pymatgen.core.periodic_table module

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

class DummySpecie(symbol: str = 'X', oxidation_state: Optional[float] = 0, properties: dict = None)

Bases: pymatgen.core.periodic_table.DummySpecies

This maps the historical grammatically inaccurate DummySpecie to DummySpecies to maintain backwards compatibility.

Parameters

• 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.

class DummySpecies(symbol: str = 'X', oxidation_state: Optional[float] = 0, properties: dict = None)

Bases: pymatgen.core.periodic_table.Species

A special specie for representing non-traditional elements or species. For example, representation of vacancies (charged or otherwise), or special sites, etc.

oxi_state

Oxidation state associated with Species.

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.

X

DummySpecies is always assigned an electronegativity of 0.

Parameters

• 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.

property X

DummySpecies is always assigned an electronegativity of 0. The effect of this is that DummySpecies are always sorted in front of actual Species.

property Z

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.

as_dict()

Returns

MSONAble dict representation.

classmethod from_dict(d)

Parameters

d – Dict representation

Returns

DummySpecies

static from_string(species_string: str)

Returns a Dummy from a string representation.

Parameters

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. –

property oxi_state

Oxidation state associated with DummySpecies

property symbol

Symbol for DummySpecies.

Type

return

class Element(value)

Bases: enum.Enum

Enum representing an element in the periodic table.

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.

Parameters

symbol (str) – Element symbol, e.g., “H”, “Fe”

Z

Atomic number

symbol

Element symbol

X

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

number

Alternative attribute for atomic number

max_oxidation_state

Maximum oxidation state for element

min_oxidation_state

Minimum oxidation state for element

oxidation_states

Tuple of all known oxidation states

common_oxidation_states

Tuple of all common oxidation states

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)]

row

Returns the periodic table row of the element.

group

Returns the periodic table group of the element.

block

Return the block character “s,p,d,f”

is_noble_gas

True if element is noble gas.

is_transition_metal

True if element is a transition metal.

is_post_transition_metal

True if element is a post transition metal.

is_rare_earth_metal

True if element is a rare earth metal.

is_metalloid

True if element is a metalloid.

is_alkali

True if element is an alkali metal.

is_alkaline

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

is_halogen

True if element is a halogen.

is_lanthanoid

True if element is a lanthanoid.

is_actinoid

True if element is a actinoid.

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.

long_name

Long name for element. E.g., “Hydrogen”.

atomic_mass

Atomic mass for the element.

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).

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).

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).

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

electrical_resistivity

Electrical resistivity

velocity_of_sound

Velocity of sound

reflectivity

Reflectivity

refractive_index

Refractice index

poissons_ratio

Poisson’s ratio

molar_volume

Molar volume

electronic_structure

Electronic structure. E.g., The electronic structure for Fe is represented as [Ar].3d6.4s2

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

thermal_conductivity

Thermal conductivity

boiling_point

Boiling point

melting_point

Melting point

critical_temperature

Critical temperature

superconduction_temperature

Superconduction temperature

liquid_range

Liquid range

bulk_modulus

Bulk modulus

youngs_modulus

Young’s modulus

brinell_hardness

Brinell hardness

rigidity_modulus

Rigidity modulus

mineral_hardness

Mineral hardness

vickers_hardness

Vicker’s hardness

density_of_solid

Density of solid phase

coefficient_of_linear_thermal_expansion

Coefficient of linear thermal expansion

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.

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.

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.

ionic_radii

All ionic radii of the element as a dict of {oxidation state: ionic radii}. Radii are given in ang.

