Source code for pymatgen.core.periodic_table

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

"""Module contains classes presenting Element and Species (Element + oxidation state) and PeriodicTable."""
import ast
import json
import re
import warnings
from collections import Counter
from enum import Enum
from io import open
from itertools import combinations, product
from pathlib import Path
from typing import Callable, Optional, Union, Dict, Tuple, List

import numpy as np
from monty.json import MSONable

from pymatgen.core.units import SUPPORTED_UNIT_NAMES, FloatWithUnit, Length, Mass, Unit
from pymatgen.util.string import formula_double_format, Stringify

# Loads element data from json file
with open(str(Path(__file__).absolute().parent / "periodic_table.json"), "rt") as f:
    _pt_data = json.load(f)

_pt_row_sizes = (2, 8, 8, 18, 18, 32, 32)


[docs]class ElementBase(Enum): """Element class defined without any enum values so it can be subclassed.""" def __init__(self, symbol: str): """ Basic immutable element object with all relevant properties. Only one instance of Element for each symbol is stored after creation, ensuring that a particular element behaves like a singleton. For all attributes, missing data (i.e., data for which is not available) is represented by a None unless otherwise stated. Args: symbol (str): Element symbol, e.g., "H", "Fe" .. attribute:: Z Atomic number .. attribute:: symbol Element symbol .. attribute:: long_name Long name for element. E.g., "Hydrogen". .. attribute:: atomic_radius_calculated Calculated atomic radius for the element. This is the empirical value. Data is obtained from http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page). .. attribute:: van_der_waals_radius Van der Waals radius for the element. This is the empirical value. Data is obtained from http://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_page). .. attribute:: mendeleev_no Mendeleev number from definition given by Pettifor, D. G. (1984). A chemical scale for crystal-structure maps. Solid State Communications, 51 (1), 31-34 .. attribute:: electrical_resistivity Electrical resistivity .. attribute:: velocity_of_sound Velocity of sound .. attribute:: reflectivity Reflectivity .. attribute:: refractive_index Refractice index .. attribute:: poissons_ratio Poisson's ratio .. attribute:: molar_volume Molar volume .. attribute:: electronic_structure Electronic structure. E.g., The electronic structure for Fe is represented as [Ar].3d6.4s2 .. attribute:: atomic_orbitals Atomic Orbitals. Energy of the atomic orbitals as a dict. E.g., The orbitals energies in eV are represented as {'1s': -1.0, '2s': -0.1} Data is obtained from https://www.nist.gov/pml/data/atomic-reference-data-electronic-structure-calculations The LDA values for neutral atoms are used .. attribute:: thermal_conductivity Thermal conductivity .. attribute:: boiling_point Boiling point .. attribute:: melting_point Melting point .. attribute:: critical_temperature Critical temperature .. attribute:: superconduction_temperature Superconduction temperature .. attribute:: liquid_range Liquid range .. attribute:: bulk_modulus Bulk modulus .. attribute:: youngs_modulus Young's modulus .. attribute:: brinell_hardness Brinell hardness .. attribute:: rigidity_modulus Rigidity modulus .. attribute:: mineral_hardness Mineral hardness .. attribute:: vickers_hardness Vicker's hardness .. attribute:: density_of_solid Density of solid phase .. attribute:: coefficient_of_linear_thermal_expansion Coefficient of linear thermal expansion .. attribute:: ground_level Ground level for element .. attribute:: ionization_energies List of ionization energies. First value is the first ionization energy, second is the second ionization energy, etc. Note that this is zero-based indexing! So Element.ionization_energies[0] refer to the 1st ionization energy. Values are from the NIST Atomic Spectra Database. Missing values are None. """ self.symbol = "%s" % symbol d = _pt_data[symbol] # Store key variables for quick access self.Z = d["Atomic no"] at_r = d.get("Atomic radius", "no data") if str(at_r).startswith("no data"): self._atomic_radius = None else: self._atomic_radius = Length(at_r, "ang") self._atomic_mass = Mass(d["Atomic mass"], "amu") self.long_name = d["Name"] self._data = d @property def X(self) -> float: """ :return: Electronegativity of element. Note that if an element does not have an electronegativity, a NaN float is returned. """ if "X" in self._data: return self._data["X"] warnings.warn( "No electronegativity for %s. Setting to NaN. " "This has no physical meaning, and is mainly done to " "avoid errors caused by the code expecting a float." % self.symbol ) return float("NaN") @property def atomic_radius(self) -> Optional[FloatWithUnit]: """ Returns: The atomic radius of the element in Ã…ngstroms. """ return self._atomic_radius @property def atomic_mass(self) -> Optional[FloatWithUnit]: """ Returns: The atomic mass of the element in amu. """ return self._atomic_mass def __getattr__(self, item): if item in [ "mendeleev_no", "electrical_resistivity", "velocity_of_sound", "reflectivity", "refractive_index", "poissons_ratio", "molar_volume", "thermal_conductivity", "boiling_point", "melting_point", "critical_temperature", "superconduction_temperature", "liquid_range", "bulk_modulus", "youngs_modulus", "brinell_hardness", "rigidity_modulus", "mineral_hardness", "vickers_hardness", "density_of_solid", "atomic_radius_calculated", "van_der_waals_radius", "atomic_orbitals", "coefficient_of_linear_thermal_expansion", "ground_state_term_symbol", "valence", "ground_level", "ionization_energies", ]: kstr = item.capitalize().replace("_", " ") val = self._data.get(kstr, None) if str(val).startswith("no data"): val = None elif isinstance(val, (list, dict)): pass else: try: val = float(val) except ValueError: nobracket = re.sub(r"\(.*\)", "", val) toks = nobracket.replace("about", "").strip().split(" ", 1) if len(toks) == 2: try: if "10<sup>" in toks[1]: base_power = re.findall(r"([+-]?\d+)", toks[1]) factor = "e" + base_power[1] if toks[0] in ["&gt;", "high"]: toks[0] = "1" # return the border value toks[0] += factor if item == "electrical_resistivity": unit = "ohm m" elif item == "coefficient_of_linear_thermal_expansion": unit = "K^-1" else: unit = toks[1] val = FloatWithUnit(toks[0], unit) else: unit = toks[1].replace("<sup>", "^").replace("</sup>", "").replace("&Omega;", "ohm") units = Unit(unit) if set(units.keys()).issubset(SUPPORTED_UNIT_NAMES): val = FloatWithUnit(toks[0], unit) except ValueError: # Ignore error. val will just remain a string. pass return val raise AttributeError("Element has no attribute %s!" % item) @property def data(self) -> dict: """ Returns dict of data for element. """ return self._data.copy() @property def ionization_energy(self) -> float: """ First ionization energy of element. """ return self._data["Ionization energies"][0] @property def electron_affinity(self) -> float: """ First ionization energy of element. """ return self._data["Electron affinity"] @property def electronic_structure(self) -> str: """ Electronic structure as string, with only valence electrons. E.g., The electronic structure for Fe is represented as '[Ar].3d6.4s2' """ return re.sub("</*sup>", "", self._data["Electronic structure"]) @property def average_ionic_radius(self) -> FloatWithUnit: """ Average ionic radius for element (with units). The average is taken over all oxidation states of the element for which data is present. """ if "Ionic radii" in self._data: radii = self._data["Ionic radii"] radius = sum(radii.values()) / len(radii) else: radius = 0.0 return FloatWithUnit(radius, "ang") @property def average_cationic_radius(self) -> FloatWithUnit: """ Average cationic radius for element (with units). The average is taken over all positive oxidation states of the element for which data is present. """ if "Ionic radii" in self._data: radii = [v for k, v in self._data["Ionic radii"].items() if int(k) > 0] if radii: return FloatWithUnit(sum(radii) / len(radii), "ang") return FloatWithUnit(0.0, "ang") @property def average_anionic_radius(self) -> float: """ Average anionic radius for element (with units). The average is taken over all negative oxidation states of the element for which data is present. """ if "Ionic radii" in self._data: radii = [v for k, v in self._data["Ionic radii"].items() if int(k) < 0] if radii: return FloatWithUnit(sum(radii) / len(radii), "ang") return FloatWithUnit(0.0, "ang") @property def ionic_radii(self) -> Dict[int, float]: """ All ionic radii of the element as a dict of {oxidation state: ionic radii}. Radii are given in ang. """ if "Ionic radii" in self._data: return {int(k): FloatWithUnit(v, "ang") for k, v in self._data["Ionic radii"].items()} return {} @property def number(self) -> int: """Alternative attribute for atomic number""" return self.Z @property def max_oxidation_state(self) -> float: """Maximum oxidation state for element""" if "Oxidation states" in self._data: return max(self._data["Oxidation states"]) return 0 @property def min_oxidation_state(self) -> float: """Minimum oxidation state for element""" if "Oxidation states" in self._data: return min(self._data["Oxidation states"]) return 0 @property def oxidation_states(self) -> Tuple: """Tuple of all known oxidation states""" return tuple(self._data.get("Oxidation states", list())) @property def common_oxidation_states(self) -> Tuple: """Tuple of common oxidation states""" return tuple(self._data.get("Common oxidation states", list())) @property def icsd_oxidation_states(self) -> Tuple: """Tuple of all oxidation states with at least 10 instances in ICSD database AND at least 1% of entries for that element""" return tuple(self._data.get("ICSD oxidation states", list())) @property def metallic_radius(self) -> float: """ Metallic radius of the element. Radius is given in ang. """ return FloatWithUnit(self._data["Metallic radius"], "ang") @property def full_electronic_structure(self) -> List[Tuple[int, str, int]]: """ Full electronic structure as tuple. E.g., The electronic structure for Fe is