4.3. The Atoms object

This example is about the Atoms object and how to set it up.

This object holds the system’s geometry and parameter.

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from eminus import Atoms

The only necessary parameters are atom and pos

atom holds the atom symbols, and pos holds the atom positions

Please note that atomic units will be used

atom = "N2"
pos = [[-1.037, 0, 0], [1.037, 0, 0]]

Create an object for dinitrogen and display it

atoms = Atoms(atom, pos)
print(f"Atoms object:\n{atoms}\n")

Cut-off energy

ecut = 20

Optional parameters with examples are listed as follows

Cell size or vacuum size

a = 20

Spin of the system, i.e., the number of unpaired electrons (2S, not 2S+1)

spin = 0

Total charge of the system

charge = 0

Spin handling

unrestricted = False

Center the system inside the box by its geometric center of mass and rotate it such that its geometric moment of inertia aligns with the coordinate axes

center = True

Level of output, larger numbers mean more output

verbose = 4

Create an Atoms object for dinitrogen and display it

atoms = Atoms(
    atom=atom,
    pos=pos,
    ecut=ecut,
    a=a,
    spin=spin,
    charge=charge,
    unrestricted=unrestricted,
    center=center,
    verbose=verbose,
)
print(f"New Atoms object:\n{atoms}\n")

Albeit discouraged, some properties can be changed after the initialization as seen below

Valence charge per atom, the charges should not differ for the same species

None will use valence charges from GTH pseudopotentials

atoms.Z = [5, 5]

Real-space sampling of the cell using an equidistant grid

atoms.s = 40

Occupation numbers per state

None will assume occupations of 2

The last state will be adjusted if the sum of f is not equal to the sum of Z

atoms.f = [2, 2, 2, 2, 2]

You can manipulate the object by displaying or editing most properties

To display the calculated cell volume

print(f"Cell volume = {atoms.Omega} a0^3")

If you edit properties of an existing object dependent properties can be updated by rebuilding the Atoms object

The atoms.build function is used to generate cell parameters for an SCF calculation, but an SCF object will call the function if necessary

Edit the cell size, rebuild the object, and display the new cell volume

atoms.a = 3
atoms.build()
print(f"New cell volume = {atoms.Omega} a0^3")

To display all relevant electronic information regarding the occupations, one can display the Occupations object every Atoms object has

print(f"\nOccupations object:\n{atoms.occ}")

More information is always available in the respective docstring

# print(f"\nAtoms docstring:\n{Atoms.__doc__}")

or:

# help(Atoms)

Download 03_atoms_objects.py