exatomic.core.two module

Atomic Two Body

This module provides functions for computing two body properties. A body can be, for example, an atom (such that two body properties correspond to inter-atomic distances - bonds), or a molecule (such that two body properties correspond to distances between molecule centers of mass). The following table provides a guide for the types of data found in two body tables provided by this module (specifically for atom two body properties).

Column	Type	Description
atom0	integer	foreign key to `Atom`
atom1	integer	foreign key to `Atom`
distance	float	distance between atom0 and atom1
bond	boolean	True if bond
frame	category	non-unique integer (req.)
symbols	category	concatenated atomic symbols

class exatomic.core.two.AtomTwo(*args, **kwargs)[source]

Bases: DataFrame

Interatomic distances.

property bonded

class exatomic.core.two.MoleculeTwo(*args, **kwargs)[source]: Bases: DataFrame

exatomic.core.two.compute_atom_two(universe, dmax=8.0, vector=False, bonds=True, **kwargs)[source]

Compute interatomic distances and determine bonds.

atom_two = compute_atom_two(uni, dmax=4.0)    # Max distance of interest as 4 bohr
atom_two = compute_atom_two(uni, vector=True) # Return distance vector components as well as distance
atom_two = compute_atom_two(uni, bonds=False) # Don't compute bonds
# Compute bonds with custom covalent radii (atomic units)
atom_two = compute_atom_two(unit, H=10.0, He=20.0, Li=30.0, bond_extra=100.0)

Parameters:

universe (Universe) – Universe object with atom table
dmax (float) – Maximum distance of interest
vector (bool) – Compute distance vector (needed for angles)
bonds (bool) – Compute bonds (default True)
kwargs – Additional keyword arguments for _compute_bonds()

exatomic.core.two.compute_pdist(universe, dmax=8.0)[source]

Compute interatomic distances for atoms in free boundary conditions.

Does return distance vector.

exatomic.core.two.compute_pdist_nv(universe, dmax=8.0)[source]

Compute interatomic distances for atoms in free boundary conditions.

Does not return distance vector.

exatomic.core.two.compute_pdist_ortho(universe, dmax=8.0)[source]

Compute interatomic distances between atoms in an orthorhombic periodic cell.

Parameters:

universe (Universe) – A universe
bonds (bool) – Compute bonds as well as distances
bond_extra (float) – Extra factor to use when determining bonds
dmax (float) – Maximum distance of interest
rtol (float) – Relative tolerance (float equivalence)
atol (float) – Absolute tolerance (float equivalence)
radii (kwargs) – Custom (covalent) radii to use when determining bonds

exatomic.core.two.compute_pdist_ortho_nv(universe, dmax=8.0)[source]

Compute interatomic distances between atoms in an orthorhombic periodic cell.

Parameters:

universe (Universe) – A universe
bonds (bool) – Compute bonds as well as distances
bond_extra (float) – Extra factor to use when determining bonds
dmax (float) – Maximum distance of interest
rtol (float) – Relative tolerance (float equivalence)
atol (float) – Absolute tolerance (float equivalence)
radii (kwargs) – Custom (covalent) radii to use when determining bonds

exatomic.core.two.compute_atom_two_out_of_core(hdfname, uni, a, **kwargs)[source]

Perform an out of core periodic two body calculation for a simple cubic unit cell with dimension a.

All data will be saved to and HDF5 file with the given filename. Key structure is per frame, i.e. frame_fdx/atom_two.

Parameters:

hdfname (str) – HDF file name
uni (Universe) – Universe
a (float) – Simple cubic unit cell dimension
kwargs – Keyword arguments for bond computation (i.e. covalent radii)