represented as: [(1, "s", 2), (2, "s", 2), (2, "p", 6), (3, "s", 2), (3, "p", 6), (3, "d", 6), (4, "s", 2)] """ estr = self.electronic_structure def parse_orbital(orbstr): m = re.match(r"(\d+)([spdfg]+)(\d+)", orbstr) if m: return int(m.group(1)), m.group(2), int(m.group(3)) return orbstr data = [parse_orbital(s) for s in estr.split(".")] if data[0][0] == "[": sym = data[0].replace("[", "").replace("]", "") data = list(Element(sym).full_electronic_structure) + data[1:] return data # type: ignore @property def valence(self): """ From full electron config obtain valence subshell angular moment (L) and number of valence e- (v_e) """ # The number of valence of noble gas is 0 if self.group == 18: return np.nan, 0 L_symbols = "SPDFGHIKLMNOQRTUVWXYZ" valence = [] full_electron_config = self.full_electronic_structure last_orbital = full_electron_config[-1] for n, l_symbol, ne in full_electron_config: l = L_symbols.lower().index(l_symbol) if ne < (2 * l + 1) * 2: valence.append((l, ne)) # check for full last shell (e.g. column 2) elif (n, l_symbol, ne) == last_orbital and ne == (2 * l + 1) * 2 and len(valence) == 0: valence.append((l, ne)) if len(valence) > 1: raise ValueError("Ambiguous valence") return valence[0] @property def term_symbols(self) -> List[List[str]]: """ All possible Russell-Saunders term symbol of the Element eg. L = 1, n_e = 2 (s2) returns [['1D2'], ['3P0', '3P1', '3P2'], ['1S0']] """ L_symbols = "SPDFGHIKLMNOQRTUVWXYZ" L, v_e = self.valence # for one electron in subshell L ml = list(range(-L, L + 1)) ms = [1 / 2, -1 / 2] # all possible configurations of ml,ms for one e in subshell L ml_ms = list(product(ml, ms)) # Number of possible configurations for r electrons in subshell L. n = (2 * L + 1) * 2 # the combination of n_e electrons configurations # C^{n}_{n_e} e_config_combs = list(combinations(range(n), v_e)) # Total ML = sum(ml1, ml2), Total MS = sum(ms1, ms2) TL = [sum([ml_ms[comb[e]][0] for e in range(v_e)]) for comb in e_config_combs] TS = [sum([ml_ms[comb[e]][1] for e in range(v_e)]) for comb in e_config_combs] comb_counter = Counter(zip(TL, TS)) term_symbols = [] while sum(comb_counter.values()) > 0: # Start from the lowest freq combination, # which corresponds to largest abs(L) and smallest abs(S) L, S = min(comb_counter) J = list(np.arange(abs(L - S), abs(L) + abs(S) + 1)) term_symbols.append([str(int(2 * (abs(S)) + 1)) + L_symbols[abs(L)] + str(j) for j in J]) # Without J # term_symbols.append(str(int(2 * (abs(S)) + 1)) \ # + L_symbols[abs(L)]) # Delete all configurations included in this term for ML in range(-L, L - 1, -1): for MS in np.arange(S, -S + 1, 1): if (ML, MS) in comb_counter: comb_counter[(ML, MS)] -= 1 if comb_counter[(ML, MS)] == 0: del comb_counter[(ML, MS)] return term_symbols @property def ground_state_term_symbol(self): """ Ground state term symbol Selected based on Hund's Rule """ L_symbols = "SPDFGHIKLMNOQRTUVWXYZ" term_symbols = self.term_symbols term_symbol_flat = { term: { "multiplicity": int(term[0]), "L": L_symbols.index(term[1]), "J": float(term[2:]), } for term in sum(term_symbols, []) } multi = [int(item["multiplicity"]) for terms, item in term_symbol_flat.items()] max_multi_terms = { symbol: item for symbol, item in term_symbol_flat.items() if item["multiplicity"] == max(multi) } Ls = [item["L"] for terms, item in max_multi_terms.items()] max_L_terms = {symbol: item for symbol, item in term_symbol_flat.items() if item["L"] == max(Ls)} J_sorted_terms = sorted(max_L_terms.items(), key=lambda k: k[1]["J"]) L, v_e = self.valence if v_e <= (2 * L + 1): return J_sorted_terms[0][0] return J_sorted_terms[-1][0] def __eq__(self, other): return isinstance(other, Element) and self.Z == other.Z def __ne__(self, other): return not self.__eq__(other) def __hash__(self): return self.Z def __repr__(self): return "Element " + self.symbol def __str__(self): return self.symbol def __lt__(self, other): """ Sets a default sort order for atomic species by electronegativity. Very useful for getting correct formulas. For example, FeO4PLi is automatically sorted into LiFePO4. """ x1 = float("inf") if self.X != self.X else self.X x2 = float("inf") if other.X != other.X else other.X if x1 != x2: return x1 < x2 # There are cases where the electronegativity are exactly equal. # We then sort by symbol. return self.symbol < other.symbol
[docs] @staticmethod def from_Z(z: int) -> "Element": """ Get an element from an atomic number. Args: z (int): Atomic number Returns: Element with atomic number z. """ for sym, data in _pt_data.items(): if data["Atomic no"] == z: return Element(sym) raise ValueError("No element with this atomic number %s" % z)
[docs] @staticmethod def from_row_and_group(row: int, group: int) -> "Element": """ Returns an element from a row and group number. Args: row (int): Row number group (int): Group number .. note:: The 18 group number system is used, i.e., Noble gases are group 18. """ for sym in _pt_data.keys(): el = Element(sym) if el.row == row and el.group == group: return el raise ValueError("No element with this row and group!")
