API

Functions

nme.nme.atomic_mass_to_atomic_number(atomic_mass)

Convert an atomic mass to an atomic number by guessing what the element is by finding the element with the closest atomic mass

nme.nme.atomic_mass_to_symbol(atomic_mass)

Convert an atomic mass to a symbol

nme.nme.atomic_number_to_atomic_mass(atomic_number)

Convert an atomic number to that element’s atomic mass

nme.nme.atomic_number_to_symbol(atomic_number)

Convert an atomic number to a symbol

nme.nme.read_xyz(filepath)

Read a .xyz file into an array of atoms

Parameters:filepath (str) – The path of the xyz file Returns:A Molecule object containing the atoms in the .xyz file Return type:Molecule

nme.nme.symbol_to_atomic_mass(symbol)

Convert an element’s symbol to its atomic mass

nme.nme.symbol_to_atomic_number(symbol)

Convert an element’s symbol to its atomic number

nme.nme.write_lammps(molecules, filename, bbox=None, boundary_margin=0.8)

Write the given molecules to a LAMMPS data file

Parameters:

• molecules – A molecule or array of molecules to be written
• filename – The path that the LAMMPS data should be written to
• bbox – (optional) The bounding box of the simulation area, specified as a pair of cartesian coordinates corresponding to the minimum coordinates and the maximum coordinates (e.g. [ [0, 0, 0], [1, 1, 1] ])
• boundary_margin – (optional) If a bounding box is not supplied, compute a bounding box automatically by padding the area taken up by the molecules by this many atoms

Atom

class nme.nme.Atom(element, xyz)

Initialize an Atom. This is the fundamental object of nme.

Parameters:

• element (int) – The atomic number of the element
• xyz – A tuple, list, or numpy array of size 3 corresponding to the atom’s coordinates

Molecule

class nme.nme.Molecule(atoms=None)

Initialize a Molecule. A Molecule acts a container for Atom objects and can be used to manipulate groups of atoms or write a group of atoms to the disk.

Parameters:atoms (list) – (optional) A list of Atom objects. If no atoms are provied then an empty molecule is returned.

append(other)

Append atoms or molecules to the atoms array

Parameters:other – An Atom, Molecule, or a list of atoms and molecules

bbox_intersects(molecule, padding=0)

Test whether the bounding box of the current molecule intersects the bounding box of another molecule

Parameters:

• molecule (Molecule) – The other molecule
• padding (float) – (optional) A number to pad the bounding boxes by to increase their size

Returns:

True if the bounding box of this molecule intersects the bounding box of another molecule; False otherwise.

Return type:

bool

copy()

Create a copy of this molecule

Returns:A copy of this molecule Return type:Molecule

find_bonds(bond_radius=1.8)

Find bonds between molecules

Parameters:bond_radius (float) – (optional) The distance, in angstroms, between two atoms under which a bond will be assumed Returns:A two-dimensional array of atoms where each pair of atoms represents a bond Return type:list

move_to(xyz)

Move the molecule such that its centroid is at the desired position

Parameters:xyz – A tuple, list, or numpy array of size 3, corresponding to the location that the molecule should be moved to

offset(offset)

Offset the current molecule

Parameters:offset – A tuple, list, or numpy array of size 3 corresponding to the translation that should be applied to all of the molecule’s atoms

rotate(theta, phi, psi, degrees=False)

Rotate the molecule about its centroid in 3D space

Parameters:

• theta (float) – The angle to rotate the molecule around its X axis
• phi (float) – The angle to rotate the molecule around its Y axis
• psi (float) – The angle to rotate the molecule around its Z axis
• degrees (bool) – (optional) If True, the angles given are assumed to be in degrees and will be converted to radians before being used

write_lammps(filename, *args, **kwargs)

Syntactic sugar: see nme.nme.write_lammps()

write_xyz(filename, comment='generated with nme')

Write the current molecule to an XYZ file

Parameters:

• filename (str) – The path that the XYZ data should be written to
• comment (str) – (optional) A comment to include in the XYZ file

Workspace

class nme.nme.Workspace

Initialize a Workspace. A Workspace is a container for :class:`Atom`s and :class:`Molecule`s. The primary purpose of a Workspace is to facilitate writing multiple atoms and molecules to a single output file.

append(object_)

Append atoms or molecules to the workspace

Parameters:object – An Atom or Molecule

write_lammps(filename, *args, **kwargs)

Syntactic sugar: see nme.nme.write_lammps()

write_xyz(filename, comment='generated with nme')

Write the current workspace to an XYZ file

Parameters:

• filename (str) – The path that the XYZ data should be written to
• comment (str) – (optional) A comment to include in the XYZ file