pymatgen.core.periodic_table module

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

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

Bases: 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: float | None = 0, properties: dict | None = None)

Bases: 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: float

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: int

DummySpecies is always assigned an atomic number equal to the hash of the symbol. The expectation is that someone would be an actual dummy to use atomic numbers for a Dummy specie.

as_dict() → dict

Returns:

MSONAble dict representation.

classmethod from_dict(d) → DummySpecies

Parameters:

d – Dict representation

Returns:

DummySpecies

static from_string(species_string: str) → DummySpecies

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 interpreted. –

property oxi_state: float | None

Oxidation state associated with DummySpecies

property symbol: str

Symbol for DummySpecies.

Type:

return

class Element(value)

Bases: ElementBase

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

long_name

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

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 determined from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental data by Bondi and later workers. The uncertainty in these values is on the order of 0.1 Å.

Data are obtained from

“Atomic Radii of the Elements” in CRC Handbook of Chemistry and Physics,

91st Ed.; Haynes, W.M., Ed.; CRC Press: Boca Raton, FL, 2010.

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

ground_level

Ground level for element

ionization_energies

List of ionization energies. First value is the first ionization energy, second is the second ionization energy, etc. Note that this is zero-based indexing! So Element.ionization_energies[0] refer to the 1st ionization energy. Values are from the NIST Atomic Spectra Database. Missing values are None.

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'

Xe = 'Xe'

Y = 'Y'

Yb = 'Yb'

Zn = 'Zn'

Zr = 'Zr'

class ElementBase(value)

Bases: Enum

Element class defined without any enum values so it can be subclassed.

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

long_name

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

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 determined from critical reviews of X-ray diffraction, gas kinetic collision cross-section, and other experimental data by Bondi and later workers. The uncertainty in these values is on the order of 0.1 Å.

Data are obtained from

“Atomic Radii of the Elements” in CRC Handbook of Chemistry and Physics,

91st Ed.; Haynes, W.M., Ed.; CRC Press: Boca Raton, FL, 2010.

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

ground_level

Ground level for element

ionization_energies

List of ionization energies. First value is the first ionization energy, second is the second ionization energy, etc. Note that this is zero-based indexing! So Element.ionization_energies[0] refer to the 1st ionization energy. Values are from the NIST Atomic Spectra Database. Missing values are None.

property X: float

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

Type:

return

as_dict() → dict[Literal['element', '@module', '@class'], str]

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

property atomic_mass: FloatWithUnit

Returns: float: The atomic mass of the element in amu.

property atomic_radius: FloatWithUnit | None

Returns: float | None: The atomic radius of the element in Ångstroms. Can be None for

some elements like noble gases.

property average_anionic_radius: float

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

property average_cationic_radius: FloatWithUnit

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

property average_ionic_radius: FloatWithUnit

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: str

Return the block character “s,p,d,f”

property common_oxidation_states: tuple[int, ...]

Tuple of common oxidation states

property data: dict[str, Any]

Returns dict of data for element.

property electron_affinity: float

The amount of energy released when an electron is attached to a neutral atom.

property electronic_structure: str

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) → Element

Get an element from an atomic number.

Parameters:

Z (int) – Atomic number

Returns:

Element with atomic number Z.

static from_dict(d) → Element

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

static from_name(name: str) → Element

Get an element from its long name.

Parameters:

name – Long name of the element, e.g. ‘Hydrogen’ or ‘Iron’. Not case-sensitive.

Returns:

Element with the name ‘name’

static from_row_and_group(row: int, group: int) → Element

Returns an element from a row and group number. Important Note: For lanthanoids and actinoids, the row number must be 8 and 9, respectively, and the group number must be between 3 (La, Ac) and 17 (Lu, Lr). This is different than the value for Element(symbol).row and Element(symbol).group for these elements.

Parameters:

• row (int) – (pseudo) row number. This is the standard row number except for the lanthanoids and actinoids for which it is 8 or 9, respectively.

• group (int) – (pseudo) group number. This is the standard group number except for the lanthanoids and actinoids for which it is 3 (La, Ac) to 17 (Lu, Lr).