[docs] @staticmethod def is_valid_symbol(symbol: str) -> bool: """ Returns true if symbol is a valid element symbol. Args: symbol (str): Element symbol Returns: True if symbol is a valid element (e.g., "H"). False otherwise (e.g., "Zebra"). """ return symbol in Element.__members__
@property def row(self) -> int: """ Returns the periodic table row of the element. """ z = self.Z total = 0 if 57 <= z <= 71: return 8 if 89 <= z <= 103: return 9 for i, size in enumerate(_pt_row_sizes): total += size if total >= z: return i + 1 return 8 @property def group(self) -> int: """ Returns the periodic table group of the element. """ z = self.Z if z == 1: return 1 if z == 2: return 18 if 3 <= z <= 18: if (z - 2) % 8 == 0: return 18 if (z - 2) % 8 <= 2: return (z - 2) % 8 return 10 + (z - 2) % 8 if 19 <= z <= 54: if (z - 18) % 18 == 0: return 18 return (z - 18) % 18 if (z - 54) % 32 == 0: return 18 if (z - 54) % 32 >= 18: return (z - 54) % 32 - 14 return (z - 54) % 32 @property def block(self) -> str: """ Return the block character "s,p,d,f" """ if (self.is_actinoid or self.is_lanthanoid) and self.Z not in [71, 103]: return "f" if self.is_actinoid or self.is_lanthanoid: return "d" if self.group in [1, 2]: return "s" if self.group in range(13, 19): return "p" if self.group in range(3, 13): return "d" raise ValueError("unable to determine block") @property def is_noble_gas(self) -> bool: """ True if element is noble gas. """ return self.Z in (2, 10, 18, 36, 54, 86, 118) @property def is_transition_metal(self) -> bool: """ True if element is a transition metal. """ ns = list(range(21, 31)) ns.extend(list(range(39, 49))) ns.append(57) ns.extend(list(range(72, 81))) ns.append(89) ns.extend(list(range(104, 113))) return self.Z in ns @property def is_post_transition_metal(self) -> bool: """ True if element is a post-transition or poor metal. """ return self.symbol in ("Al", "Ga", "In", "Tl", "Sn", "Pb", "Bi") @property def is_rare_earth_metal(self) -> bool: """ True if element is a rare earth metal. """ return self.is_lanthanoid or self.is_actinoid @property def is_metal(self) -> bool: """ :return: True if is a metal. """ return ( self.is_alkali or self.is_alkaline or self.is_post_transition_metal or self.is_transition_metal or self.is_lanthanoid or self.is_actinoid ) @property def is_metalloid(self) -> bool: """ True if element is a metalloid. """ return self.symbol in ("B", "Si", "Ge", "As", "Sb", "Te", "Po") @property def is_alkali(self) -> bool: """ True if element is an alkali metal. """ return self.Z in (3, 11, 19, 37, 55, 87) @property def is_alkaline(self) -> bool: """ True if element is an alkaline earth metal (group II). """ return self.Z in (4, 12, 20, 38, 56, 88) @property def is_halogen(self) -> bool: """ True if element is a halogen. """ return self.Z in (9, 17, 35, 53, 85) @property def is_chalcogen(self) -> bool: """ True if element is a chalcogen. """ return self.Z in (8, 16, 34, 52, 84) @property def is_lanthanoid(self) -> bool: """ True if element is a lanthanoid. """ return 56 < self.Z < 72 @property def is_actinoid(self) -> bool: """ True if element is a actinoid. """ return 88 < self.Z < 104 @property def is_quadrupolar(self) -> bool: """ Checks if this element can be quadrupolar """ return len(self.data.get("NMR Quadrupole Moment", {})) > 0 @property def nmr_quadrupole_moment(self) -> dict: """ Get a dictionary the nuclear electric quadrupole moment in units of e*millibarns for various isotopes """ return {k: FloatWithUnit(v, "mbarn") for k, v in self.data.get("NMR Quadrupole Moment", {}).items()} @property def iupac_ordering(self): """ Ordering according to Table VI of "Nomenclature of Inorganic Chemistry (IUPAC Recommendations 2005)". This ordering effectively follows the groups and rows of the periodic table, except the Lanthanides, Actanides and hydrogen. """ return self._data["IUPAC ordering"] def __deepcopy__(self, memo): return Element(self.symbol)
[docs] @staticmethod def from_dict(d) -> "Element": """ Makes Element obey the general json interface used in pymatgen for easier serialization. """ return Element(d["element"])
[docs] def as_dict(self) -> dict: """ Makes Element obey the general json interface used in pymatgen for easier serialization. """ return { "@module": self.__class__.__module__, "@class": self.__class__.__name__, "element": self.symbol, }
