pymatgen.analysis.bond_valence module¶

class
BVAnalyzer
(symm_tol=0.1, max_radius=4, max_permutations=100000, distance_scale_factor=1.015, charge_neutrality_tolerance=1e05, forbidden_species=None)[source]¶ Bases:
object
This class implements a maximum a posteriori (MAP) estimation method to determine oxidation states in a structure. The algorithm is as follows: 1) The bond valence sum of all symmetrically distinct sites in a structure is calculated using the elementbased parameters in M. O’Keefe, & N. Brese, JACS, 1991, 113(9), 32263229. doi:10.1021/ja00009a002. 2) The posterior probabilities of all oxidation states is then calculated using: P(oxi_state/BV) = K * P(BV/oxi_state) * P(oxi_state), where K is a constant factor for each element. P(BV/oxi_state) is calculated as a Gaussian with mean and std deviation determined from an analysis of the ICSD. The posterior P(oxi_state) is determined from a frequency analysis of the ICSD. 3) The oxidation states are then ranked in order of decreasing probability and the oxidation state combination that result in a charge neutral cell is selected.
Initializes the BV analyzer, with useful defaults.
 Parameters
symm_tol – Symmetry tolerance used to determine which sites are symmetrically equivalent. Set to 0 to turn off symmetry.
max_radius – Maximum radius in Angstrom used to find nearest neighbors.
max_permutations – The maximum number of permutations of oxidation states to test.
distance_scale_factor – A scale factor to be applied. This is useful for scaling distances, esp in the case of calculationrelaxed structures which may tend to under (GGA) or over bind (LDA). The default of 1.015 works for GGA. For experimental structure, set this to 1.
charge_neutrality_tolerance – Tolerance on the charge neutrality when unordered structures are at stake.
forbidden_species – List of species that are forbidden (example : [“O“] cannot be used) It is used when e.g. someone knows that some oxidation state cannot occur for some atom in a structure or list of structures.

CHARGE_NEUTRALITY_TOLERANCE
= 1e05¶

get_oxi_state_decorated_structure
(structure)[source]¶ Get an oxidation state decorated structure. This currently works only for ordered structures only.
 Parameters
structure – Structure to analyze
 Returns
A modified structure that is oxidation state decorated.
 Raises
ValueError if the valences cannot be determined. –

get_valences
(structure)[source]¶ Returns a list of valences for the structure. This currently works only for ordered structures only.
 Parameters
structure – Structure to analyze
 Returns
A list of valences for each site in the structure (for an ordered structure), e.g., [1, 1, 2] or a list of lists with the valences for each fractional element of each site in the structure (for an unordered structure), e.g., [[2, 4], [3], [2], [2], [2]]
 Raises
A ValueError if the valences cannot be determined. –

add_oxidation_state_by_site_fraction
(structure, oxidation_states)[source]¶ Add oxidation states to a structure by fractional site.
 Parameters
oxidation_states (list) – List of list of oxidation states for each site fraction for each site. E.g., [[2, 4], [3], [2], [2], [2]]

calculate_bv_sum
(site, nn_list, scale_factor=1.0)[source]¶ Calculates the BV sum of a site.
 Parameters
site – The site
nn_list – List of nearest neighbors in the format [(nn_site, dist), …].
scale_factor – A scale factor to be applied. This is useful for scaling distance, esp in the case of calculationrelaxed structures which may tend to under (GGA) or over bind (LDA).

calculate_bv_sum_unordered
(site, nn_list, scale_factor=1)[source]¶ Calculates the BV sum of a site for unordered structures.
 Parameters
site – The site
nn_list – List of nearest neighbors in the format [(nn_site, dist), …].
scale_factor – A scale factor to be applied. This is useful for scaling distance, esp in the case of calculationrelaxed structures which may tend to under (GGA) or over bind (LDA).

get_z_ordered_elmap
(comp)[source]¶ Arbitrary ordered elmap on the elements/species of a composition of a given site in an unordered structure. Returns a list of tuples ( element_or_specie: occupation) in the arbitrary order.
The arbitrary order is based on the Z of the element and the smallest fractional occupations first. Example : {“Ni3+”: 0.2, “Ni4+”: 0.2, “Cr3+”: 0.15, “Zn2+”: 0.34, “Cr4+”: 0.11} will yield the species in the following order : Cr4+, Cr3+, Ni3+, Ni4+, Zn2+ … or Cr4+, Cr3+, Ni4+, Ni3+, Zn2+