
False, False)
h = Header(struct, source, comment2)
return h
else:
return "Header not generated by pymatgen, cannot return header object"
def __str__(self):
"""
String representation of Header.
"""
def to_s(x):
return "%0.6f" % x
output = ["* This FEFF.inp file generated by pymatgen",
''.join(["TITLE comment: ", self.comment]),
''.join(["TITLE Source: ", self.source]),
"TITLE Structure Summary: {}".format(self.struct.composition.formula),
"TITLE Reduced formula: {}".format(self.struct.composition.reduced_formula),
"TITLE space group: ({}), space number: ({})".format(self.space_group, self.space_number),
"TITLE abc:{}".format(" ".join([to_s(i).rjust(10) for i in self.struct.lattice.abc])),
"TITLE angles:{}".format(" ".join([to_s(i).rjust(10) for i in self.struct.lattice.angles])),
"TITLE sites: {}".format(self.struct.num_sites)]
for i, site in enumerate(self.struct):
output.append(" ".join(["*", str(i + 1), site.species_string,
" ".join([to_s(j).rjust(12) for j in site.frac_coords])]))
return "\n".join(output)
[docs] def write_file(self, filename='HEADER'):
"""
Writes Header into filename on disk.
Args:
filename: Filename and path for file to be written to disk
"""
with open(filename, "w") as f:
f.write(str(self) + "\n")
[docs]class Atoms(MSONable):
"""
Atomic cluster centered around the absorbing atom.
"""
def __init__(self, struct, absorbing_atom, radius):
"""
Args:
struct (Structure): input structure
absorbing_atom (str/int): Symbol for absorbing atom or site index
radius (float): radius of the atom cluster in Angstroms.
"""
if struct.is_ordered:
self.struct = struct
self.pot_dict = get_atom_map(struct)
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
self.absorbing_atom, self.center_index = \
get_absorbing_atom_symbol_index(absorbing_atom, struct)
self.radius = radius
self._cluster = self._set_cluster()
def _set_cluster(self):
"""
Compute and set the cluster of atoms as a Molecule object. The siteato
coordinates are translated such that the absorbing atom(aka central
atom) is at the origin.
Returns:
Molecule
"""
center = self.struct[self.center_index].coords
sphere = self.struct.get_neighbors(self.struct[self.center_index], self.radius)
symbols = [self.absorbing_atom]
coords = [[0, 0, 0]]
for i, site_dist in enumerate(sphere):
site_symbol = re.sub(r"[^aA-zZ]+", "", site_dist[0].species_string)
symbols.append(site_symbol)
coords.append(site_dist[0].coords - center)
return Molecule(symbols, coords)
@property
def cluster(self):
"""
Returns the atomic cluster as a Molecule object.
"""
return self._cluster
[docs] @staticmethod
def atoms_string_from_file(filename):
"""
Reads atomic shells from file such as feff.inp or ATOMS file
The lines are arranged as follows:
x y z ipot Atom Symbol Distance Number
with distance being the shell radius and ipot an integer identifying
the potential used.
Args:
filename: File name containing atomic coord data.
Returns:
Atoms string.
"""
with zopen(filename, "rt") as fobject:
f = fobject.readlines()
coords = 0
atoms_str = []
for line in f:
if coords == 0:
find_atoms = line.find("ATOMS")
if find_atoms >= 0:
coords = 1
if coords == 1 and not ("END" in line):
atoms_str.append(line.replace("\r", ""))
return ''.join(atoms_str)
[docs] @staticmethod
def cluster_from_file(filename):
"""
Parse the feff input file and return the atomic cluster as a Molecule
object.
Args:
filename (str): path the feff input file
Returns:
Molecule: the atomic cluster as Molecule object. The absorbing atom
is the one at the origin.
"""
atoms_string = Atoms.atoms_string_from_file(filename)
line_list = [l.split() for l in atoms_string.splitlines()[3:]]
coords = []
symbols = []
for l in line_list:
if l:
coords.append([float(i) for i in l[:3]])
symbols.append(l[4])
return Molecule(symbols, coords)
[docs] def get_lines(self):
"""
Returns a list of string representations of the atomic configuration
information(x, y, z, ipot, atom_symbol, distance, id).