[docs] @staticmethod def print_periodic_table(filter_function: Optional[Callable] = None): """ A pretty ASCII printer for the periodic table, based on some filter_function. Args: filter_function: A filtering function taking an Element as input and returning a boolean. For example, setting filter_function = lambda el: el.X > 2 will print a periodic table containing only elements with electronegativity > 2. """ for row in range(1, 10): rowstr = [] for group in range(1, 19): try: el = Element.from_row_and_group(row, group) except ValueError: el = None # type: ignore if el and ((not filter_function) or filter_function(el)): rowstr.append("{:3s}".format(el.symbol)) else: rowstr.append(" ") print(" ".join(rowstr))
[docs]class Element(ElementBase): """Enum representing an element in the periodic table.""" # This name = value convention is redundant and dumb, but unfortunately is # necessary to preserve backwards compatibility with a time when Element is # a regular object that is constructed with Element(symbol). H = "H" He = "He" Li = "Li" Be = "Be" B = "B" C = "C" N = "N" O = "O" F = "F" Ne = "Ne" Na = "Na" Mg = "Mg" Al = "Al" Si = "Si" P = "P" S = "S" Cl = "Cl" Ar = "Ar" K = "K" Ca = "Ca" Sc = "Sc" Ti = "Ti" V = "V" Cr = "Cr" Mn = "Mn" Fe = "Fe" Co = "Co" Ni = "Ni" Cu = "Cu" Zn = "Zn" Ga = "Ga" Ge = "Ge" As = "As" Se = "Se" Br = "Br" Kr = "Kr" Rb = "Rb" Sr = "Sr" Y = "Y" Zr = "Zr" Nb = "Nb" Mo = "Mo" Tc = "Tc" Ru = "Ru" Rh = "Rh" Pd = "Pd" Ag = "Ag" Cd = "Cd" In = "In" Sn = "Sn" Sb = "Sb" Te = "Te" I = "I" Xe = "Xe" Cs = "Cs" Ba = "Ba" La = "La" Ce = "Ce" Pr = "Pr" Nd = "Nd" Pm = "Pm" Sm = "Sm" Eu = "Eu" Gd = "Gd" Tb = "Tb" Dy = "Dy" Ho = "Ho" Er = "Er" Tm = "Tm" Yb = "Yb" Lu = "Lu" Hf = "Hf" Ta = "Ta" W = "W" Re = "Re" Os = "Os" Ir = "Ir" Pt = "Pt" Au = "Au" Hg = "Hg" Tl = "Tl" Pb = "Pb" Bi = "Bi" Po = "Po" At = "At" Rn = "Rn" Fr = "Fr" Ra = "Ra" Ac = "Ac" Th = "Th" Pa = "Pa" U = "U" Np = "Np" Pu = "Pu" Am = "Am" Cm = "Cm" Bk = "Bk" Cf = "Cf" Es = "Es" Fm = "Fm" Md = "Md" No = "No" Lr = "Lr" Rf = "Rf" Db = "Db" Sg = "Sg" Bh = "Bh" Hs = "Hs" Mt = "Mt" Ds = "Ds" Rg = "Rg" Cn = "Cn" Nh = "Nh" Fl = "Fl" Mc = "Mc" Lv = "Lv" Ts = "Ts" Og = "Og"
[docs]class Species(MSONable, Stringify): """ An extension of Element with an oxidation state and other optional properties. Properties associated with Species should be "idealized" values, not calculated values. For example, high-spin Fe2+ may be assigned an idealized spin of +5, but an actual Fe2+ site may be calculated to have a magmom of +4.5. Calculated properties should be assigned to Site objects, and not Species. """ STRING_MODE = "SUPERSCRIPT" supported_properties = ("spin",) def __init__( self, symbol: str, oxidation_state: Optional[float] = 0.0, properties: Optional[dict] = None, ): """ Initializes a Species. Args: symbol (str): Element symbol, e.g., Fe oxidation_state (float): Oxidation state of element, e.g., 2 or -2 properties: Properties associated with the Species, e.g., {"spin": 5}. Defaults to None. Properties must be one of the Species supported_properties. .. attribute:: oxi_state Oxidation state associated with Species .. attribute:: ionic_radius Ionic radius of Species (with specific oxidation state). .. versionchanged:: 2.6.7 Properties are now checked when comparing two Species for equality. """ self._el = Element(symbol) self._oxi_state = oxidation_state self._properties = properties if properties else {} for k, _ in self._properties.items(): if k not in Species.supported_properties: raise ValueError("{} is not a supported property".format(k)) def __getattr__(self, a): # overriding getattr doesn't play nice with pickle, so we # can't use self._properties p = object.__getattribute__(self, "_properties") if a in p: return p[a] return getattr(self._el, a) def __eq__(self, other): """ Species is equal to other only if element and oxidation states are exactly the same. """ return ( isinstance(other, Species) and self.symbol == other.symbol and self.oxi_state == other.oxi_state and self._properties == other._properties ) def __ne__(self, other): return not self.__eq__(other) def __hash__(self): """ Equal Species should have the same str representation, hence should hash equally. Unequal Species will have differnt str representations. """ return self.__str__().