4.5. Input and output¶

This example is about input and output functionalities.

Reading and writing file formats will be explained.

from eminus import Atoms, read, SCF
from eminus.units import bohr2ang

Some file standards are supported to be read from

atom, pos = read("CH4.xyz")

To immediately create an Atoms object you can do the following

atoms = Atoms(*read("CH4.xyz"))

CUBE files are supported as well

Here, lattice information and field information are given as well

atom, pos, Z, a, s, field = read("CH4.cube")

Create an Atoms object with it and start a DFT calculation

atoms = Atoms(atom=atom, pos=pos, a=a)
atoms.s = s
scf = SCF(atoms)
scf.run()

Write the total density to a CUBE file, e.g., to visualize it

scf.write("CH4_density.cube", scf.n)

Please note that XYZ files will use Angstrom as length units

CUBE files have no standard, but atomic units will be assumed

Units can always be converted using the unit conversion functionality

print(f"\nMethane coordinates in Bohr:\n{pos}")
print(f"\nMethane coordinates in Angstrom:\n{bohr2ang(pos)}")

You can also save the Atoms or SCF object directly to load them later

read and write are unified functions that determine the corresponding function using the file ending

atoms.write("CH4")
atoms = read("CH4.json")