Note

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

property full_electronic_structure: list[tuple[int, str, int]]

Full electronic structure as tuple. E.g., The electronic structure for Fe is represented as: [(1, “s”, 2), (2, “s”, 2), (2, “p”, 6), (3, “s”, 2), (3, “p”, 6), (3, “d”, 6), (4, “s”, 2)]

property ground_state_term_symbol

Ground state term symbol Selected based on Hund’s Rule

property group: int

Returns the periodic table group of the element. Note: For lanthanoids and actinoids, the group is always 3.

property icsd_oxidation_states: tuple[int, ...]

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: dict[int, float]

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

property ionization_energy: float

First ionization energy of element.

property is_actinoid: bool

True if element is a actinoid.

property is_alkali: bool

True if element is an alkali metal.

property is_alkaline: bool

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

property is_chalcogen: bool

True if element is a chalcogen.

property is_halogen: bool

True if element is a halogen.

property is_lanthanoid: bool

True if element is a lanthanoid.

property is_metal: bool

True if is a metal.

property is_metalloid: bool

True if element is a metalloid.

property is_noble_gas: bool

True if element is noble gas.

property is_post_transition_metal: bool

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

property is_quadrupolar: bool

Checks if this element can be quadrupolar.

property is_rare_earth_metal: bool

True if element is a rare earth metal.

property is_transition_metal: bool

True if element is a transition metal.

static is_valid_symbol(symbol: str) → bool

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, Actinides and hydrogen.

property max_oxidation_state: float

Maximum oxidation state for element

property metallic_radius: float

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

property min_oxidation_state: float

Minimum oxidation state for element

property nmr_quadrupole_moment: dict[str, pymatgen.core.units.FloatWithUnit]

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

property number: int

Alternative attribute for atomic number Z

property oxidation_states: tuple[int, ...]

Tuple of all known oxidation states

static print_periodic_table(filter_function: Callable | None = 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: int

Returns the periodic table row of the element. Note: For lanthanoids and actinoids, the row is always 6 or 7, respectively.

property term_symbols: list[list[str]]

All possible Russell-Saunders term symbol of the Element. eg. L = 1, n_e = 2 (s2) returns [[‘1D2’], [‘3P0’, ‘3P1’, ‘3P2’], [‘1S0’]]

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: float | None = 0.0, properties: dict | None = None)

Bases: 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: float | None = 0.0, properties: dict | None = None)

Bases: MSONable, Stringify

An extension of Element with an oxidation state and other optional properties. Properties associated with Species should be “idealized” values, not calculated values. For example, high-spin Fe2+ may be assigned an idealized spin of +5, but an actual Fe2+ site may be calculated to have a magmom of +4.5. Calculated properties should be assigned to Site objects, and not Species.

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.

STRING_MODE = 'SUPERSCRIPT'

as_dict() → dict

Returns:

Json-able dictionary representation.

property element

Underlying element object

classmethod from_dict(d) → Species

Parameters:

d – Dict representation.

Returns:

Species.

static from_string(species_string: str) → Species

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 interpreted. –

get_crystal_field_spin(coordination: Literal['oct', 'tet'] = 'oct', spin_config: Literal['low', 'high'] = 'high') → float

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

Parameters:

• coordination ("oct" | "tet") – Tetrahedron or octahedron crystal site coordination

• spin_config ("low" | "high") – Whether the species is in a high or low spin state

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: str | None = None) → float

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: Literal['', 'Low Spin', 'High Spin'] = '', radius_type: Literal['ionic', 'crystal'] = 'ionic') → float

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: float | None

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

property oxi_state: float | None

Oxidation state of Species.

supported_properties = ('spin',)

to_pretty_string() → str

Returns:

String without properties.

get_el_sp(obj) → Element | Species | DummySpecies

Utility method to get an Element or Species from an input obj. If obj is in itself an element or a specie, it is returned automatically. If obj is an int or a string representing an integer, the Element with the atomic number obj is returned. If obj is a string, Species parsing will be attempted (e.g., Mn2+), failing which Element parsing will be attempted (e.g., Mn), failing which DummyElement parsing will be attempted.

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. –