__hash__() def __lt__(self, other): """ Sets a default sort order for atomic species by electronegativity, followed by oxidation state, followed by spin. """ x1 = float("inf") if self.X != self.X else self.X x2 = float("inf") if other.X != other.X else other.X if x1 != x2: return x1 < x2 if self.symbol != other.symbol: # There are cases where the electronegativity are exactly equal. # We then sort by symbol. return self.symbol < other.symbol if self.oxi_state: other_oxi = 0 if (isinstance(other, Element) or other.oxi_state is None) else other.oxi_state return self.oxi_state < other_oxi if getattr(self, "spin", False): other_spin = getattr(other, "spin", 0) return self.spin < other_spin return False @property def element(self): """ Underlying element object """ return self._el @property def ionic_radius(self) -> Optional[float]: """ Ionic radius of specie. Returns None if data is not present. """ if self._oxi_state in self.ionic_radii: return self.ionic_radii[self._oxi_state] if self._oxi_state: d = self._el.data oxstr = str(int(self._oxi_state)) if oxstr in d.get("Ionic radii hs", {}): warnings.warn("No default ionic radius for %s. Using hs data." % self) return d["Ionic radii hs"][oxstr] if oxstr in d.get("Ionic radii ls", {}): warnings.warn("No default ionic radius for %s. Using ls data." % self) return d["Ionic radii ls"][oxstr] warnings.warn("No ionic radius for {}!".format(self)) return None @property def oxi_state(self) -> Optional[float]: """ Oxidation state of Species. """ return self._oxi_state
[docs] @staticmethod def from_string(species_string: str) -> "Species": """ Returns a Species from a string representation. Args: species_string (str): A typical string representation of a species, e.g., "Mn2+", "Fe3+", "O2-". Returns: A Species object. Raises: ValueError if species_string cannot be intepreted. """ # e.g. Fe2+,spin=5 # 1st group: ([A-Z][a-z]*) --> Fe # 2nd group: ([0-9.]*) --> "2" # 3rd group: ([+\-]) --> + # 4th group: (.*) --> everything else, ",spin=5" m = re.search(r"([A-Z][a-z]*)([0-9.]*)([+\-]*)(.*)", species_string) if m: # parse symbol sym = m.group(1) # parse oxidation state (optional) if not m.group(2) and not m.group(3): oxi = None else: oxi = 1 if m.group(2) == "" else float(m.group(2)) oxi = -oxi if m.group(3) == "-" else oxi # parse properties (optional) properties = None if m.group(4): toks = m.group(4).replace(",", "").split("=") properties = {toks[0]: ast.literal_eval(toks[1])} # but we need either an oxidation state or a property if oxi is None and properties is None: raise ValueError("Invalid Species String") return Species(sym, 0 if oxi is None else oxi, properties) raise ValueError("Invalid Species String")
def __repr__(self): return "Species " + self.__str__() def __str__(self): output = self.symbol if self.oxi_state is not None: if self.oxi_state >= 0: output += formula_double_format(self.oxi_state) + "+" else: output += formula_double_format(-self.oxi_state) + "-" for p, v in self._properties.items(): output += ",%s=%s" % (p, v) return output
[docs] def to_pretty_string(self) -> str: """ :return: String without properties. """ output = self.symbol if self.oxi_state is not None: if self.oxi_state >= 0: output += formula_double_format(self.oxi_state) + "+" else: output += formula_double_format(-self.oxi_state) + "-" return output
[docs] def get_nmr_quadrupole_moment(self, isotope: Optional[str] = None) -> float: """ Gets the nuclear electric quadrupole moment in units of e*millibarns Args: isotope (str): the isotope to get the quadrupole moment for default is None, which gets the lowest mass isotope """ quad_mom = self._el.nmr_quadrupole_moment if not quad_mom: return 0.0 if isotope is None: isotopes = list(quad_mom.keys()) isotopes.sort(key=lambda x: int(x.split("-")[1]), reverse=False) return quad_mom.get(isotopes[0], 0.0) if isotope not in quad_mom: raise ValueError("No quadrupole moment for isotope {}".format(isotope)) return quad_mom.get(isotope, 0.0)
[docs] def get_shannon_radius(self, cn: str, spin: str = "", radius_type: str = "ionic") -> float: """ Get the local environment specific ionic radius for species. Args: cn (str): Coordination using roman letters. Supported values are I-IX, as well as IIIPY, IVPY and IVSQ. spin (str): Some species have different radii for different spins. You can get specific values using "High Spin" or "Low Spin". Leave it as "" if not available. If only one spin data is available, it is returned and this spin parameter is ignored. radius_type (str): Either "crystal" or "ionic" (default). Returns: Shannon radius for specie in the specified environment. """ radii = self._el.data["Shannon radii"] radii = radii[str(int(self._oxi_state))][cn] # type: ignore if len(radii) == 1: # type: ignore k, data = list(radii.items())[0] # type: ignore if k != spin: warnings.warn( "Specified spin state of %s not consistent with database " "spin of %s. Only one spin data available, and " "that value is returned." % (spin, k) ) else: data = radii[spin] return data["%s_radius" % radius_type]
