Elements

mdapy.elements holds the chemical symbols, standard atomic weights and radii used everywhere in mdapy. The atomic weights are those of IUPAC (Meija et al. (2016)); for an element without stable isotopes, the mass of its longest-lived isotope. The covalent radii are those of Cordero et al. (2008), with sp³ carbon and low-spin manganese, iron and cobalt; the van der Waals radii those of Alvarez (2013).

from mdapy import elements

elements.atomic_numbers(["Cu", "Ni"])  # array([29, 28])
elements.atomic_masses(["Cu", "Ni"])  # array([63.546 , 58.6934])
elements.element_from_mass(26.98)  # 'Al'

Contents

Name	Meaning
SYMBOLS	The 118 chemical symbols, indexed by atomic number. Index 0 is "X", an unknown element.
ATOMIC_MASSES	Standard atomic weights in amu, indexed by atomic number. Read-only.
ELEMENT_DTYPE	The polars type of the element column.
atomic_numbers(symbols)	Atomic numbers of chemical symbols.
atomic_masses(elements)	Atomic weights of symbols or atomic numbers.
COVALENT_RADII, VDW_RADII	Covalent and van der Waals radii in Å, indexed by atomic number; NaN where there is none. Read-only.
covalent_radii(elements), vdw_radii(elements)	The radii of symbols or atomic numbers; InvalidParameter for an element without one.
element_from_mass(mass, tolerance=0.01, candidates=None)	The element whose atomic weight matches a mass.

The element column

Per-atom chemical symbols are stored with the polars type ELEMENT_DTYPE, an enumeration of SYMBOLS in order of atomic number. Each atom takes one byte, symbols are checked when the column is created, and the underlying integer of each value is its atomic number:

import polars as pl

s = pl.Series(["Cu", "Ni"], dtype=elements.ELEMENT_DTYPE)
s.to_physical()  # [29, 28]

Identifying elements from masses

Some files, such as LAMMPS data files, give masses but no chemical symbols. element_from_mass returns the element whose atomic weight lies within tolerance (0.01 amu by default) of the mass, and raises InvalidParameter when no element or more than one element matches.

By default only elements with at least one stable isotope are considered: H to Bi, except Tc and Pm. No two of them have atomic weights within 0.02 amu of each other, so the match is unique. Radioactive elements must be listed in candidates, because their atomic weights can be almost equal to another element's: ²⁰⁹Po and Bi differ by 0.002 amu, ²⁴⁷Cm and ²⁴⁷Bk by 0.00004 amu.