pymatgen.core.periodic_table — pymatgen 2020.7.3 documentation

# 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 Specie (Element + oxidation state) and PeriodicTable."""

    import re
    import json
    import warnings
    from io import open
    from pathlib import Path
    from enum import Enum
    from typing import Optional, Callable
    from itertools import product, \
        combinations
    from collections import Counter

    import numpy as np

    from pymatgen.core.units import Mass, Length, FloatWithUnit, Unit, \
        SUPPORTED_UNIT_NAMES
    from pymatgen.util.string import formula_double_format
    from monty.json import MSONable

    # 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)

    class Element(Enum):
        """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"

        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:: X

                Pauling electronegativity. Elements without an electronegativity
                number are assigned a value of zero by default.

            .. attribute:: number

                Alternative attribute for atomic number

            .. attribute:: max_oxidation_state

                Maximum oxidation state for element

            .. attribute:: min_oxidation_state

                Minimum oxidation state for element

            .. attribute:: oxidation_states

                Tuple of all known oxidation states

            .. attribute:: common_oxidation_states

                Tuple of all common oxidation states

            .. attribute:: full_electronic_structure

                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)]

            .. attribute:: row

                Returns the periodic table row of the element.

            .. attribute:: group

                Returns the periodic table group of the element.

            .. attribute:: block

                Return the block character "s,p,d,f"

            .. attribute:: is_noble_gas

                True if element is noble gas.

            .. attribute:: is_transition_metal

                True if element is a transition metal.

            .. attribute:: is_post_transition_metal

                True if element is a post transition metal.

            .. attribute:: is_rare_earth_metal

                True if element is a rare earth metal.

            .. attribute:: is_metalloid

                True if element is a metalloid.

            .. attribute:: is_alkali

                True if element is an alkali metal.

            .. attribute:: is_alkaline

                True if element is an alkaline earth metal (group II).

            .. attribute:: is_halogen

                True if element is a halogen.

            .. attribute:: is_lanthanoid

                True if element is a lanthanoid.

            .. attribute:: is_actinoid

                True if element is a actinoid.

            .. attribute:: iupac_ordering

                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.

            .. attribute:: long_name

               Long name for element. E.g., "Hydrogen".

            .. attribute:: atomic_mass

                Atomic mass for the element.

            .. attribute:: atomic_radius

                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:: 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:: average_ionic_radius

                Average ionic radius for element in ang. The average is taken over all
                oxidation states of the element for which data is present.

            .. attribute:: average_cationic_radius

                Average cationic radius for element in ang. The average is taken over all
                positive oxidation states of the element for which data is present.

            .. attribute:: average_anionic_radius

                Average ionic radius for element in ang. The average is taken over all
                negative oxidation states of the element for which data is present.

            .. attribute:: ionic_radii

                All ionic radii of the element as a dict of
                {oxidation state: ionic radii}. Radii are given in ang.
            """
            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):
            """
            :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):
            """
            Returns: The atomic radius of the element in Ångstroms.
            """
            return self._atomic_radius

        @property
        def atomic_mass(self):
            """
            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"]:
                kstr = item.capitalize().replace("_", " ")
                val = self._data.get(kstr, None)
                if str(val).startswith("no data"):
                    val = None
                elif isinstance(val, 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 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):
            """
            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):
            """
            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):
            """
            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):
            """
            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):
            """Alternative attribute for atomic number"""
            return self.Z

        @property
        def max_oxidation_state(self):
            """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):
            """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 of all known oxidation states"""
            return tuple(self._data.get("Oxidation states", list()))

        @property
        def common_oxidation_states(self):
            """Tuple of all known oxidation states"""
            return tuple(self._data.get("Common oxidation states", list()))

        @property
        def icsd_oxidation_states(self):
            """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):
            """
            Metallic radius of the element. Radius is given in ang.
            """
            return FloatWithUnit(self._data["Metallic radius"], "ang")

        @property
        def full_electronic_structure(self):
            """
            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 = Element(sym).full_electronic_structure + data[1:]
            return data

        @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
            for _, l_symbol, ne in full_electron_config[::-1]:
                l = L_symbols.lower().index(l_symbol)
                if ne < (2 * l + 1) * 2:
                    valence.append((l, ne))
            if len(valence) > 1:
                raise ValueError("Ambiguous valence")

            return valence[0]

        @property
        def term_symbols(self):
            """
            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([r for r in 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

        @staticmethod
        def from_Z(z: int):
            """
            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)

        @staticmethod
        def from_row_and_group(row: int, group: int):
            """
            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!")

        @staticmethod
        def is_valid_symbol(symbol: str):
            """
            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):
            """
            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):
            """
            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):
            """
            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):
            """
            True if element is noble gas.
            """
            return self.Z in (2, 10, 18, 36, 54, 86, 118)

        @property
        def is_transition_metal(self):
            """
            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):
            """
            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):
            """
            True if element is a halogen.
            """
            return self.Z in (9, 17, 35, 53, 85)

        @property
        def is_chalcogen(self):
            """
            True if element is a chalcogen.
            """
            return self.Z in (8, 16, 34, 52, 84)

        @property
        def is_lanthanoid(self):
            """
            True if element is a lanthanoid.
            """
            return 56 < self.Z < 72

        @property
        def is_actinoid(self):
            """
            True if element is a actinoid.
            """
            return 88 < self.Z < 104

        @property
        def is_quadrupolar(self):
            """
            Checks if this element can be quadrupolar
            """
            return len(self.data.get("NMR Quadrupole Moment", {})) > 0

        @property
        def nmr_quadrupole_moment(self):
            """
            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)

        @staticmethod
        def from_dict(d):
            """
            Makes Element obey the general json interface used in pymatgen for
            easier serialization.
            """
            return Element(d["element"])

        def as_dict(self):
            """
            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}

        @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
                    if el and ((not filter_function) or filter_function(el)):
                        rowstr.append("{:3s}".format(el.symbol))
                    else:
                        rowstr.append("   ")
                print(" ".join(rowstr))

    class Specie(MSONable):
        """
        An extension of Element with an oxidation state and other optional
        properties. Properties associated with Specie 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 Specie.
        """

        supported_properties = ("spin",)

        def __init__(self, symbol: str,
                     oxidation_state: float = 0.0,
                     properties: dict = None):
            """
            Initializes a Specie.