[docs] def get_crystal_field_spin(self, coordination: str = "oct", spin_config: str = "high") -> float: """ Calculate the crystal field spin based on coordination and spin configuration. Only works for transition metal species. Args: coordination (str): Only oct and tet are supported at the moment. spin_config (str): Supported keywords are "high" or "low". Returns: Crystal field spin in Bohr magneton. Raises: AttributeError if species is not a valid transition metal or has an invalid oxidation state. ValueError if invalid coordination or spin_config. """ if coordination not in ("oct", "tet") or spin_config not in ("high", "low"): raise ValueError("Invalid coordination or spin config.") elec = self.full_electronic_structure if len(elec) < 4 or elec[-1][1] != "s" or elec[-2][1] != "d": raise AttributeError("Invalid element {} for crystal field calculation.".format(self.symbol)) nelectrons = elec[-1][2] + elec[-2][2] - self.oxi_state if nelectrons < 0 or nelectrons > 10: raise AttributeError("Invalid oxidation state {} for element {}".format(self.oxi_state, self.symbol)) if spin_config == "high": if nelectrons <= 5: return nelectrons return 10 - nelectrons if spin_config == "low": if coordination == "oct": if nelectrons <= 3: return nelectrons if nelectrons <= 6: return 6 - nelectrons if nelectrons <= 8: return nelectrons - 6 return 10 - nelectrons if coordination == "tet": if nelectrons <= 2: return nelectrons if nelectrons <= 4: return 4 - nelectrons if nelectrons <= 7: return nelectrons - 4 return 10 - nelectrons raise RuntimeError()
def __deepcopy__(self, memo): return Species(self.symbol, self.oxi_state, self._properties)
[docs] def as_dict(self) -> dict: """ :return: Json-able dictionary representation. """ d = { "@module": self.__class__.__module__, "@class": self.__class__.__name__, "element": self.symbol, "oxidation_state": self._oxi_state, } if self._properties: d["properties"] = self._properties return d
[docs] @classmethod def from_dict(cls, d) -> "Species": """ :param d: Dict representation. :return: Species. """ return cls(d["element"], d["oxidation_state"], d.get("properties", None))
[docs]class DummySpecies(Species): """ A special specie for representing non-traditional elements or species. For example, representation of vacancies (charged or otherwise), or special sites, etc. .. attribute:: oxi_state Oxidation state associated with Species. .. attribute:: Z DummySpecies is always assigned an atomic number equal to the hash number of the symbol. Obviously, it makes no sense whatsoever to use the atomic number of a Dummy specie for anything scientific. The purpose of this is to ensure that for most use cases, a DummySpecies behaves no differently from an Element or Species. .. attribute:: X DummySpecies is always assigned an electronegativity of 0. """ def __init__( self, symbol: str = "X", oxidation_state: Optional[float] = 0, properties: Optional[dict] = None, ): """ Args: symbol (str): An assigned symbol for the dummy specie. Strict rules are applied to the choice of the symbol. The dummy symbol cannot have any part of first two letters that will constitute an Element symbol. Otherwise, a composition may be parsed wrongly. E.g., "X" is fine, but "Vac" is not because Vac contains V, a valid Element. oxidation_state (float): Oxidation state for dummy specie. Defaults to zero. """ # enforce title case to match other elements, reduces confusion # when multiple DummySpecies in a "formula" string symbol = symbol.title() for i in range(1, min(2, len(symbol)) + 1): if Element.is_valid_symbol(symbol[:i]): raise ValueError("{} contains {}, which is a valid element " "symbol.".format(symbol, symbol[:i])) # Set required attributes for DummySpecies to function like a Species in # most instances. self._symbol = symbol self._oxi_state = oxidation_state self._properties = properties if properties else {} for k, _ in self._properties.items(): if k not in Species.supported_properties: raise ValueError("{} is not a supported property".format(k)) def __getattr__(self, a): # overriding getattr doens't play nice with pickle, so we # can't use self._properties p = object.__getattribute__(self, "_properties") if a in p: return p[a] raise AttributeError(a) def __hash__(self): return self.symbol.__hash__() def __eq__(self, other): """ Species is equal to other only if element and oxidation states are exactly the same. """ if not isinstance(other, DummySpecies): return False return ( isinstance(other, Species) and self.symbol == other.symbol and self.oxi_state == other.oxi_state and self._properties == other._properties ) def __ne__(self, other): return not self.