Returns:
list: list of strings, sorted by the distance from the absorbing
atom.
"""
lines = [["{:f}".format(self._cluster[0].x),
"{:f}".format(self._cluster[0].y),
"{:f}".format(self._cluster[0].z),
0, self.absorbing_atom, "0.0", 0]]
for i, site in enumerate(self._cluster[1:]):
site_symbol = re.sub(r"[^aA-zZ]+", "", site.species_string)
ipot = self.pot_dict[site_symbol]
lines.append(["{:f}".format(site.x), "{:f}".format(site.y),
"{:f}".format(site.z), ipot, site_symbol,
"{:f}".format(self._cluster.get_distance(0, i + 1)), i + 1])
return sorted(lines, key=itemgetter(5))
def __str__(self):
"""
String representation of Atoms file.
"""
lines_sorted = self.get_lines()
# TODO: remove the formatting and update the unittests
lines_formatted = str(tabulate(lines_sorted,
headers=["* x", "y", "z", "ipot",
"Atom", "Distance", "Number"]))
atom_list = lines_formatted.replace("--", "**")
return ''.join(["ATOMS\n", atom_list, "\nEND\n"])
[docs] def write_file(self, filename='ATOMS'):
"""
Write Atoms list to file.
Args:
filename: path for file to be written
"""
with zopen(filename, "wt") as f:
f.write(str(self) + "\n")
[docs]class Tags(dict):
"""
FEFF control parameters.
"""
def __init__(self, params=None):
"""
Args:
params: A set of input parameters as a dictionary.
"""
super().__init__()
if params:
self.update(params)
def __setitem__(self, key, val):
"""
Add parameter-val pair. Warns if parameter is not in list of valid
Feff tags. Also cleans the parameter and val by stripping leading and
trailing white spaces.
Arg:
key: dict key value
value: value associated with key in dictionary
"""
if key.strip().upper() not in VALID_FEFF_TAGS:
warnings.warn(key.strip() + " not in VALID_FEFF_TAGS list")
super().__setitem__(key.strip(), Tags.proc_val(key.strip(), val.strip()) if isinstance(val, str) else val)
[docs] def as_dict(self):
"""
Dict representation.
Returns:
Dictionary of parameters from fefftags object
"""
tags_dict = dict(self)
tags_dict['@module'] = self.__class__.__module__
tags_dict['@class'] = self.__class__.__name__
return tags_dict
[docs] @staticmethod
def from_dict(d):
"""
Creates Tags object from a dictionary.
Args:
d: Dict of feff parameters and values.
Returns:
Tags object
"""
i = Tags()
for k, v in d.items():
if k not in ("@module", "@class"):
i[k] = v
return i
[docs] def get_string(self, sort_keys=False, pretty=False):
"""
Returns a string representation of the Tags. The reason why this
method is different from the __str__ method is to provide options
for pretty printing.
Args:
sort_keys: Set to True to sort the Feff parameters alphabetically.
Defaults to False.
pretty: Set to True for pretty aligned output. Defaults to False.
Returns:
String representation of Tags.
"""
keys = self.keys()
if sort_keys:
keys = sorted(keys)
lines = []
for k in keys:
if isinstance(self[k], dict):
if k in ["ELNES", "EXELFS"]:
lines.append([k, self._stringify_val(self[k]["ENERGY"])])
beam_energy = self._stringify_val(self[k]["BEAM_ENERGY"])
beam_energy_list = beam_energy.split()
if int(beam_energy_list[1]) == 0: # aver=0, specific beam direction
lines.append([beam_energy])
lines.append([self._stringify_val(self[k]["BEAM_DIRECTION"])])
else:
# no cross terms for orientation averaged spectrum
beam_energy_list[2] = str(0)
lines.append([self._stringify_val(beam_energy_list)])
lines.append([self._stringify_val(self[k]["ANGLES"])])
lines.append([self._stringify_val(self[k]["MESH"])])
lines.append([self._stringify_val(self[k]["POSITION"])])
else:
lines.append([k, self._stringify_val(self[k])])
if pretty:
return tabulate(lines)
else:
return str_delimited(lines, None, " ")
@staticmethod
def _stringify_val(val):
"""
Convert the given value to string.
