src.easycrystallography.Elements

periodic_table

DummySpecie

Bases: DummySpecies

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

DummySpecies

Bases: Species

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

.. attribute:: oxi_state

Oxidation state associated with Species.

.. attribute:: Z

DummySpecies is always assigned an atomic number equal to the hash
number of the symbol. Obviously, it makes no sense whatsoever to use
the atomic number of a Dummy specie for anything scientific. The purpose
of this is to ensure that for most use cases, a DummySpecies behaves no
differently from an Element or Species.

.. attribute:: X

DummySpecies is always assigned an electronegativity of 0.

X: float property

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

Z: int property

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.

oxi_state: Optional[float] property

Oxidation state associated with DummySpecies

symbol: str property

:return: Symbol for DummySpecies.

__eq__(other)

Species is equal to other only if element and oxidation states are exactly the same.

__init__(symbol='X', oxidation_state=0, properties=None)

Parameters:

Name	Type	Description	Default
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.	'X'
oxidation_state	float	Oxidation state for dummy specie. Defaults to zero.	0

__lt__(other)

Sets a default sort order for atomic species by electronegativity, followed by oxidation state.

as_dict()

:return: MSONAble dict representation.

from_dict(d, skip=None) classmethod

:param d: Dict representation :return: DummySpecies

from_string(species_string) staticmethod

Returns a Dummy from a string representation.

Parameters:

Name	Type	Description	Default
species_string	str	A string representation of a dummy species, e.g., "X2+", "X3+".	required

Returns:

Type	Description
	A DummySpecies object.

Element

Bases: Enum

Enum representing an element in the periodic table.

X property

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

atomic_mass property

Returns: The atomic mass of the element in amu.

atomic_radius property

Returns: The atomic radius of the element in Ångstroms.

average_anionic_radius property

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

average_cationic_radius property

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

average_ionic_radius property

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

block property

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

common_oxidation_states property

Tuple of all known oxidation states

data: dict property

Returns dict of data for element.

electronic_structure: str property

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

full_electronic_structure property

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)]

ground_state_term_symbol property

Ground state term symbol Selected based on Hund's Rule

group property

Returns the periodic table group of the element.

icsd_oxidation_states property

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

ionic_radii property

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

is_actinoid property

True if element is a actinoid.

is_alkali: bool property

True if element is an alkali metal.

is_alkaline: bool property

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

is_chalcogen property

True if element is a chalcogen.

is_halogen property

True if element is a halogen.

is_lanthanoid property

True if element is a lanthanoid.

is_metal: bool property

:return: True if is a metal.

is_metalloid: bool property

True if element is a metalloid.

is_noble_gas property

True if element is noble gas.

is_post_transition_metal property

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

is_quadrupolar property

Checks if this element can be quadrupolar

is_rare_earth_metal: bool property

True if element is a rare earth metal.

is_transition_metal property

True if element is a transition metal.

iupac_ordering property

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.

max_oxidation_state property

Maximum oxidation state for element

metallic_radius property

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

min_oxidation_state property

Minimum oxidation state for element

nmr_quadrupole_moment property

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

number property

Alternative attribute for atomic number

oxidation_states property

Tuple of all known oxidation states

row property

Returns the periodic table row of the element.

term_symbols property

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

valence property

From full electron config obtain valence subshell

angular moment (L) and number of valence e- (v_e)

__init__(symbol)

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:

Name	Type	Description	Default
symbol	str	Element symbol, e.g., "H", "Fe"	required

.. 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.

__lt__(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.

as_dict(skip=None)

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

from_Z(z) staticmethod

Get an element from an atomic number.

Parameters:

Name	Type	Description	Default
z	int	Atomic number	required

Returns:

Type	Description
	Element with atomic number z.

from_dict(d) staticmethod

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

from_row_and_group(row, group) staticmethod

Returns an element from a row and group number.

Parameters:

Name	Type	Description	Default
row	int	Row number	required
group	int	Group number	required

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

is_valid_symbol(symbol) staticmethod

Returns true if symbol is a valid element symbol.

Parameters:

Name	Type	Description	Default
symbol	str	Element symbol	required

Returns:

Type	Description
	True if symbol is a valid element (e.g., "H"). False otherwise
	(e.g., "Zebra").

print_periodic_table(filter_function=None) staticmethod

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

Parameters:

Name	Type	Description	Default
filter_function	Optional[Callable]	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.	None

Specie

Bases: Species

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

Species

Bases: ComponentSerializer

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.

element property

Underlying element object

ionic_radius property

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

oxi_state property

Oxidation state of Species.

__eq__(other)

Species is equal to other only if element and oxidation states are exactly the same.

__hash__()

Equal Species should have the same str representation, hence should hash equally. Unequal Species will have differnt str representations.

__init__(symbol, oxidation_state=0.0, properties=None)

Initializes a Species.

Parameters:

Name	Type	Description	Default
symbol	str	Element symbol, e.g., Fe	required
oxidation_state	float	Oxidation state of element, e.g., 2 or -2	0.0
properties	dict	Properties associated with the Species, e.g., {"spin": 5}. Defaults to None. Properties must be one of the Species supported_properties.	None

.. attribute:: oxi_state

Oxidation state associated with Species

.. attribute:: ionic_radius

Ionic radius of Species (with specific oxidation state).

.. versionchanged:: 2.6.7

Properties are now checked when comparing two Species for equality.

__lt__(other)

Sets a default sort order for atomic species by electronegativity, followed by oxidation state, followed by spin.

as_dict(skip=None)

:return: Json-able dictionary representation.

from_dict(d) classmethod

:param d: Dict representation. :return: Species.

from_string(species_string) staticmethod

Returns a Species from a string representation.

Parameters:

Name	Type	Description	Default
species_string	str	A typical string representation of a species, e.g., "Mn2+", "Fe3+", "O2-".	required

Returns:

Type	Description
	A Species object.

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

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

Parameters:

Name	Type	Description	Default
coordination	str	Only oct and tet are supported at the moment.	'oct'
spin_config	str	Supported keywords are "high" or "low".	'high'

Returns:

Type	Description
	Crystal field spin in Bohr magneton.

get_nmr_quadrupole_moment(isotope=None)

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

Parameters:

Name	Type	Description	Default
isotope	str	the isotope to get the quadrupole moment for default is None, which gets the lowest mass isotope	None

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

Get the local environment specific ionic radius for species.

Parameters:

Name	Type	Description	Default
cn	str	Coordination using roman letters. Supported values are I-IX, as well as IIIPY, IVPY and IVSQ.	required
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).	'ionic'

Returns:

Type	Description
	Shannon radius for specie in the specified environment.

formula_double_format(afloat, ignore_ones=True, tol=1e-08)

This function is used to make pretty formulas by formatting the amounts. Instead of Li1.0 Fe1.0 P1.0 O4.0, you get LiFePO4. Args: afloat (float): a float ignore_ones (bool): if true, floats of 1 are ignored. tol (float): Tolerance to round to nearest int. i.e. 2.0000000001 -> 2 Returns: A string representation of the float for formulas.

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:

Name	Type	Description	Default
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).	required

Returns:

Type	Description
	Species or Element, with a bias for the maximum number of properties
	that can be determined.