smact.screening module

smact.screening.eneg_states_test(ox_states, enegs)[source]

Internal function for checking electronegativity criterion

This implementation is fast as it ‘short-circuits’ as soon as it finds an invalid combination. However it may be that in some cases redundant comparisons are made. Performance is very close between this method and eneg_states_test_alternate.

Parameters:
  • ox_states (list) – oxidation states corresponding to species in compound
  • enegs (list) – Electronegativities corresponding to species in compound
Returns:

True if cations have higher electronegativity than

anions, otherwise False
Return type:

bool
smact.screening.eneg_states_test_alternate(ox_states, enegs)[source]

Internal function for checking electronegativity criterion

This implementation appears to be slightly slower than eneg_states_test, but further testing is needed.

Parameters:
  • ox_states (list) – oxidation states corresponding to species in compound
  • enegs (list) – Electronegativities corresponding to species in compound
Returns:

True if cations have higher electronegativity than

anions, otherwise False
Return type:

bool
smact.screening.eneg_states_test_threshold(ox_states, enegs, threshold=0)[source]

Internal function for checking electronegativity criterion

This implementation is fast as it ‘short-circuits’ as soon as it finds an invalid combination. However it may be that in some cases redundant comparisons are made. Performance is very close between this method and eneg_states_test_alternate.

A ‘threshold’ option is added so that this constraint may be relaxed somewhat.

Parameters:
  • ox_states (list) – oxidation states corresponding to species in compound
  • enegs (list) – Electronegativities corresponding to species in compound
  • threshold (Option(float)) – a tolerance for the allowed deviation from the Pauling criterion
Returns:

True if cations have higher electronegativity than

anions, otherwise False
Return type:

bool
smact.screening.ml_rep_generator(composition, stoichs=None)[source]

Function to take a composition of Elements and return a list of values between 0 and 1 that describes the composition, useful for machine learning.

The list is of length 103 as there are 103 elements considered in total in SMACT.

e.g. Li2O –> [0, 0, 2/3, 0, 0, 0, 0, 1/3, 0 ….]

Inspired by the representation used by Legrain et al. DOI: 10.1021/acs.chemmater.7b00789

Parameters:
  • composition (list) – Element objects in composition OR symbols of elements in composition
  • stoichs (list) – Corresponding stoichiometries in the composition
Returns:

List of floats representing the composition that sum

to one
Return type:

norm (list)
smact.screening.pauling_test(oxidation_states, electronegativities, symbols=[], repeat_anions=True, repeat_cations=True, threshold=0.0)[source]
Check if a combination of ions makes chemical sense,
(i.e. positive ions should be of lower electronegativity).
Parameters:
  • ox (list) – oxidation states of elements in the compound
  • paul (list) – the corresponding Pauling electronegativities of the elements in the compound
  • symbols (list) – chemical symbols of each site
  • threshold (float) – a tolerance for the allowed deviation from the Pauling criterion
  • repeat_anions – boolean, allow an anion to repeat in different oxidation states in the same compound
  • repeat_cations – as above, but for cations
Returns:

True if positive ions have lower electronegativity than negative ions
Return type:

bool
smact.screening.pauling_test_old(ox, paul, symbols, repeat_anions=True, repeat_cations=True, threshold=0.0)[source]

Check if a combination of ions makes chemical sense, (i.e. positive ions should be of lower Pauling electronegativity). This function should give the same results as pauling_test but is not optimised for speed.

Parameters:
  • ox (list) – oxidation states of the compound
  • paul (list) – the corresponding Pauling electronegativities of the elements in the compound
  • symbols (list) – chemical symbols of each site.
  • threshold (float) – a tolerance for the allowed deviation from the Pauling criterion
  • repeat_anions – boolean, allow an anion to repeat in different oxidation states in the same compound.
  • repeat_cations – as above, but for cations.
Returns:

True if positive ions have lower electronegativity than negative ions
Return type:

(bool)
smact.screening.smact_filter(els, threshold=8, species_unique=True, oxidation_states_set='default')[source]

Function that applies the charge neutrality and electronegativity tests in one go for simple application in external scripts that wish to apply the general ‘smact test’.

Parameters:
  • els (tuple/list) – A list of smact.Element objects
  • threshold (int) – Threshold for stoichiometry limit, default = 8
  • species_unique (bool) – Whether or not to consider elements in different oxidation states as unique in the results.
  • oxidation_states_set (string) – A string to choose which set of oxidation states should be chosen. Options are ‘default’, ‘icsd’, ‘pymatgen’ and ‘wiki’ for the default, icsd, pymatgen structure predictor and Wikipedia (https://en.wikipedia.org/wiki/Template:List_of_oxidation_states_of_the_elements) oxidation states.
Returns:

Allowed compositions for that chemical system in the form [(elements), (oxidation states), (ratios)] if species_unique=True or in the form [(elements), (ratios)] if species_unique=False.
Return type:

allowed_comps (list)