Source code for pymatgen.core.periodic_table

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

from __future__ import division, unicode_literals, print_function

import os
import re
import json
import warnings
from io import open
from enum import Enum

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

"""
Module contains classes presenting Element and Specie (Element + oxidation
state) and PeriodicTable.
"""


__author__ = "Shyue Ping Ong, Michael Kocher"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "2.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__status__ = "Production"
__date__ = "Sep 23, 2011"


# Loads element data from json file
with open(os.path.join(os.path.dirname(__file__),
                       "periodic_table.json"), "rt") as f:
    _pt_data = json.load(f)

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


[docs]class Element(Enum): """ 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_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:: 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 .. 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. Simplified form with HTML formatting. E.g., The electronic structure for Fe is represented as [Ar].3d<sup>6</sup>.4s<sup>2</sup> .. 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:: ionic_radii All ionic radii of the element as a dict of {oxidation state: ionic radii}. Radii are given in ang. """ # 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" def __init__(self, symbol): 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._data = d @property def X(self): if "X" in self._data: return self._data["X"] else: warnings.warn("No electronegativity for %s. Setting to infinity. " "This has no physical meaning, and is mainly done to " "avoid errors caused by the code expecting a float." % self.symbol) return float("inf") def __getattr__(self, item): if item in ["mendeleev_no", "electrical_resistivity", "velocity_of_sound", "reflectivity", "refractive_index", "poissons_ratio", "molar_volume", "electronic_structure", "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", "coefficient_of_linear_thermal_expansion"]: kstr = item.capitalize().replace("_", " ") val = self._data.get(kstr, None) if str(val).startswith("no data"): val = None 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 as ex: # Ignore error. val will just remain a string. pass return val raise AttributeError @property def data(self): """ Returns dict of data for element. """ return self._data.copy() @property @unitized("ang") 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"] return sum(radii.values()) / len(radii) else: return 0 @property @unitized("ang") 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): v for k, v in self._data["Ionic radii"].items()} else: 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 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._data["Electronic structure"] def parse_orbital(orbstr): m = re.match(r"(\d+)([spdfg]+)<sup>(\d+)</sup>", 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 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. """ if self.X != other.X: return self.X < other.X else: # 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): """ 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, group): """ 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): """ 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"). """ try: Element(symbol) return True except: return False
@property def row(self): """ Returns the periodic table row of the element. """ z = self.Z total = 0 if 57 <= z <= 71: return 8 elif 89 <= z <= 103: return 9 for i in range(len(_pt_row_sizes)): total += _pt_row_sizes[i] 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 elif (z - 2) % 8 <= 2: return (z - 2) % 8 else: return 10 + (z - 2) % 8 if 19 <= z <= 54: if (z - 18) % 18 == 0: return 18 else: return (z - 18) % 18 if (z - 54) % 32 == 0: return 18 elif (z - 54) % 32 >= 18: return (z - 54) % 32 - 14 else: return (z - 54) % 32 @property def block(self): """ Return the block character "s,p,d,f" """ block = "" if (self.is_actinoid or self.is_lanthanoid) and \ self.Z not in [71, 103]: block = "f" elif self.is_actinoid or self.is_lanthanoid: block = "d" elif self.group in [1, 2]: block = "s" elif self.group in range(13, 19): block = "p" elif self.group in range(3, 13): block = "d" else: raise ValueError("unable to determine block") return 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_rare_earth_metal(self): """ True if element is a rare earth metal. """ return self.is_lanthanoid or self.is_actinoid @property def is_metalloid(self): """ True if element is a metalloid. """ return self.symbol in ("B", "Si", "Ge", "As", "Sb", "Te", "Po") @property def is_alkali(self): """ True if element is an alkali metal. """ return self.Z in (3, 11, 19, 37, 55, 87) @property def is_alkaline(self): """ 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 def __deepcopy__(self, memo): return Element(self.symbol)
[docs] @staticmethod def from_dict(d): """ Makes Element obey the general json interface used in pymatgen for easier serialization. """ return Element(d["element"])