Ac = 'Ac'

Ag = 'Ag'

Al = 'Al'

Am = 'Am'

Ar = 'Ar'

As = 'As'

At = 'At'

Au = 'Au'

B = 'B'

Ba = 'Ba'

Be = 'Be'

Bh = 'Bh'

Bi = 'Bi'

Bk = 'Bk'

Br = 'Br'

C = 'C'

Ca = 'Ca'

Cd = 'Cd'

Ce = 'Ce'

Cf = 'Cf'

Cl = 'Cl'

Cm = 'Cm'

Cn = 'Cn'

Co = 'Co'

Cr = 'Cr'

Cs = 'Cs'

Cu = 'Cu'

Db = 'Db'

Ds = 'Ds'

Dy = 'Dy'

Er = 'Er'

Es = 'Es'

Eu = 'Eu'

F = 'F'

Fe = 'Fe'

Fl = 'Fl'

Fm = 'Fm'

Fr = 'Fr'

Ga = 'Ga'

Gd = 'Gd'

Ge = 'Ge'

H = 'H'

He = 'He'

Hf = 'Hf'

Hg = 'Hg'

Ho = 'Ho'

Hs = 'Hs'

I = 'I'

In = 'In'

Ir = 'Ir'

K = 'K'

Kr = 'Kr'

La = 'La'

Li = 'Li'

Lr = 'Lr'

Lu = 'Lu'

Lv = 'Lv'

Mc = 'Mc'

Md = 'Md'

Mg = 'Mg'

Mn = 'Mn'

Mo = 'Mo'

Mt = 'Mt'

N = 'N'

Na = 'Na'

Nb = 'Nb'

Nd = 'Nd'

Ne = 'Ne'

Nh = 'Nh'

Ni = 'Ni'

No = 'No'

Np = 'Np'

O = 'O'

Og = 'Og'

Os = 'Os'

P = 'P'

Pa = 'Pa'

Pb = 'Pb'

Pd = 'Pd'

Pm = 'Pm'

Po = 'Po'

Pr = 'Pr'

Pt = 'Pt'

Pu = 'Pu'

Ra = 'Ra'

Rb = 'Rb'

Re = 'Re'

Rf = 'Rf'

Rg = 'Rg'

Rh = 'Rh'

Rn = 'Rn'

Ru = 'Ru'

S = 'S'

Sb = 'Sb'

Sc = 'Sc'

Se = 'Se'

Sg = 'Sg'

Si = 'Si'

Sm = 'Sm'

Sn = 'Sn'

Sr = 'Sr'

Ta = 'Ta'

Tb = 'Tb'

Tc = 'Tc'

Te = 'Te'

Th = 'Th'

Ti = 'Ti'

Tl = 'Tl'

Tm = 'Tm'

Ts = 'Ts'

U = 'U'

V = 'V'

W = 'W'

property X

Electronegativity of element. Note that if an element does not have an electronegativity, a NaN float is returned.

Type

return

Xe = 'Xe'

Y = 'Y'

Yb = 'Yb'

Zn = 'Zn'

Zr = 'Zr'

as_dict()

Makes Element obey the general json interface used in pymatgen for easier serialization.

property atomic_mass

The atomic mass of the element in amu.

Type

Returns

property atomic_radius

The atomic radius of the element in Ångstroms.

Type

Returns

property average_anionic_radius

Average anionic radius for element (with units). The average is taken over all negative oxidation states of the element for which data is present.

property average_cationic_radius

Average cationic radius for element (with units). The average is taken over all positive oxidation states of the element for which data is present.

property average_ionic_radius

Average ionic radius for element (with units). The average is taken over all oxidation states of the element for which data is present.

property block

Return the block character “s,p,d,f”

property common_oxidation_states

Tuple of all known oxidation states

property data

Returns dict of data for element.

property electronic_structure

Electronic structure as string, with only valence electrons. E.g., The electronic structure for Fe is represented as ‘[Ar].3d6.4s2’

static from_Z(z: int)

Get an element from an atomic number.

Parameters

z (int) – Atomic number

Returns

Element with atomic number z.

static from_dict(d)

Makes Element obey the general json interface used in pymatgen for easier serialization.

static from_row_and_group(row: int, group: int)

Returns an element from a row and group number.

