.. _05_input_output:

.. include:: ../../examples/05_input_output/README.rst

----

.. code-block:: python

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

Some file standards are supported to be read from

.. code-block:: python

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

To immediately create an :code:`Atoms` object you can do the following

.. code-block:: python

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

CUBE files are supported as well

Here, lattice information and field information are given as well

.. code-block:: python

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

Create an :code:`Atoms` object with it and start a DFT calculation

.. code-block:: python

   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

.. code-block:: python

   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

.. code-block:: python

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

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

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

.. code-block:: python

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

Download :download:`05_input_output.py <../../examples/05_input_output/05_input_output.py>` :download:`CH4.cube <../../examples/05_input_output/CH4.cube>` :download:`CH4.xyz <../../examples/05_input_output/CH4.xyz>`