[docs] 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}
[docs] @staticmethod def print_periodic_table(filter_function=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))
[docs]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. 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. """ cache = {} def __new__(cls, *args, **kwargs): key = (cls,) + args + tuple(kwargs.items()) try: inst = Specie.cache.get(key, None) except TypeError: # Can't cache this set of arguments inst = key = None if inst is None: inst = object.__new__(cls) if key is not None: Specie.cache[key] = inst return inst supported_properties = ("spin",) def __init__(self, symbol, oxidation_state=None, properties=None): 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] try: return getattr(self._el, a) except: raise AttributeError(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. """ if self.X != other.X: return self.X < other.X elif self.symbol != other.symbol: # There are cases where the electronegativity are exactly equal. # We then sort by symbol. return self.symbol < other.symbol else: other_oxi = 0 if isinstance(other, Element) else other.oxi_state return self.oxi_state < other_oxi @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] elif 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
[docs] @staticmethod def from_string(species_string): """ 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) else: 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
[docs] def get_crystal_field_spin(self, coordination="oct", spin_config="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": return nelectrons if nelectrons <= 5 else 10 - nelectrons elif spin_config == "low": if coordination == "oct": if nelectrons <= 3: return nelectrons elif nelectrons <= 6: return 6 - nelectrons elif nelectrons <= 8: return nelectrons - 6 else: return 10 - nelectrons elif coordination == "tet": if nelectrons <= 2: return nelectrons elif nelectrons <= 4: return 4 - nelectrons elif nelectrons <= 7: return nelectrons - 4 else: return 10 - nelectrons
def __deepcopy__(self, memo): return Specie(self.symbol, self.oxi_state, self._properties)
[docs] def as_dict(self): 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): return cls(d["element"], d["oxidation_state"], d.get("properties", None))
[docs]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. 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. .. attribute:: symbol Symbol for the DummySpecie. .. attribute:: oxi_state Oxidation state associated with Specie. .. attribute:: Z DummySpecie is always assigned an atomic number of 0. .. attribute:: X DummySpecie is always assigned an electronegativity of 0. """ def __init__(self, symbol="X", oxidation_state=0, properties=None): 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] try: return getattr(self._el, a) except: 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 self.symbol == other.symbol \ and self._oxi_state == other._oxi_state 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 elif self.symbol != other.symbol: # There are cases where the electronegativity are exactly equal. # We then sort by symbol. return self.symbol < other.symbol else: other_oxi = 0 if isinstance(other, Element) else other.oxi_state return self.oxi_state < other_oxi @property def Z(self): """ 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): """ Oxidation state associated with DummySpecie """ return self._oxi_state @property def X(self): """ 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 @property def symbol(self): return self._symbol def __deepcopy__(self, memo): return DummySpecie(self.symbol, self._oxi_state)
[docs] @staticmethod def from_string(species_string): """ 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-Z][a-z]*)([0-9.]*)([+\-]*)(.*)", species_string) if m: sym = m.group(1) if m.group(2) == "" and m.group(3) == "": oxi = 0 else: 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).split("=") properties = {toks[0]: float(toks[1])} return DummySpecie(sym, oxi, properties) raise ValueError("Invalid DummySpecies String")
[docs] @classmethod def safe_from_composition(cls, comp, oxidation_state=0): """ Returns a DummySpecie object that can be safely used with (i.e. not present in) a given composition """ # We don't want to add a DummySpecie with the same # symbol as anything in the composition, even if the # oxidation state is different els = comp.element_composition.elements for c in 'abcdfghijklmnopqrstuvwxyz': if DummySpecie('X' + c) not in els: return DummySpecie('X' + c, oxidation_state) raise ValueError("All attempted DummySpecies already " "present in {}".format(comp))
[docs] def as_dict(self): 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): 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 >= 0: output += formula_double_format(self._oxi_state) + "+" else: output += formula_double_format(-self._oxi_state) + "-" return output
[docs]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: raise ValueError("Can't parse Element or String from type" " %s: %s." % (type(obj), obj))