Parameters

• row (int) – Row number

• group (int) – Group number

Note

The 18 group number system is used, i.e., Noble gases are group 18.

property 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)]

property ground_state_term_symbol

Ground state term symbol Selected based on Hund’s Rule

property group

Returns the periodic table group of the element.

property icsd_oxidation_states

Tuple of all oxidation states with at least 10 instances in ICSD database AND at least 1% of entries for that element

property ionic_radii

All ionic radii of the element as a dict of {oxidation state: ionic radii}. Radii are given in ang.

property is_actinoid

True if element is a actinoid.

property is_alkali

True if element is an alkali metal.

property is_alkaline

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

property is_chalcogen

True if element is a chalcogen.

property is_halogen

True if element is a halogen.

property is_lanthanoid

True if element is a lanthanoid.

property is_metal

True if is a metal.

Type

return

property is_metalloid

True if element is a metalloid.

property is_noble_gas

True if element is noble gas.

property is_post_transition_metal

True if element is a post-transition or poor metal.

property is_quadrupolar

Checks if this element can be quadrupolar

property is_rare_earth_metal

True if element is a rare earth metal.

property is_transition_metal

True if element is a transition metal.

static is_valid_symbol(symbol: str)

Returns true if symbol is a valid element symbol.

Parameters

symbol (str) – Element symbol

Returns

True if symbol is a valid element (e.g., “H”). False otherwise (e.g., “Zebra”).

property 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.

property max_oxidation_state

Maximum oxidation state for element

property metallic_radius

Metallic radius of the element. Radius is given in ang.

property min_oxidation_state

Minimum oxidation state for element

property nmr_quadrupole_moment

Get a dictionary the nuclear electric quadrupole moment in units of e*millibarns for various isotopes

property number

Alternative attribute for atomic number

property oxidation_states

Tuple of all known oxidation states

static print_periodic_table(filter_function: Optional[Callable] = None)

A pretty ASCII printer for the periodic table, based on some filter_function.

Parameters

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.

property row

Returns the periodic table row of the element.

property term_symbols

All possible Russell-Saunders term symbol of the Element eg. L = 1, n_e = 2 (s2) returns

[[‘1D2’], [‘3P0’, ‘3P1’, ‘3P2’], [‘1S0’]]

property valence

# From full electron config obtain valence subshell # angular moment (L) and number of valence e- (v_e)

class Specie(symbol: str, oxidation_state: Optional[float] = 0.0, properties: dict = None)

Bases: pymatgen.core.periodic_table.Species

This maps the historical grammatically inaccurate Specie to Species to maintain backwards compatibility.

Initializes a Species.

Parameters

• 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.

oxi_state

Oxidation state associated with Species

ionic_radius

Ionic radius of Species (with specific oxidation state).

Changed in version 2.6.7: Properties are now checked when comparing two Species for equality.

class Species(symbol: str, oxidation_state: Optional[float] = 0.0, properties: dict = None)

Bases: monty.json.MSONable

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.

Initializes a Species.

Parameters

• 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.

oxi_state

Oxidation state associated with Species

ionic_radius

Ionic radius of Species (with specific oxidation state).

Changed in version 2.6.7: Properties are now checked when comparing two Species for equality.

as_dict()

Returns

Json-able dictionary representation.

property element

Underlying element object

classmethod from_dict(d)

Parameters

d – Dict representation.

Returns

Species.

static from_string(species_string: str)

Returns a Species from a string representation.

Parameters

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. –

get_crystal_field_spin(coordination: str = 'oct', spin_config: str = 'high')

Calculate the crystal field spin based on coordination and spin configuration. Only works for transition metal species.

Parameters

• 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. –

get_nmr_quadrupole_moment(isotope=None)

Gets the nuclear electric quadrupole moment in units of e*millibarns

Parameters

isotope (str) – the isotope to get the quadrupole moment for default is None, which gets the lowest mass isotope

get_shannon_radius(cn: str, spin: str = '', radius_type: str = 'ionic')

Get the local environment specific ionic radius for species.

Parameters

• 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.

property ionic_radius

Ionic radius of specie. Returns None if data is not present.

property oxi_state

Oxidation state of Species.

supported_properties = ('spin',)

get_el_sp(obj)

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.

Parameters

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. –