"""
if isinstance(val, list):
return " ".join([str(i) for i in val])
else:
return str(val)
def __str__(self):
return self.get_string()
[docs] def write_file(self, filename='PARAMETERS'):
"""
Write Tags to a Feff parameter tag file.
Args:
filename: filename and path to write to.
"""
with zopen(filename, "wt") as f:
f.write(self.__str__() + "\n")
[docs] @staticmethod
def from_file(filename="feff.inp"):
"""
Creates a Feff_tag dictionary from a PARAMETER or feff.inp file.
Args:
filename: Filename for either PARAMETER or feff.inp file
Returns:
Feff_tag object
"""
with zopen(filename, "rt") as f:
lines = list(clean_lines(f.readlines()))
params = {}
eels_params = []
ieels = -1
ieels_max = -1
for i, line in enumerate(lines):
m = re.match(r"([A-Z]+\d*\d*)\s*(.*)", line)
if m:
key = m.group(1).strip()
val = m.group(2).strip()
val = Tags.proc_val(key, val)
if key not in ("ATOMS", "POTENTIALS", "END", "TITLE"):
if key in ["ELNES", "EXELFS"]:
ieels = i
ieels_max = ieels + 5
else:
params[key] = val
if ieels >= 0:
if i >= ieels and i <= ieels_max:
if i == ieels + 1:
if int(line.split()[1]) == 1:
ieels_max -= 1
eels_params.append(line)
if eels_params:
if len(eels_params) == 6:
eels_keys = ['BEAM_ENERGY', 'BEAM_DIRECTION', 'ANGLES', 'MESH', 'POSITION']
else:
eels_keys = ['BEAM_ENERGY', 'ANGLES', 'MESH', 'POSITION']
eels_dict = {"ENERGY": Tags._stringify_val(eels_params[0].split()[1:])}
for k, v in zip(eels_keys, eels_params[1:]):
eels_dict[k] = str(v)
params[str(eels_params[0].split()[0])] = eels_dict
return Tags(params)
[docs] @staticmethod
def proc_val(key, val):
"""
Static helper method to convert Feff parameters to proper types, e.g.
integers, floats, lists, etc.
Args:
key: Feff parameter key
val: Actual value of Feff parameter.
"""
list_type_keys = list(VALID_FEFF_TAGS)
del list_type_keys[list_type_keys.index("ELNES")]
del list_type_keys[list_type_keys.index("EXELFS")]
boolean_type_keys = ()
float_type_keys = ("S02", "EXAFS", "RPATH")
def smart_int_or_float(numstr):
if numstr.find(".") != -1 or numstr.lower().find("e") != -1:
return float(numstr)
else:
return int(numstr)
try:
if key.lower() == 'cif':
m = re.search(r"\w+.cif", val)
return m.group(0)
if key in list_type_keys:
output = list()
toks = re.split(r"\s+", val)
for tok in toks:
m = re.match(r"(\d+)\*([\d\.\-\+]+)", tok)
if m:
output.extend([smart_int_or_float(m.group(2))] *
int(m.group(1)))
else:
output.append(smart_int_or_float(tok))
return output
if key in boolean_type_keys:
m = re.search(r"^\W+([TtFf])", val)
if m:
if m.group(1) == "T" or m.group(1) == "t":
return True
else:
return False
raise ValueError(key + " should be a boolean type!")
if key in float_type_keys:
return float(val)
except ValueError:
return val.capitalize()
return val.capitalize()
[docs] def diff(self, other):
"""
Diff function. Compares two PARAMETER files and indicates which
parameters are the same and which are not. Useful for checking whether
two runs were done using the same parameters.