__eq__(other) def __lt__(self, other): """ Sets a default sort order for atomic species by electronegativity, followed by oxidation state. """ if self.X != other.X: return self.X < other.X if self.symbol != other.symbol: # There are cases where the electronegativity are exactly equal. # We then sort by symbol. return self.symbol < other.symbol other_oxi = 0 if isinstance(other, Element) else other.oxi_state return self.oxi_state < other_oxi @property def Z(self) -> int: """ DummySpecies is always assigned an atomic number equal to the hash of the symbol. The expectation is that someone would be an actual dummy to use atomic numbers for a Dummy specie. """ return self.symbol.__hash__() @property def oxi_state(self) -> Optional[float]: """ Oxidation state associated with DummySpecies """ return self._oxi_state @property def X(self) -> float: """ DummySpecies is always assigned an electronegativity of 0. The effect of this is that DummySpecies are always sorted in front of actual Species. """ return 0.0 @property def symbol(self) -> str: """ :return: Symbol for DummySpecies. """ return self._symbol def __deepcopy__(self, memo): return DummySpecies(self.symbol, self._oxi_state)
[docs] @staticmethod def from_string(species_string: str) -> "DummySpecies": """ Returns a Dummy from a string representation. Args: species_string (str): A string representation of a dummy species, e.g., "X2+", "X3+". Returns: A DummySpecies object. Raises: ValueError if species_string cannot be intepreted. """ m = re.search(r"([A-ZAa-z]*)([0-9.]*)([+\-]*)(.*)", species_string) if m: sym = m.group(1) if m.group(2) == "" and m.group(3) == "": oxi = 0.0 else: oxi = 1.0 if m.group(2) == "" else float(m.group(2)) oxi = -oxi if m.group(3) == "-" else oxi properties = None if m.group(4): toks = m.group(4).split("=") properties = {toks[0]: float(toks[1])} return DummySpecies(sym, oxi, properties) raise ValueError("Invalid DummySpecies String")
[docs] def as_dict(self) -> dict: """ :return: MSONAble dict representation. """ d = { "@module": self.__class__.__module__, "@class": self.__class__.__name__, "element": self.symbol, "oxidation_state": self._oxi_state, } if self._properties: d["properties"] = self._properties # type: ignore return d
[docs] @classmethod def from_dict(cls, d) -> "DummySpecies": """ :param d: Dict representation :return: DummySpecies """ return cls(d["element"], d["oxidation_state"], d.get("properties", None))
def __repr__(self): return "DummySpecies " + self.__str__() def __str__(self): output = self.symbol if self.oxi_state is not None: if self.oxi_state >= 0: output += formula_double_format(self.oxi_state) + "+" else: output += formula_double_format(-self.oxi_state) + "-" for p, v in self._properties.items(): output += ",%s=%s" % (p, v) return output
[docs]class Specie(Species): """ This maps the historical grammatically inaccurate Specie to Species to maintain backwards compatibility. """ pass
[docs]class DummySpecie(DummySpecies): """ This maps the historical grammatically inaccurate DummySpecie to DummySpecies to maintain backwards compatibility. """ pass
[docs]def get_el_sp(obj) -> Union[Element, Species, DummySpecies]: """ Utility method to get an Element or Species from an input obj. If obj is in itself an element or a specie, it is returned automatically. If obj is an int or a string representing an integer, the Element with the atomic number obj is returned. If obj is a string, Species parsing will be attempted (e.g., Mn2+), failing which Element parsing will be attempted (e.g., Mn), failing which DummyElement parsing will be attempted. Args: obj (Element/Species/str/int): An arbitrary object. Supported objects are actual Element/Species objects, integers (representing atomic numbers) or strings (element symbols or species strings). Returns: Species or Element, with a bias for the maximum number of properties that can be determined. Raises: ValueError if obj cannot be converted into an Element or Species. """ if isinstance(obj, (Element, Species, DummySpecies)): return obj try: c = float(obj) i = int(c) i = i if i == c else None # type: ignore except (ValueError, TypeError): i = None # type: ignore if i is not None: return Element.from_Z(i) try: return Species.from_string(obj) except (ValueError, KeyError): try: return Element(obj) except (ValueError, KeyError): try: return DummySpecies.from_string(obj) except Exception: raise ValueError("Can't parse Element or String from type" " %s: %s." % (type(obj), obj))