            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 Specie, e.g.,
                    {"spin": 5}. Defaults to None. Properties must be one of the
                    Specie supported_properties.

            .. attribute:: oxi_state

                Oxidation state associated with Specie

            .. attribute:: ionic_radius

                Ionic radius of Specie (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.keys():
                if k not in Specie.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):
            """
            Specie is equal to other only if element and oxidation states are
            exactly the same.
            """
            return (isinstance(other, Specie) 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 Specie should have the same str representation, hence
            should hash equally. Unequal Specie 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):
            """
            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]
            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):
            """
            Oxidation state of Specie.
            """
            return self._oxi_state

        @staticmethod
        def from_string(species_string: str):
            """
            Returns a Specie from a string representation.

            Args:
                species_string (str): A typical string representation of a
                    species, e.g., "Mn2+", "Fe3+", "O2-".

            Returns:
                A Specie object.

            Raises:
                ValueError if species_string cannot be intepreted.
            """
            m = re.search(r"([A-Z][a-z]*)([0-9.]*)([+\-])(.*)", species_string)
            if m:
                sym = m.group(1)
                oxi = 1 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).replace(",", "").split("=")
                    properties = {toks[0]: float(toks[1])}
                return Specie(sym, oxi, properties)
            raise ValueError("Invalid Species String")

        def __repr__(self):
            return "Specie " + 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

        def get_nmr_quadrupole_moment(self, isotope=None):
            """
            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)

        def get_shannon_radius(self, cn: str, spin: str = "",
                               radius_type: str = "ionic"):
            """
            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]

        def get_crystal_field_spin(self, coordination: str = "oct",
                                   spin_config: str = "high"):
            """
            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 Specie(self.symbol, self.oxi_state, self._properties)

        def as_dict(self):
            """
            :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

        @classmethod
        def from_dict(cls, d):
            """
            :param d: Dict representation.
            :return: Specie.
            """
            return cls(d["element"], d["oxidation_state"],
                       d.get("properties", None))

    class DummySpecie(Specie):
        """
        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 Specie.

        .. attribute:: Z

            DummySpecie 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 DummySpecie behaves no
            differently from an Element or Specie.

        .. attribute:: X

            DummySpecie is always assigned an electronegativity of 0.
        """

        def __init__(self,
                     symbol: str = "X",
                     oxidation_state: float = 0,
                     properties: 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 DummySpecie 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 DummySpecie to function like a Specie in
            # most instances.
            self._symbol = symbol
            self._oxi_state = oxidation_state
            self._properties = properties if properties else {}
            for k in self._properties.keys():
                if k not in Specie.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):
            """
            Specie is equal to other only if element and oxidation states are
            exactly the same.
            """
            if not isinstance(other, DummySpecie):
                return False
            return (isinstance(other, Specie) 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:
            """
            DummySpecie 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) -> float:
            """
            Oxidation state associated with DummySpecie
            """
            return self._oxi_state

        @property
        def X(self) -> float:
            """
            DummySpecie is always assigned an electronegativity of 0. The effect of
            this is that DummySpecie are always sorted in front of actual Specie.
            """
            return 0.0

        @property
        def symbol(self) -> str:
            """
            :return: Symbol for DummySpecie.
            """
            return self._symbol

        def __deepcopy__(self, memo):
            return DummySpecie(self.symbol, self._oxi_state)

        @staticmethod
        def from_string(species_string: str):
            """
            Returns a Dummy from a string representation.

            Args:
                species_string (str): A string representation of a dummy
                    species, e.g., "X2+", "X3+".

            Returns:
                A DummySpecie 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 DummySpecie(sym, oxi, properties)
            raise ValueError("Invalid DummySpecies String")

        def as_dict(self):
            """
            :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
            return d

        @classmethod
        def from_dict(cls, d):
            """
            :param d: Dict representation
            :return: DummySpecie
            """
            return cls(d["element"], d["oxidation_state"],
                       d.get("properties", None))

        def __repr__(self):
            return "DummySpecie " + 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

    def get_el_sp(obj):
        """
        Utility method to get an Element or Specie 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, Specie 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/Specie/str/int): An arbitrary object.  Supported objects
                are actual Element/Specie objects, integers (representing atomic
                numbers) or strings (element symbols or species strings).

        Returns:
            Specie 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 Specie.
        """
        if isinstance(obj, (Element, Specie, DummySpecie)):
            return obj

        if isinstance(obj, (list, tuple)):
            return [get_el_sp(o) for o in obj]

        try:
            c = float(obj)
            i = int(c)
            i = i if i == c else None
        except (ValueError, TypeError):
            i = None

        if i is not None:
            return Element.from_Z(i)

        try:
            return Specie.from_string(obj)
        except (ValueError, KeyError):
            try:
                return Element(obj)
            except (ValueError, KeyError):
                try:
                    return DummySpecie.from_string(obj)
                except Exception:
                    raise ValueError("Can't parse Element or String from type"
                                     " %s: %s." % (type(obj), obj))