Args:
other: The other PARAMETER dictionary to compare to.
Returns:
Dict of the format {"Same" : parameters_that_are_the_same,
"Different": parameters_that_are_different} Note that the
parameters are return as full dictionaries of values.
"""
similar_param = {}
different_param = {}
for k1, v1 in self.items():
if k1 not in other:
different_param[k1] = {"FEFF_TAGS1": v1,
"FEFF_TAGS2": "Default"}
elif v1 != other[k1]:
different_param[k1] = {"FEFF_TAGS1": v1,
"FEFF_TAGS2": other[k1]}
else:
similar_param[k1] = v1
for k2, v2 in other.items():
if k2 not in similar_param and k2 not in different_param:
if k2 not in self:
different_param[k2] = {"FEFF_TAGS1": "Default",
"FEFF_TAGS2": v2}
return {"Same": similar_param, "Different": different_param}
def __add__(self, other):
"""
Add all the values of another Tags object to this object
Facilitates the use of "standard" Tags
"""
params = dict(self)
for k, v in other.items():
if k in self and v != self[k]:
raise ValueError("Tags have conflicting values!")
else:
params[k] = v
return Tags(params)
[docs]class Potential(MSONable):
"""
FEFF atomic potential.
"""
def __init__(self, struct, absorbing_atom):
"""
Args:
struct (Structure): Structure object.
absorbing_atom (str/int): Absorbing atom symbol or site index
"""
if struct.is_ordered:
self.struct = struct
self.pot_dict = get_atom_map(struct)
else:
raise ValueError("Structure with partial occupancies cannot be "
"converted into atomic coordinates!")
self.absorbing_atom, _ = \
get_absorbing_atom_symbol_index(absorbing_atom, struct)
[docs] @staticmethod
def pot_string_from_file(filename='feff.inp'):
"""
Reads Potential parameters from a feff.inp or FEFFPOT file.
The lines are arranged as follows:
ipot Z element lmax1 lmax2 stoichometry spinph
Args:
filename: file name containing potential data.
Returns:
FEFFPOT string.
"""
with zopen(filename, "rt") as f_object:
f = f_object.readlines()
ln = -1
pot_str = ["POTENTIALS\n"]
pot_tag = -1
pot_data = 0
pot_data_over = 1
sep_line_pattern = [re.compile('ipot.*Z.*tag.*lmax1.*lmax2.*spinph'),
re.compile('^[*]+.*[*]+$')]
for line in f:
if pot_data_over == 1:
ln += 1
if pot_tag == -1:
pot_tag = line.find("POTENTIALS")
ln = 0
if pot_tag >= 0 and ln > 0 and pot_data_over > 0:
try:
if len(sep_line_pattern[0].findall(line)) > 0 or \
len(sep_line_pattern[1].findall(line)) > 0:
pot_str.append(line)
elif int(line.split()[0]) == pot_data:
pot_data += 1
pot_str.append(line.replace("\r", ""))
except (ValueError, IndexError):
if pot_data > 0:
pot_data_over = 0
return ''.join(pot_str).rstrip('\n')
[docs] @staticmethod
def pot_dict_from_string(pot_data):
"""
Creates atomic symbol/potential number dictionary
forward and reverse
Arg:
pot_data: potential data in string format
Returns:
forward and reverse atom symbol and potential number dictionaries.
"""
pot_dict = {}
pot_dict_reverse = {}
begin = 0
ln = -1
for line in pot_data.split("\n"):
try:
if begin == 0 and line.split()[0] == "0":
begin += 1
ln = 0
if begin == 1:
ln += 1
if ln > 0:
atom = line.split()[2]
index = int(line.split()[0])
pot_dict[atom] = index
pot_dict_reverse[index] = atom
except (ValueError, IndexError):
pass
return pot_dict, pot_dict_reverse
def __str__(self):
"""
Returns a string representation of potential parameters to be used in
the feff.inp file,
determined from structure object.
