atomic_feature

Atomic features are one-hot codes.

all_elements

All element symbols in the periodic table. Some radioactive elements are not included:

['Ac', 'Ag', 'Al', 'Am', 'Ar', 'As', 'At', 'Au', 'B',  'Ba',
 'Be', 'Bh', 'Bi', 'Bk', 'Br', 'C',  'Ca', 'Cd', 'Ce', 'Cf',
 'Cl', 'Cm', 'Cn', 'Co', 'Cr', 'Cs', 'Cu', 'Db', 'Ds', 'Dy',
 'Er', 'Es', 'Eu', 'F',  'Fe', 'Fl', 'Fm', 'Fr', 'Ga', 'Gd',
 'Ge', 'H',  'He', 'Hf', 'Hg', 'Ho', 'Hs', 'I',  'In', 'Ir',
 'K',  'Kr', 'La', 'Li', 'Lr', 'Lu', 'Lv', 'Mc', 'Md', 'Mg',
 'Mn', 'Mo', 'Mt', 'N',  'Na', 'Nb', 'Nd', 'Ne', 'Nh', 'Ni',
 'No', 'Np', 'O',  'Og', 'Os', 'P',  'Pa', 'Pb', 'Pd', 'Pm',
 'Po', 'Pr', 'Pt', 'Pu', 'Ra', 'Rb', 'Re', 'Rf', 'Rg', 'Rh',
 'Rn', 'Ru', 'S',  'Sb', 'Sc', 'Se', 'Sg', 'Si', 'Sm', 'Sn',
 'Sr', 'Ta', 'Tb', 'Tc', 'Te', 'Th', 'Ti', 'Tl', 'Tm', 'Ts',
 'U',  'V',  'W',  'Xe', 'Y',  'Yb', 'Zn', 'Zr']

elements

Common elements:

['Ac', 'Ag', 'Al', 'Am', 'As', 'Au', 'B',  'Ba', 'Be',
 'Bi', 'Br', 'C',  'Ca', 'Cd', 'Ce', 'Cl', 'Co', 'Cr', 'Cs',
 'Cu', 'Dy', 'Er', 'Eu', 'F',  'Fe', 'Ga', 'Gd', 'Ge', 'H',
 'Hf', 'Hg', 'Ho', 'I',  'In', 'Ir', 'K',  'La', 'Li', 'Lu',
 'Mg', 'Mn', 'Mo', 'N',  'Na', 'Nb', 'Nd', 'Ni', 'Np', 'O',
 'Os', 'P',  'Pb', 'Pd', 'Pm', 'Po', 'Pr', 'Pt', 'Pu', 'Ra',
 'Rb', 'Re', 'Rh', 'Ru', 'S',  'Sb', 'Sc', 'Se', 'Si', 'Sm',
 'Sn', 'Sr', 'Ta', 'Tb', 'Tc', 'Te', 'Th', 'Ti', 'Tl', 'Tm',
 'U',  'V',  'W',  'Y',  'Yb', 'Zn', 'Zr']

selected_elements

Selected elements for a specific system. For example:

['H', 'He', 'Li', 'Be', 'B']

Elements_used

Elements used for one-hot coding.

Important

This variable defines the elements used for a well-trained model. Make sure the atomistic representation for the training and prediction are same. Normally, Elements_used = elements is robust.

get_atomic_features()

Encode atomistic features with physical properties. For more input features, please refer to: https://pymatgen.org/pymatgen.core.periodic_table.html. For now, the following properties are included.

Note

This function will be deprecated in the short future.

Property Code	Property
Z	atomic number
atomic_radius	atomic radius
molar_volume	molar volume
atomic_mass	atomic mass
mendeleev_no	mendeleev number
X	electronegativity
boiling_point	boiling point
melting_point	melting point
row	row number in the periodic table
group	group number in the periodic table
max_oxidation_state	maximum oxidation state
min_oxidation_state	minimum oxidation state

Returns:

atom_feat: atomic features of all elements.

get_atomic_feature_onehot(Elements_used)

Get the one-hot code of all considered elements. The elements are sorted by their atomic number:

atomic_number = [atomic_numbers[x] for x in Elements_used]
atoms_dict = dict(zip(atomic_number, Elements_used))

atomic_number.sort()

Elements_sorted = [atoms_dict[x] for x in atomic_number]

Parameters:

Elements_used (list) – Elements used to encode atomic representations.

Returns:

atom_feat: one-hot code representation of all considered elements.