The lines are arranged as follows:
ipot Z element lmax1 lmax2 stoichiometry spinph
Returns:
String representation of Atomic Coordinate Shells.
"""
central_element = Element(self.absorbing_atom)
ipotrow = [[0, central_element.Z, central_element.symbol, -1, -1, .0001, 0]]
for el, amt in self.struct.composition.items():
ipot = self.pot_dict[el.symbol]
ipotrow.append([ipot, el.Z, el.symbol, -1, -1, amt, 0])
ipot_sorted = sorted(ipotrow, key=itemgetter(0))
ipotrow = str(tabulate(ipot_sorted,
headers=["*ipot", "Z", "tag", "lmax1",
"lmax2", "xnatph(stoichometry)",
"spinph"]))
ipotlist = ipotrow.replace("--", "**")
ipotlist = ''.join(["POTENTIALS\n", ipotlist])
return ipotlist
[docs] def write_file(self, filename='POTENTIALS'):
"""
Write to file.
Args:
filename: filename and path to write potential file to.
"""
with zopen(filename, "wt") as f:
f.write(str(self) + "\n")
[docs]class Paths(MSONable):
"""
Set FEFF scattering paths('paths.dat' file used by the 'genfmt' module).
"""
def __init__(self, atoms, paths, degeneracies=None):
"""
Args:
atoms (Atoms): Atoms object
paths (list(list)): list of paths. Each path is a list of atom indices in the atomic
cluster(the molecular cluster created by Atoms class).
e.g. [[0, 1, 2], [5, 9, 4, 1]] -> 2 paths: one with 3 legs and the other with 4 legs.
degeneracies (list): list of degeneracies, one for each path. Set to 1 if not specified.
"""
self.atoms = atoms
self.paths = paths
self.degeneracies = degeneracies or [1] * len(paths)
assert len(self.degeneracies) == len(self.paths)
def __str__(self):
lines = ["PATH", "---------------"]
# max possible, to avoid name collision count down from max value.
path_index = 9999
for i, legs in enumerate(self.paths):
lines.append("{} {} {}".format(path_index, len(legs), self.degeneracies[i]))
lines.append("x y z ipot label")
for l in legs:
coords = self.atoms.cluster[l].coords.tolist()
tmp = "{:.6f} {:.6f} {:.6f}".format(*tuple(coords))
element = str(self.atoms.cluster[l].specie.name)
# the potential index for the absorbing atom(the one at the cluster origin) is 0
potential = 0 if np.linalg.norm(coords) <= 1e-6 else self.atoms.pot_dict[element]
tmp = "{} {} {}".format(tmp, potential, element)
lines.append(tmp)
path_index -= 1
return "\n".join(lines)
[docs] def write_file(self, filename="paths.dat"):
"""
Write paths.dat.
"""
with zopen(filename, "wt") as f:
f.write(str(self) + "\n")
[docs]class FeffParserError(Exception):
"""
Exception class for Structure.
Raised when the structure has problems, e.g., atoms that are too close.
"""
[docs]def get_atom_map(structure):
"""
Returns a dict that maps each atomic symbol to a unique integer starting
from 1.
Args:
structure (Structure)
Returns:
dict
"""
syms = [site.specie.symbol for site in structure]
unique_pot_atoms = []
[unique_pot_atoms.append(i) for i in syms if not unique_pot_atoms.count(i)]
atom_map = {}
for i, atom in enumerate(unique_pot_atoms):
atom_map[atom] = i + 1
return atom_map
[docs]def get_absorbing_atom_symbol_index(absorbing_atom, structure):
"""
Return the absorbing atom symboll and site index in the given structure.
Args:
absorbing_atom (str/int): symbol or site index
structure (Structure)
Returns:
str, int: symbol and site index
"""
if isinstance(absorbing_atom, str):
return absorbing_atom, structure.indices_from_symbol(absorbing_atom)[0]
elif isinstance(absorbing_atom, int):
return str(structure[absorbing_atom].specie), absorbing_atom
else:
raise ValueError("absorbing_atom must be either specie symbol or site index")